A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ 

A

A - Static variable in class org.biojava3.aaproperties.Constraints
 
AA - Static variable in class org.biojava3.data.sequence.SequenceUtil
Valid Amino acids
aa - Static variable in class org.biojava3.phylo.ResidueProperties
 
aa2CTerminalPka - Static variable in class org.biojava3.aaproperties.Constraints
 
aa2ExtinctionCoefficient - Static variable in class org.biojava3.aaproperties.Constraints
 
aa2Hydrophathicity - Static variable in class org.biojava3.aaproperties.Constraints
 
aa2MolecularWeight - Static variable in class org.biojava3.aaproperties.Constraints
 
aa2NTerminalPka - Static variable in class org.biojava3.aaproperties.Constraints
 
aa2PKa - Static variable in class org.biojava3.aaproperties.Constraints
 
aa2Triplet - Static variable in class org.biojava3.phylo.ResidueProperties
 
aa3Hash - Static variable in class org.biojava3.phylo.ResidueProperties
 
aaIndex - Static variable in class org.biojava3.phylo.ResidueProperties
 
AAindexFactory - Class in org.biojava3.alignment.aaindex
Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.
AAindexFactory() - Constructor for class org.biojava3.alignment.aaindex.AAindexFactory
 
AAIndexFileParser - Class in org.biojava3.alignment.aaindex
 
AAIndexFileParser() - Constructor for class org.biojava3.alignment.aaindex.AAIndexFileParser
 
AAIndexProvider - Interface in org.biojava3.alignment.aaindex
 
aaScore(char, char) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
AboutDialog - Class in org.biojava.bio.structure.align.gui
 
AboutDialog() - Constructor for class org.biojava.bio.structure.align.gui.AboutDialog
 
AbstractBean - Class in org.biojava.bio.structure.io.mmcif.model
a generic class that implements the toString method for a bean
AbstractBean() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AbstractBean
 
AbstractCompound - Class in org.biojava3.core.sequence.template
The details of a Compound
AbstractCompound(String) - Constructor for class org.biojava3.core.sequence.template.AbstractCompound
 
AbstractCompoundSet<C extends Compound> - Class in org.biojava3.core.sequence.template
 
AbstractCompoundSet() - Constructor for class org.biojava3.core.sequence.template.AbstractCompoundSet
 
AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava3.core.sequence.template
 
AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.features
A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
AbstractFeature(String, String) - Constructor for class org.biojava3.core.sequence.features.AbstractFeature
A feature has a type and a source
AbstractLocation - Class in org.biojava3.core.sequence.location.template
Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
AbstractLocation() - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
 
AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
Default constructor
AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
Default constructor
AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
Implements common code for an Aligner which builds a score matrix during computation.
AbstractMatrixAligner() - Constructor for class org.biojava3.alignment.template.AbstractMatrixAligner
Before running an alignment, data must be sent in via calls to AbstractMatrixAligner.setGapPenalty(GapPenalty) and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractMatrixAligner
Prepares for an alignment.
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava3.alignment.template.AbstractMatrixAligner
Prepares for an alignment.
AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.template
 
AbstractNucleotideCompoundSet() - Constructor for class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
 
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
Implements common code for an Aligner for a pair of Sequences.
AbstractPairwiseSequenceAligner() - Constructor for class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
Prepares for a pairwise sequence alignment.
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
Implements common code for an Aligner for a pair of Profiles.
AbstractProfileProfileAligner() - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.template.AbstractProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
AbstractScorer - Class in org.biojava3.alignment.template
Implements common code for algorithms which compute a score.
AbstractScorer() - Constructor for class org.biojava3.alignment.template.AbstractScorer
 
AbstractSequence<C extends Compound> - Class in org.biojava3.core.sequence.template
The base class for DNA, RNA and Protein sequences.
AbstractSequence() - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
 
AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
Create a Sequence from a simple string where the values should be found in compoundSet
AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
AbstractSequence.AnnotationType - Enum in org.biojava3.core.sequence.template
 
AbstractStructureAlignment - Class in org.biojava.bio.structure.align
 
AbstractStructureAlignment() - Constructor for class org.biojava.bio.structure.align.AbstractStructureAlignment
 
AbstractUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
 
AbstractUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
accept(PDBHeader) - Method in interface org.biojava.bio.structure.server.PDBFilter
return true if this PDBHeader is passing this filter.
AccesionedLocation - Interface in org.biojava3.core.sequence.location.template
A location which is bound to an AccessionID.
ACCESSION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Accession - Class in org.forester.phylogeny.data
 
Accession(String, String) - Constructor for class org.forester.phylogeny.data.Accession
 
ACCESSION_SOURCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Accessioned - Interface in org.biojava3.core.sequence.template
Indicates an entity is accessioned
AccessionID - Class in org.biojava3.core.sequence
Used in Sequences as the unique indentifier.
AccessionID() - Constructor for class org.biojava3.core.sequence.AccessionID
 
AccessionID(String) - Constructor for class org.biojava3.core.sequence.AccessionID
 
AccessionID(String, DataSource) - Constructor for class org.biojava3.core.sequence.AccessionID
 
AccessionParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.ChooseDirAction
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.DBResultTable
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
Invoked when the user presses the stop button.
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
The user selected one of the Combo boxes...
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.JPrintPanel
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyAlignmentLoadListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyDistMaxListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyExportListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MyOpenPdbFileListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.MySaveFileListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.align.gui.ShowPDBIDListener
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.ArchaeopteryxE
 
actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.FontChooser
 
actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.MainFrame
Action performed.
actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.MainFrameApplication
 
actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.TreePanel
 
AD - Variable in class org.biojava.bio.structure.domain.pdp.CutValues
 
adapter - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
 
adapter - Static variable in class org.biojava3.structure.gui.JmolViewerImpl
 
add(int, int, int, int) - Method in class org.biojava.bio.structure.align.helper.JointFragments
 
add(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
add two atoms ( a + b).
add(FeatureI) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Add specified feature to the end of the list.
add(Collection<FeatureI>) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Add all features in the specified list or collection to this list.
addAlgorithm(StructureAlignment) - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
Adds a new StructureAlignment algorithm to the list.
addAlignedSequence(S) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
A sequence that has been aligned to other sequences will have inserts.
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
addAlignmentProgressListener(AlignmentProgressListener) - Method in class org.biojava.bio.structure.align.FarmJob
 
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains, SortedSet<BinaryDomainCombination>) - Static method in class org.forester.surfacing.SurfacingUtil
 
addAllDomainIdsToSet(GenomeWideCombinableDomains, SortedSet<DomainId>) - Static method in class org.forester.surfacing.SurfacingUtil
 
addAltLoc(Group) - Method in interface org.biojava.bio.structure.Group
Add a group that is an alternate location for this group.
addAltLoc(Group) - Method in class org.biojava.bio.structure.HetatomImpl
 
addAnchors(AlignerHelper.Cut[], short[], boolean, int[]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
addAnnotation(Annotation) - Method in class org.forester.phylogeny.data.Sequence
 
addAsChild(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.
addAsChild(PhylogenyNodeI) - Method in class org.forester.phylogeny.PhylogenyNode
Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.
addAsChild(PhylogenyNodeI) - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
addAsSibling(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
 
addAtom(Atom) - Method in interface org.biojava.bio.structure.Group
add an atom to this group.
addAtom(Atom) - Method in class org.biojava.bio.structure.HetatomImpl
add an atom to this group.
addAtomLinkage(StructureAtomLinkage) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
Add a linkage.
addAtomLinkage(StructureAtomLinkage) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
addAtomLinkages(Collection<StructureAtomLinkage>) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
Add a collections of linkages.
addAtomLinkages(Collection<StructureAtomLinkage>) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
addCDS(AccessionID, int, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
Add a Coding Sequence region with phase to the transcript sequence
addChain(Chain) - Method in class org.biojava.bio.structure.Compound
 
addChain(Chain) - Method in interface org.biojava.bio.structure.Structure
add a new chain.
addChain(Chain, int) - Method in interface org.biojava.bio.structure.Structure
add a new chain, if several models are available.
addChain(Chain) - Method in class org.biojava.bio.structure.StructureImpl
add a new chain.
addChain(Chain, int) - Method in class org.biojava.bio.structure.StructureImpl
add a new chain, if several models are available.
addChemComp(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
add a new component to the dictionary
addChildElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
 
addChildElement(XmlElement) - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
addCombinableDomain(DomainId) - Method in class org.forester.surfacing.BasicCombinableDomains
 
addCombinableDomain(DomainId) - Method in interface org.forester.surfacing.CombinableDomains
To add a new combinable domain.
addCompound(C, C, Iterable<C>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
addCompound(C, C, C...) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
addCompound(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
addCompounds(F, T...) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
addCompoundToLists(List<List<T>>, T) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
addConfidence(Confidence) - Method in class org.forester.phylogeny.data.BranchData
 
addDomain(ProteinDomain) - Method in class org.forester.phylogeny.data.DomainArchitecture
 
addDomainIdToIgnore(DomainId) - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
addEquivalent(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
addExon(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
Add an ExonSequence mainly used to mark as a feature
addExtension(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
addExtension(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
addExtension(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
add a known File extension.
addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
addFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Add a feature to this sequence.
addGainedCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters
 
addGene(AccessionID, int, int, Strand) - Method in class org.biojava3.core.sequence.ChromosomeSequence
Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
addGoId(GoId) - Method in class org.forester.surfacing.BasicDomain
 
addGoId(GoId) - Method in interface org.forester.surfacing.Domain
 
addGoId(GoId) - Method in class org.forester.surfacing.DomainId
 
addGoId(GoId) - Method in class org.forester.surfacing.SimpleDomain
 
addGroup(Group) - Method in interface org.biojava.bio.structure.Chain
add a group to the list of ATOM record group of this chain.
addGroup(Group) - Method in class org.biojava.bio.structure.ChainImpl
add a group to the list of ATOM record group of this chain.
addHtmlHead(Writer, String) - Static method in class org.forester.surfacing.SurfacingUtil
 
addIntron(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
Add an Intron Currently used to mark an IntronSequence as a feature
addIntronsUsingExons() - Method in class org.biojava3.core.sequence.GeneSequence
Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.
addKeyword(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Add a keyword associate with the PTM.
addKeywords(Collection<String>) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
 
addLength(Species, int) - Method in class org.forester.surfacing.DomainLengths
 
addLengths(List<Protein>) - Method in class org.forester.surfacing.DomainLengthsTable
 
addLostCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters
 
addMatrixListener(MatrixListener) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
addMatrixListener(MatrixListener) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.
addMMcifConsumer(MMcifConsumer) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
addModel(List<Chain>) - Method in interface org.biojava.bio.structure.Structure
add a new model.
addModel(List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
add a new model.
addNote(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Add notes about this sequence that will get exported for GFF3
addNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
 
addOneSystemProperty(String) - Method in class org.biojava.bio.structure.align.gui.SystemInfo
 
addPDBFilter(PDBFilter) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
addPDBFilter(PDBFilter) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
addPDBFilter(PDBFilter) - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
add a filter for PDB files.
addPresentCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters
 
addProgessListener(NJTreeProgressListener) - Method in class org.biojava3.phylo.TreeConstructor
 
addProgressListener(AlignmentProgressListener) - Method in class org.biojava.bio.structure.align.StructurePairAligner
 
addProperty(String, String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
Add a property and type to associate with this DBReferenceInfo
addProperty(Property) - Method in class org.forester.phylogeny.data.PropertiesMap
 
addProteinDomain(Domain) - Method in class org.forester.surfacing.BasicProtein
 
addProteinDomain(Domain) - Method in interface org.forester.surfacing.Protein
 
addQuantity(Number) - Method in class org.biojava3.core.sequence.features.QuantityFeature
 
addResidue(SiftsResidue) - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
addSegment(SiftsSegment) - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
addSequence(Sequence, boolean) - Method in class org.forester.development.BasicMsa
 
addSSBond(SSBond) - Method in interface org.biojava.bio.structure.Structure
add a single SSBond to this structure
addSSBond(SSBond) - Method in class org.biojava.bio.structure.StructureImpl
add a single SSBond to this structure
addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
 
addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
 
addStrings(String, String...) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
addStructureListener(StructureListener) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
addStructureListener(StructureListener) - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
Deprecated.
 
addStructureListener(StructureListener) - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
addToCache(String, File) - Static method in class org.biojava3.core.util.FlatFileCache
 
addTranscript(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
Add a transcription sequence to a gene which describes a ProteinSequence
addValue(double) - Method in class org.forester.util.BasicDescriptiveStatistics
 
addValue(double) - Method in interface org.forester.util.DescriptiveStatistics
 
AdjactantDirectedBinaryDomainCombination - Class in org.forester.surfacing
 
AdjactantDirectedBinaryDomainCombination(DomainId, DomainId) - Constructor for class org.forester.surfacing.AdjactantDirectedBinaryDomainCombination
 
AdjactantDirectedBinaryDomainCombination(String, String) - Constructor for class org.forester.surfacing.AdjactantDirectedBinaryDomainCombination
 
AdjactantDirectedCombinableDomains - Class in org.forester.surfacing
 
AdjactantDirectedCombinableDomains(DomainId, Species) - Constructor for class org.forester.surfacing.AdjactantDirectedCombinableDomains
 
AFP - Class in org.biojava.bio.structure.align.model
A class to represent a FATCAT AFP
AFP() - Constructor for class org.biojava.bio.structure.align.model.AFP
 
afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.bio.structure.align.AFPTwister
Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
AFPAlignmentDisplay - Class in org.biojava.bio.structure.align.util
 
AFPAlignmentDisplay() - Constructor for class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
AFPCalculator - Class in org.biojava.bio.structure.align.fatcat.calc
a class that performs calculations on AFPCHains
AFPCalculator() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
 
AFPChain - Class in org.biojava.bio.structure.align.model
a bean to contain the core of an alignment The FatCat aligner class is working on the AFPChain class.
AFPChain() - Constructor for class org.biojava.bio.structure.align.model.AFPChain
 
AFPChain(AFPChain) - Constructor for class org.biojava.bio.structure.align.model.AFPChain
Copy constructor
AFPChainCoordManager - Class in org.biojava.bio.structure.align.gui.aligpanel
 
AFPChainCoordManager() - Constructor for class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
 
AFPChainer - Class in org.biojava.bio.structure.align.fatcat.calc
a class to chain AFPs to an alignment
AFPChainer() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
 
AFPChainFlipper - Class in org.biojava.bio.structure.align.xml
 
AFPChainFlipper() - Constructor for class org.biojava.bio.structure.align.xml.AFPChainFlipper
 
AFPChainScorer - Class in org.biojava.bio.structure.align.util
 
AFPChainScorer() - Constructor for class org.biojava.bio.structure.align.util.AFPChainScorer
 
AfpChainWriter - Class in org.biojava.bio.structure.align.model
A class to convert the data in an AfpChain object to various String outputs.
AfpChainWriter() - Constructor for class org.biojava.bio.structure.align.model.AfpChainWriter
 
AFPChainXMLConverter - Class in org.biojava.bio.structure.align.xml
 
AFPChainXMLConverter() - Constructor for class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
 
AFPChainXMLParser - Class in org.biojava.bio.structure.align.xml
 
AFPChainXMLParser() - Constructor for class org.biojava.bio.structure.align.xml.AFPChainXMLParser
 
AFPOptimizer - Class in org.biojava.bio.structure.align.fatcat.calc
 
AFPOptimizer() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
 
afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
//Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
AFPPostProcessor - Class in org.biojava.bio.structure.align.fatcat.calc
does post processing after alignment chaingin
AFPPostProcessor() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
 
AFPTwister - Class in org.biojava.bio.structure.align
 
AFPTwister() - Constructor for class org.biojava.bio.structure.align.AFPTwister
 
Ala - Static variable in class org.biojava3.phylo.ResidueProperties
 
algorithmName - Static variable in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
algorithmName - Static variable in class org.biojava.bio.structure.align.ce.CeCPMain
 
algorithmName - Static variable in class org.biojava.bio.structure.align.ce.CeMain
 
algorithmName - Static variable in class org.biojava.bio.structure.align.ce.CeSideChainMain
 
algorithmName - Static variable in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
algorithmName - Static variable in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
algorithmName - Static variable in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
algorithmName - Static variable in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
ALIGFACTOR - Static variable in class org.biojava.bio.structure.align.pairwise.Gotoh
 
AligMatEl - Class in org.biojava.bio.structure.align.helper
 
AligMatEl() - Constructor for class org.biojava.bio.structure.align.helper.AligMatEl
 
align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.ce.CeCPMain
Aligns ca1 and ca2 using a heuristic to check for CPs.
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.ce.CeMain
Align ca2 onto ca1.
align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeMain
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
 
align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
align(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
align(Atom[], Atom[], Object) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
align(Atom[], Atom[]) - Method in interface org.biojava.bio.structure.align.StructureAlignment
Run an alignment while specifying the atoms to be aligned.
align(Atom[], Atom[], Object) - Method in interface org.biojava.bio.structure.align.StructureAlignment
run an alignment and also send a bean containing the parameters.
align(Structure, Structure) - Method in class org.biojava.bio.structure.align.StructurePairAligner
Calculate the alignment between the two full structures with default parameters
align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
Calculate the alignment between the two full structures with user provided parameters
align(Structure, String, Structure, String) - Method in class org.biojava.bio.structure.align.StructurePairAligner
Align two chains from the structures.
align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
Aligns two chains from the structures using user provided parameters.
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
calculate the protein structure superimposition, between two sets of atoms.
align(Structure, List<Chain>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
align(List<Group>, List<Group>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
aligns two chains of groups, where the first parent is representing the list of amino acids as obtained from the SEQRES records, and the second parent represents the groups obtained from the ATOM records (and containing the actual ATOM information).
align() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.bio.structure.align.pairwise.AligNPE
Align w/o penalizing endpags.
Alignable - Interface in org.biojava.bio.structure.align.pairwise
 
AlignedPosition - Class in org.biojava.bio.structure.gui.util
 
AlignedPosition() - Constructor for class org.biojava.bio.structure.gui.util.AlignedPosition
 
AlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step - Enum in org.biojava3.alignment.template
Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
Aligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an algorithm which computes an alignment Profile from a list of Sequences.
AlignerHelper - Class in org.biojava3.alignment.routines
Static utility to construct alignment routines from a common library of methods.
AlignerHelper() - Constructor for class org.biojava3.alignment.routines.AlignerHelper
 
AlignerHelper.Cut - Class in org.biojava3.alignment.routines
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
AlignerHelper.Cut(int, int[]) - Constructor for class org.biojava3.alignment.routines.AlignerHelper.Cut
 
AlignerHelper.Last - Enum in org.biojava3.alignment.routines
Defines a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
 
ALIGNMENT_PANEL - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
alignmentAsMap(AFPChain) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
AlignmentCalc - Class in org.biojava.bio.structure.align.gui
A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.bio.structure.align.gui.AlignmentCalc
requests an alignment of pdb1 vs pdb 2.
AlignmentCalc - Class in org.biojava.bio.structure.gui.util
A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure) - Constructor for class org.biojava.bio.structure.gui.util.AlignmentCalc
requests an alignment of pdb1 vs pdb 2.
AlignmentCalcDB - Class in org.biojava.bio.structure.align.gui
 
AlignmentCalcDB(AlignmentGui, Structure, String, UserConfiguration, String, Boolean) - Constructor for class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
AlignmentCalculationRunnable - Interface in org.biojava.bio.structure.align.gui
 
alignmentEnded() - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
alignmentEnded() - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
 
alignmentEnded() - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
AlignmentGui - Class in org.biojava.bio.structure.align.gui
A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.
AlignmentPositionListener - Interface in org.biojava.bio.structure.gui.events
 
AlignmentProgressListener - Interface in org.biojava.bio.structure.align.events
 
AlignmentProgressListener - Class in org.biojava.bio.structure.align.pairwise
A class to listen to progress of the structure alignmnent calcualtions
AlignmentProgressListener() - Constructor for class org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
 
AlignmentResult - Class in org.biojava.bio.structure.align.pairwise
A class to track the alignment results in a flat file
AlignmentResult() - Constructor for class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
Alignments - Class in org.biojava3.alignment
Static utility to easily run alignment routines.
Alignments.PairInProfileScorerType - Enum in org.biojava3.alignment
List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType - Enum in org.biojava3.alignment
List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType - Enum in org.biojava3.alignment
List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType - Enum in org.biojava3.alignment
List of implemented profile-profile alignment routines.
Alignments.RefinerType - Enum in org.biojava3.alignment
List of implemented profile refinement routines.
alignmentStarted(String, String) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
alignmentStarted(String, String) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
 
alignmentStarted(String, String) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
AlignmentTextPanel - Class in org.biojava.bio.structure.align.gui
 
AlignmentTextPanel() - Constructor for class org.biojava.bio.structure.align.gui.AlignmentTextPanel
 
AlignmentTools - Class in org.biojava.bio.structure.align.util
Some utility methods for analyzing and manipulating AFPChains.
AlignmentTools() - Constructor for class org.biojava.bio.structure.align.util.AlignmentTools
 
AlignmentTools.IdentityMap<K> - Class in org.biojava.bio.structure.align.util
A Map can be viewed as a function from K to V.
AlignmentTools.IdentityMap() - Constructor for class org.biojava.bio.structure.align.util.AlignmentTools.IdentityMap
 
alignNucleotideGroups(List<Group>, List<Group>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
alignPair(String, String) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
alignPair(String, String, String) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
AligNPE - Class in org.biojava.bio.structure.align.pairwise
 
AligNPE() - Constructor for class org.biojava.bio.structure.align.pairwise.AligNPE
 
alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
Aligns ca1 with ca2 permuted by cp residues.
alignRigid(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
 
alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.bio.structure.align.fatcat.FatCat
 
AlignTools - Class in org.biojava.bio.structure.align.helper
 
AlignTools() - Constructor for class org.biojava.bio.structure.align.helper.AlignTools
 
AligPanel - Class in org.biojava.bio.structure.align.gui.aligpanel
A JPanel that can display an AFPChain in a nice way and interact with Jmol.
AligPanel() - Constructor for class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
AligPanelMouseMotionListener - Class in org.biojava.bio.structure.align.gui.aligpanel
 
AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
AligUIManager - Class in org.biojava.bio.structure.align.webstart
 
AligUIManager() - Constructor for class org.biojava.bio.structure.align.webstart.AligUIManager
 
aliphatic - Static variable in class org.biojava3.phylo.ResidueProperties
 
ALL_PFAMS_ENCOUNTERED_SUFFIX - Static variable in class org.forester.application.surfacing
 
ALL_PFAMS_ENCOUNTERED_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX - Static variable in class org.forester.application.surfacing
 
ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
ALL_PFAMS_GAINED_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing
 
ALL_PFAMS_GAINED_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing
 
ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
ALL_PFAMS_LOST_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing
 
ALL_PFAMS_LOST_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing
 
ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
ALL_POLYMER_TYPES - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Convenience Set of all polymer types.
AllChemCompProvider - Class in org.biojava.bio.structure.io.mmcif
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
 
allComponents() - Static method in class org.biojava3.protmod.Component
 
allComponents() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
allIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
allKeywords() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
allModifications() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
ALLOW_MULTIPLE_PARENTS_DEFAULT - Static variable in class org.forester.phylogeny.Phylogeny
 
allPdbccIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
allPsimodIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
allResidIds() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
AltAligComparator - Class in org.biojava.bio.structure.align.pairwise
a comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
AltAligComparator() - Constructor for class org.biojava.bio.structure.align.pairwise.AltAligComparator
 
AlternativeAlignment - Class in org.biojava.bio.structure.align.pairwise
Implements a class which handles one possible (alternative) solution.
AlternativeAlignment() - Constructor for class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
AlternativeAlignmentFrame - Class in org.biojava.bio.structure.gui.util
a frame showing the alternative alignments, which are the result of a structure superimposition
AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
 
AmbiguityDNACompoundSet - Class in org.biojava3.core.sequence.compound
 
AmbiguityDNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
 
AmbiguityRNACompoundSet - Class in org.biojava3.core.sequence.compound
 
AmbiguityRNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
 
AMBIGUOUS_AA - Static variable in class org.biojava3.data.sequence.SequenceUtil
Same as AA pattern but with two additional letters - XU
AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava3.data.sequence.SequenceUtil
Ambiguous nucleotide
AMIGO_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
AminoAcid - Interface in org.biojava.bio.structure
A Group that represents an AminoAcid.
AMINOACID - Static variable in class org.biojava.bio.structure.GroupType
the type for amino acids
AminoAcid - Class in org.forester.development
 
AminoAcidComposition - Class in org.biojava3.aaproperties.xml
 
AminoAcidComposition() - Constructor for class org.biojava3.aaproperties.xml.AminoAcidComposition
 
AminoAcidComposition(String, String, String, List<Name2Count>, List<Name2Count>) - Constructor for class org.biojava3.aaproperties.xml.AminoAcidComposition
 
AminoAcidCompositionTable - Class in org.biojava3.aaproperties.xml
 
AminoAcidCompositionTable() - Constructor for class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
AminoAcidCompositionTable(List<AminoAcidComposition>) - Constructor for class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
AminoAcidCompound - Class in org.biojava3.core.sequence.compound
Used to describe an Amino Acid.
AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava3.core.sequence.compound.AminoAcidCompound
 
AminoAcidCompoundSet - Class in org.biojava3.core.sequence.compound
Set of proteinogenic amino acids.
AminoAcidCompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
AminoAcidImpl - Class in org.biojava.bio.structure
AminoAcid inherits most from Hetatom.
AminoAcidImpl() - Constructor for class org.biojava.bio.structure.AminoAcidImpl
 
aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
AminoAcidSequence - Class in org.forester.development
 
AminoAcidSequence(int) - Constructor for class org.forester.development.AminoAcidSequence
 
AminoAcidSequence(String, byte[]) - Constructor for class org.forester.development.AminoAcidSequence
 
AminoAcidSequence(String, String) - Constructor for class org.forester.development.AminoAcidSequence
 
amount(Atom) - Static method in class org.biojava.bio.structure.Calc
amount.
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.routines
This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int, int[]) - Constructor for class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Prepares for a pairwise global sequence alignment.
anchors - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
angle(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
angle.
angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
 
ANNOTATION - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
ANNOTATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Annotation - Class in org.forester.phylogeny.data
 
Annotation() - Constructor for class org.forester.phylogeny.data.Annotation
 
ANNOTATION_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
ANNOTATION_EVIDENCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
ANNOTATION_REF_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
ANNOTATION_SOURCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
ANNOTATION_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
AnnotationParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
APACHE_FEATURES_VALIDATION_SCHEMA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
APACHE_FEATURES_VALIDATION_SCHEMA - Static variable in class org.forester.io.parsers.tol.TolParser
 
APACHE_FEATURES_VALIDATION_SCHEMA_FULL - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
APACHE_FEATURES_VALIDATION_SCHEMA_FULL - Static variable in class org.forester.io.parsers.tol.TolParser
 
APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION - Static variable in class org.forester.io.parsers.tol.TolParser
 
apairs_from_idxlst(JointFragments) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
Set apairs according to a seed position.
App - Class in org.biojava3.genome
Hello world!
App() - Constructor for class org.biojava3.genome.App
 
App - Class in org.biojava3.phylo
Hello world!
App() - Constructor for class org.biojava3.phylo.App
 
append(T, Fastq...) - Method in interface org.biojava3.sequencing.io.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
append(T, Iterable<Fastq>) - Method in interface org.biojava3.sequencing.io.fastq.FastqWriter
Append the specified FASTQ formatted sequences to the specified appendable.
appendClose(Writer, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendElement(Writer, String, String, String, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendOpen(Writer, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendOpen(Writer, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendOpen(Writer, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendOpen(Writer, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendOpen(Writer, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendOpen(Writer, String, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
appendQuality(String) - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified quality scores appended to its current quality scores.
appendQuality(String) - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this listener of a quality line.
appendSeparatorIfNotEmpty(StringBuffer, char) - Static method in class org.forester.util.ForesterUtil
 
appendSequence(String) - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified sequence appended to its current sequence.
appendSequence(String) - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this parse listener of an additional sequence line.
appendValue(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
applyFilters() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
applyValues() - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
 
ARACYC_STR - Static variable in interface org.forester.go.GoXRef
 
Archaeopteryx - Class in org.forester.archaeopteryx
 
Archaeopteryx() - Constructor for class org.forester.archaeopteryx.Archaeopteryx
 
ArchaeopteryxA - Class in org.forester.archaeopteryx
 
ArchaeopteryxA() - Constructor for class org.forester.archaeopteryx.ArchaeopteryxA
 
ArchaeopteryxE - Class in org.forester.archaeopteryx
 
ArchaeopteryxE() - Constructor for class org.forester.archaeopteryx.ArchaeopteryxE
 
areAllChildrenDuplications(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
Arg - Static variable in class org.biojava3.phylo.ResidueProperties
 
arithmeticMean() - Method in class org.forester.util.BasicDescriptiveStatistics
 
arithmeticMean() - Method in interface org.forester.util.DescriptiveStatistics
 
aromatic - Static variable in class org.biojava3.phylo.ResidueProperties
 
arrayLeftDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Element-by-element left division in place, A = A.\B
ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader
 
ArrayListProxySequenceReader() - Constructor for class org.biojava3.core.sequence.loader.ArrayListProxySequenceReader
 
ArrayListSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
Stores a Sequence as a collection of compounds in an ArrayList
ArrayListSequenceReader() - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
arrayRightDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Element-by-element multiplication in place, A = A.*B
AsciiHistogram - Class in org.forester.util
 
AsciiHistogram(DescriptiveStatistics) - Constructor for class org.forester.util.AsciiHistogram
 
AsciiHistogram(DescriptiveStatistics, String) - Constructor for class org.forester.util.AsciiHistogram
 
Asn - Static variable in class org.biojava3.phylo.ResidueProperties
 
Asp - Static variable in class org.biojava3.phylo.ResidueProperties
 
assertLocation() - Method in class org.biojava3.core.sequence.location.InsdcLocations.BondLocation
 
assertLocation() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
assign(Structure) - Method in class org.biojava.bio.structure.secstruc.SecStruc
assigns the secondary structure to the groups in this Structure object and set the results in the group properties.
AssignmentXMLSerializer - Class in org.biojava.bio.structure.domain
 
AssignmentXMLSerializer() - Constructor for class org.biojava.bio.structure.domain.AssignmentXMLSerializer
 
asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
asSimpleText() - Method in class org.forester.development.AminoAcidSequence
 
asSimpleText() - Method in class org.forester.go.BasicGoTerm
 
asSimpleText() - Method in class org.forester.phylogeny.data.Accession
 
asSimpleText() - Method in class org.forester.phylogeny.data.Annotation
 
asSimpleText() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
asSimpleText() - Method in class org.forester.phylogeny.data.BranchColor
 
asSimpleText() - Method in class org.forester.phylogeny.data.BranchData
 
asSimpleText() - Method in class org.forester.phylogeny.data.BranchWidth
 
asSimpleText() - Method in class org.forester.phylogeny.data.Confidence
 
asSimpleText() - Method in class org.forester.phylogeny.data.Date
 
asSimpleText() - Method in class org.forester.phylogeny.data.Distribution
 
asSimpleText() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
asSimpleText() - Method in class org.forester.phylogeny.data.Event
 
asSimpleText() - Method in class org.forester.phylogeny.data.Identifier
 
asSimpleText() - Method in class org.forester.phylogeny.data.NodeData
 
asSimpleText() - Method in interface org.forester.phylogeny.data.PhylogenyData
 
asSimpleText() - Method in class org.forester.phylogeny.data.Point
 
asSimpleText() - Method in class org.forester.phylogeny.data.PropertiesMap
 
asSimpleText() - Method in class org.forester.phylogeny.data.Property
 
asSimpleText() - Method in class org.forester.phylogeny.data.ProteinDomain
 
asSimpleText() - Method in class org.forester.phylogeny.data.Reference
 
asSimpleText() - Method in class org.forester.phylogeny.data.Sequence
 
asSimpleText() - Method in class org.forester.phylogeny.data.SequenceRelation
 
asSimpleText() - Method in class org.forester.phylogeny.data.Taxonomy
 
asSimpleText() - Method in class org.forester.phylogeny.data.Uri
 
asString() - Method in interface org.forester.pccx.Coverage
 
asString() - Method in interface org.forester.pccx.CoverageCalculationOptions
 
asString() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
asString() - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions
 
asSummary() - Method in class org.forester.util.BasicDescriptiveStatistics
 
asSummary() - Method in interface org.forester.util.DescriptiveStatistics
 
asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
asText() - Method in class org.forester.development.AminoAcidSequence
 
asText() - Method in class org.forester.go.BasicGoTerm
 
asText() - Method in class org.forester.phylogeny.data.Accession
 
asText() - Method in class org.forester.phylogeny.data.Annotation
 
asText() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
asText() - Method in class org.forester.phylogeny.data.BranchColor
 
asText() - Method in class org.forester.phylogeny.data.BranchData
 
asText() - Method in class org.forester.phylogeny.data.BranchWidth
 
asText() - Method in class org.forester.phylogeny.data.Confidence
 
asText() - Method in class org.forester.phylogeny.data.Date
 
asText() - Method in class org.forester.phylogeny.data.Distribution
 
asText() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
asText() - Method in class org.forester.phylogeny.data.Event
 
asText() - Method in class org.forester.phylogeny.data.Identifier
 
asText() - Method in class org.forester.phylogeny.data.NodeData
 
asText() - Method in interface org.forester.phylogeny.data.PhylogenyData
 
asText() - Method in class org.forester.phylogeny.data.Point
 
asText() - Method in class org.forester.phylogeny.data.PropertiesMap
 
asText() - Method in class org.forester.phylogeny.data.Property
 
asText() - Method in class org.forester.phylogeny.data.ProteinDomain
 
asText() - Method in class org.forester.phylogeny.data.Reference
 
asText() - Method in class org.forester.phylogeny.data.Sequence
 
asText() - Method in class org.forester.phylogeny.data.SequenceRelation
 
asText() - Method in class org.forester.phylogeny.data.Taxonomy
 
asText() - Method in class org.forester.phylogeny.data.Uri
 
Atom - Interface in org.biojava.bio.structure
A simple interface for an Atom.
ATOM_CA_THRESHOLD - Static variable in class org.biojava.bio.structure.io.FileParsingParameters
the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
AtomCache - Class in org.biojava.bio.structure.align.util
A utility class that provides easy access to Structure objects.
AtomCache() - Constructor for class org.biojava.bio.structure.align.util.AtomCache
Default AtomCache constructor.
AtomCache(String, boolean) - Constructor for class org.biojava.bio.structure.align.util.AtomCache
Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(UserConfiguration) - Constructor for class org.biojava.bio.structure.align.util.AtomCache
Creates a new AtomCache object based on the provided UserConfiguration.
AtomImpl - Class in org.biojava.bio.structure
Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.bio.structure.AtomImpl
 
AtomInfo - Class in org.biojava.bio.structure.align.gui.jmol
This class uniquely describes an atom
AtomInfo() - Constructor for class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
AtomInfoParser - Class in org.biojava.bio.structure.align.gui.jmol
 
AtomInfoParser() - Constructor for class org.biojava.bio.structure.align.gui.jmol.AtomInfoParser
 
AtomIterator - Class in org.biojava.bio.structure
an iterator over all atoms of a structure / group.
AtomIterator(Structure) - Constructor for class org.biojava.bio.structure.AtomIterator
Constructs an AtomIterator object.
AtomIterator(Group) - Constructor for class org.biojava.bio.structure.AtomIterator
Constructs an AtomIterator object.
ATOMRECORD - Static variable in interface org.biojava.bio.structure.AminoAcid
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
atoms - Variable in class org.biojava.bio.structure.HetatomImpl
 
AtomSite - Class in org.biojava.bio.structure.io.mmcif.model
 
AtomSite() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
attribute(String, String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
attribute(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
attribute(String, String, String) - Method in interface org.biojava3.core.util.XMLWriter
Add an attribute to an element.
attribute(String, String) - Method in interface org.biojava3.core.util.XMLWriter
Add an un-qualified attribute to an element.
attributeEqualsValue(XmlElement, String, String) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
 
attributeEqualsValue(XmlElement, String, String) - Static method in class org.forester.io.parsers.tol.TolXmlHandler
 
attributes() - Method in class org.biojava3.genome.parsers.gff.Feature
Get the string of key/value attributes.
attributeValues(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a collection of the unique values for the specified key.
AuditAuthor - Class in org.biojava.bio.structure.io.mmcif.model
 
AuditAuthor() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AuditAuthor
 
AUTHDATE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
Author - Class in org.biojava.bio.structure
Describes author attributes for author information in a PDB file.
Author() - Constructor for class org.biojava.bio.structure.Author
 
AUTHORITY - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
AutoSuggestProvider - Interface in org.biojava.bio.structure.align.gui.autosuggest
A class that provides auto-completion suggestions for JAutoSuggest
available() - Method in class org.biojava3.core.util.UncompressInputStream
 

B

backboneAtomNames - Static variable in class org.biojava.bio.structure.StructureTools
The names of the Atoms that form the backbone.
BACKGROUND_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing
 
BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing_old
 
BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing
 
BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing_old
 
BasicBinaryDomainCombination - Class in org.forester.surfacing
 
BasicBinaryDomainCombination(DomainId, DomainId) - Constructor for class org.forester.surfacing.BasicBinaryDomainCombination
 
BasicBinaryDomainCombination(String, String) - Constructor for class org.forester.surfacing.BasicBinaryDomainCombination
 
BasicCharacterStateMatrix<S> - Class in org.forester.phylogenyinference
 
BasicCharacterStateMatrix(int, int) - Constructor for class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
BasicCharacterStateMatrix(int, int, S) - Constructor for class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
BasicCharacterStateMatrix(List<List<S>>) - Constructor for class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
BasicCharacterStateMatrix(S[][]) - Constructor for class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
BasicCombinableDomains - Class in org.forester.surfacing
 
BasicCombinableDomains(DomainId, Species) - Constructor for class org.forester.surfacing.BasicCombinableDomains
 
BasicDescriptiveStatistics - Class in org.forester.util
 
BasicDescriptiveStatistics() - Constructor for class org.forester.util.BasicDescriptiveStatistics
 
BasicDomain - Class in org.forester.surfacing
 
BasicDomain(String) - Constructor for class org.forester.surfacing.BasicDomain
 
BasicDomain(String, int, int, short, short, double, double) - Constructor for class org.forester.surfacing.BasicDomain
 
BasicDomain(String, int, int, short, short, double, double, double, double) - Constructor for class org.forester.surfacing.BasicDomain
 
BasicDomainSimilarityCalculator - Class in org.forester.surfacing
 
BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField, boolean, boolean) - Constructor for class org.forester.surfacing.BasicDomainSimilarityCalculator
 
BasicExternalNodeBasedCoverageExtender - Class in org.forester.pccx
 
BasicExternalNodeBasedCoverageExtender() - Constructor for class org.forester.pccx.BasicExternalNodeBasedCoverageExtender
 
BasicGenomeWideCombinableDomains - Class in org.forester.surfacing
 
BasicGoRelationship - Class in org.forester.go
 
BasicGoRelationship(String) - Constructor for class org.forester.go.BasicGoRelationship
 
BasicGoRelationship(String, String) - Constructor for class org.forester.go.BasicGoRelationship
 
BasicGoRelationship(GoRelationship.Type, GoId) - Constructor for class org.forester.go.BasicGoRelationship
 
BasicGoSubset - Class in org.forester.go
 
BasicGoSubset(String) - Constructor for class org.forester.go.BasicGoSubset
 
BasicGoSubset(GoSubset.Type) - Constructor for class org.forester.go.BasicGoSubset
 
BasicGoTerm - Class in org.forester.go
 
BasicGoTerm(GoId, String, GoNameSpace, boolean) - Constructor for class org.forester.go.BasicGoTerm
 
BasicGoTerm(String, String, String, boolean) - Constructor for class org.forester.go.BasicGoTerm
 
BasicGoXRef - Class in org.forester.go
 
BasicGoXRef(String) - Constructor for class org.forester.go.BasicGoXRef
 
BasicGoXRef(GoXRef.Type, String) - Constructor for class org.forester.go.BasicGoXRef
 
BasicMsa - Class in org.forester.development
 
BasicMsa() - Constructor for class org.forester.development.BasicMsa
 
BasicPhylogeniesWebserviceClient - Class in org.forester.archaeopteryx.webservices
 
BasicPhylogeniesWebserviceClient(String, String, String, String, WebservicesManager.WsPhylogenyFormat, ForesterUtil.PhylogenyNodeField, String, boolean, String, Object) - Constructor for class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
BasicPhylogenyFactory - Class in org.forester.phylogeny.factories
 
BasicPhylogenyFactory() - Constructor for class org.forester.phylogeny.factories.BasicPhylogenyFactory
 
BasicProtein - Class in org.forester.surfacing
 
BasicProtein(String, String) - Constructor for class org.forester.surfacing.BasicProtein
 
BasicSequence<C extends Compound> - Class in org.biojava3.core.sequence
Bare bones version of the Sequence object to be used sparingly.
BasicSequence(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.BasicSequence
 
BasicSequence(ProxySequenceReader<C>) - Constructor for class org.biojava3.core.sequence.BasicSequence
 
BasicSpecies - Class in org.forester.surfacing
 
BasicSpecies(String) - Constructor for class org.forester.surfacing.BasicSpecies
 
BasicSymmetricalDistanceMatrix - Class in org.forester.phylogenyinference
 
BasicSymmetricalDistanceMatrix(int) - Constructor for class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
BasicTable<E> - Class in org.forester.util
 
BasicTable() - Constructor for class org.forester.util.BasicTable
 
BasicTableParser - Class in org.forester.util
 
BDC_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing
 
BDC_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing_old
 
BEGIN_CHARACTERS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
BEGIN_TAXA - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
BEGIN_TREES - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
BerkeleyScopInstallation - Class in org.biojava.bio.structure.scop
 
BerkeleyScopInstallation() - Constructor for class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
bestTrace1 - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTrace1 - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
bestTrace2 - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTrace2 - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
bestTraces1 - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTraces1 - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
bestTraces2 - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTraces2 - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
bestTraceScore - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTraceScore - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
bestTracesN - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTracesN - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
bestTracesScores - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
bestTracesScores - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
BigSqrt - Class in org.biojava.bio.structure.secstruc
calculate a more precise SQRT.
BigSqrt() - Constructor for class org.biojava.bio.structure.secstruc.BigSqrt
 
BINARY_CHARACTER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_GAINED - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_GAINED_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_LOST - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_LOST_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_PRESENT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_PRESENT_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_CHARACTERS_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BINARY_DOMAIN_COMBINATIONS - Static variable in class org.forester.io.parsers.nhx.NHXtags
Deprecated.
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing
 
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing_old
 
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing
 
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing_old
 
BinaryCharacters - Class in org.forester.phylogeny.data
 
BinaryCharacters() - Constructor for class org.forester.phylogeny.data.BinaryCharacters
 
BinaryCharacters(SortedSet<String>, SortedSet<String>, SortedSet<String>, String) - Constructor for class org.forester.phylogeny.data.BinaryCharacters
 
BinaryCharacters(SortedSet<String>, SortedSet<String>, SortedSet<String>, String, int, int, int) - Constructor for class org.forester.phylogeny.data.BinaryCharacters
 
BinaryCharactersParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
BinaryDomainCombination - Interface in org.forester.surfacing
 
BinaryDomainCombination.DomainCombinationType - Enum in org.forester.surfacing
 
BinaryDomainCombination.OutputFormat - Enum in org.forester.surfacing
 
bioEnd() - Method in class org.biojava3.genome.parsers.gff.Location
Get end index, in biocoordinates.
BiojavaJmol - Class in org.biojava.bio.structure.gui
A class that provides a simple GUI for Jmol
BiojavaJmol() - Constructor for class org.biojava.bio.structure.gui.BiojavaJmol
 
BioJavaStructureAlignment - Class in org.biojava.bio.structure.align
Wrapper for the BioJava Structure Alignment Implementation
BioJavaStructureAlignment() - Constructor for class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
BIOLOGICAL_PROCESS_STR - Variable in class org.forester.go.GoNameSpace
 
bioStart() - Method in class org.biojava3.genome.parsers.gff.Location
Get start index, in biocoordinates.
bioStrand() - Method in class org.biojava3.genome.parsers.gff.Location
Get character representation of strand.
bitMask() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
This method should return the bit mask to be used to extract the bytes you are interested in working with.
bitMask() - Method in class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
bitMask() - Method in class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
BitSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
An implementation of the popular bit encodings.
BitSequenceReader(BitSequenceReader.BitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader
Instance which allows you to supply a different @{BitArrayWorker} object.
BitSequenceReader.BitArrayWorker<C extends Compound> - Class in org.biojava3.core.sequence.storage
The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.
BitSequenceReader.BitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
BitSequenceReader.BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
BitSequenceReader.BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
BitSequenceReader.BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
bitsPerCompound() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns how many bits are used to represent a compound e.g.
BLACK_WHITE_GRADIENT - Static variable in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
Blast - Class in org.forester.archaeopteryx
 
Blast() - Constructor for class org.forester.archaeopteryx.Blast
 
BlastAlignmentParameterEnum - Enum in org.biojava3.ws.alignment.qblast
Alignment request parameters accepted by QBlast service.
Not all are mandatory.
BlastHomologyHits - Class in org.biojava3.genome.homology
 
BlastHomologyHits() - Constructor for class org.biojava3.genome.homology.BlastHomologyHits
 
BlastJob - Class in org.biojava3.ws.alignment.qblast
Information about QBlast search job
BlastJob() - Constructor for class org.biojava3.ws.alignment.qblast.BlastJob
 
BlastMatrixEnum - Enum in org.biojava3.ws.alignment.qblast
Enum representing matrices supported by QBlast
BlastOutputAlignmentFormatEnum - Enum in org.biojava3.ws.alignment.qblast
Enum representing available output alignment types.
BlastOutputFormatEnum - Enum in org.biojava3.ws.alignment.qblast
Enum representing available output formats.
BlastOutputParameterEnum - Enum in org.biojava3.ws.alignment.qblast
Output parameters accepted by QBlast service.
BlastProgramEnum - Enum in org.biojava3.ws.alignment.qblast
Enum representing available blast programs.
BlastXMLQuery - Class in org.biojava3.genome.query
 
BlastXMLQuery(String) - Constructor for class org.biojava3.genome.query.BlastXMLQuery
 
blockInfo(AFPChain) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
get the afp list and residue list for each block
Blosum62 - Static variable in class org.biojava3.ronn.RonnConstraint
 
Bond - Class in org.biojava.bio.structure
Simple bond - it's just an edge/vertex for two Atom nodes.
Bond() - Constructor for class org.biojava.bio.structure.Bond
 
Bond(double, BondType, Group, Atom, Group, Atom) - Constructor for class org.biojava.bio.structure.Bond
 
BondType - Enum in org.biojava.bio.structure
Work in progress - NOT final!
bounds() - Method in class org.biojava3.genome.parsers.gff.FeatureList
The union of all locations of all features in this list, mapped to the positive strand.
BRANCH_LENGTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
BRANCH_WIDTH - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
BRANCH_WIDTH_DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.BranchWidth
 
BranchColor - Class in org.forester.phylogeny.data
 
BranchColor() - Constructor for class org.forester.phylogeny.data.BranchColor
 
BranchColor(Color) - Constructor for class org.forester.phylogeny.data.BranchColor
 
BranchCountingBasedScoringMethod - Class in org.forester.pccx
 
BranchCountingBasedScoringMethod() - Constructor for class org.forester.pccx.BranchCountingBasedScoringMethod
 
BranchData - Class in org.forester.phylogeny.data
 
BranchData() - Constructor for class org.forester.phylogeny.data.BranchData
 
BranchLengthBasedScoringMethod - Class in org.forester.pccx
 
BranchLengthBasedScoringMethod() - Constructor for class org.forester.pccx.BranchLengthBasedScoringMethod
 
BranchWidth - Class in org.forester.phylogeny.data
 
BranchWidth() - Constructor for class org.forester.phylogeny.data.BranchWidth
 
BranchWidth(double) - Constructor for class org.forester.phylogeny.data.BranchWidth
 
BranchWidthParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
broadcastComplete() - Method in class org.biojava3.phylo.TreeConstructor
 
BrowserOpener - Class in org.biojava.bio.structure.align.webstart
 
BrowserOpener() - Constructor for class org.biojava.bio.structure.align.webstart.BrowserOpener
 
BufferedReaderBytesRead - Class in org.biojava3.core.sequence.io
Need to keep track of actual bytes read and take advantage of buffered reader performance.
BufferedReaderBytesRead(Reader, int) - Constructor for class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Creates a buffering character-input stream that uses an input buffer of the specified size.
BufferedReaderBytesRead(Reader) - Constructor for class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Creates a buffering character-input stream that uses a default-sized input buffer.
build() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
The method to finish any calls to the builder with which returns a transcription engine.
build() - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
 
build() - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Build and return a new FASTQ formatted sequence configured from the properties of this builder.
buildFeatureAtrributeIndex(String, FeatureList) - Static method in class org.biojava3.genome.parsers.gff.FeatureHelper
Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index
buildTranslators() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
buried - Static variable in class org.biojava3.phylo.ResidueProperties
 
buriedmax - Static variable in class org.biojava3.phylo.ResidueProperties
 
buriedmin - Static variable in class org.biojava3.phylo.ResidueProperties
 
BYTES_PER_INT - Static variable in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 

C

c - Variable in class org.biojava.bio.structure.align.ce.CeCPMain.CPRange
first allowed c-term
C - Static variable in class org.biojava3.aaproperties.Constraints
 
CA_AND_SIDE_CHAIN_ANGLE_SCORING - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
CA_MIN_DIST - Static variable in class org.biojava.bio.structure.secstruc.SecStruc
the minimal distance of two CA atoms if H-bonds are allowed to form.
caAtomName - Static variable in class org.biojava.bio.structure.StructureTools
The Atom name of C-alpha atoms.
cache(K, V) - Method in class org.biojava.bio.structure.domain.SerializableCache
This will not cache null values.
CACHE_PROPERTY - Static variable in class org.biojava3.core.util.InputStreamProvider
 
CachedRemoteScopInstallation - Class in org.biojava.bio.structure.scop
An extension of the RemoteScopInstallation that caches some of the data locally.
CachedRemoteScopInstallation() - Constructor for class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
CachedRemoteScopInstallation(boolean) - Constructor for class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
CacheFactory - Class in org.biojava.bio.structure.align.util
provides a SoftHashMap singleton.
cacheFileName - Variable in class org.biojava.bio.structure.domain.SerializableCache
 
CAConverter - Class in org.biojava.bio.structure.io
Converts full atom representations to Calpha only ones.
CAConverter() - Constructor for class org.biojava.bio.structure.io.CAConverter
 
calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
//return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
Calc - Class in org.biojava.bio.structure
utility operations on Atoms, AminoAcids, etc.
Calc() - Constructor for class org.biojava.bio.structure.Calc
 
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.bio.structure.align.ce.CECalculator
superimpose and get rmsd
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
superimpose and get rmsd
calcColor(double, double, double, Color, Color) - Static method in class org.forester.util.ForesterUtil
This calculates a color.
calcColor(double, double, double, double, Color, Color, Color) - Static method in class org.forester.util.ForesterUtil
This calculates a color.
calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
calcScale(int) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
a value of 100 means that the whole sequence should be displayed in the current visible window a factor of 1 means that one amino acid shoud be drawn as big as possible
calcScores(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
calculates scores for this alignment ( %id )
calcSimilarity() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
calculateCopyNumberDifferences(List<GenomeWideCombinableDomains>, SortedMap<Species, List<Protein>>, List<String>, List<String>, List<String>, int, Double, File, File, File, Map<DomainId, List<GoId>>, Map<GoId, GoTerm>, File, File, File) - Static method in class org.forester.surfacing.DomainCountsDifferenceUtil
 
calculateCoverage(List<Phylogeny>, List<String>, CoverageCalculationOptions, boolean) - Method in interface org.forester.pccx.CoverageCalculationMethod
 
calculateCoverage(List<Phylogeny>, List<String>, boolean) - Method in class org.forester.pccx.CoverageCalculator
 
calculateCoverage(List<Phylogeny>, List<String>, CoverageCalculationOptions, boolean) - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethod
 
calculateDepth(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity>) - Static method in class org.forester.surfacing.SurfacingUtil
 
calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
 
calculateDistance(PhylogenyNode, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyMethods
Calculates the distance between PhylogenyNodes node1 and node2.
calculateDistanceToRoot(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
calculateFurthestDistance(Phylogeny) - Method in class org.forester.phylogeny.PhylogenyMethods
 
calculateHBondEnergy(SecStrucGroup, SecStrucGroup) - Method in class org.biojava.bio.structure.secstruc.SecStruc
calculate HBond energy of two groups in cal/mol ...
calculateIndirectAmbiguities() - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
Loops through all known nucelotides and attempts to find which are equivalent to each other.
calculateMaxBranchesToLeaf(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
calculateMaxDepth(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
calculateMaxDistanceToRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
calculateMaximumNumberOfDescendantsPerNode(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
calculateMeanBasedStatistics() - Method in class org.forester.surfacing.DomainLengths
Returns descriptive statistics based on the arithmetic means for each species.
calculateMeanBasedStatisticsForAllSpecies() - Method in class org.forester.surfacing.DomainLengthsTable
 
calculateMeanBasedStatisticsForDomain(DomainId) - Method in class org.forester.surfacing.DomainLengthsTable
 
calculateMeanBasedStatisticsForSpecies(Species) - Method in class org.forester.surfacing.DomainLengthsTable
 
calculateMinCP(int[], int, int, int) - Static method in class org.biojava.bio.structure.align.ce.CeCPMain
Finds the alignment index of the residues minCPlength before and after the duplication.
calculateOverlap(Domain, List<Boolean>) - Static method in class org.forester.surfacing.SurfacingUtil
 
calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double>, Phylogeny, PhylogenyNode, CoverageCalculationOptions) - Method in class org.forester.pccx.BranchCountingBasedScoringMethod
 
calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double>, Phylogeny, PhylogenyNode, CoverageCalculationOptions) - Method in interface org.forester.pccx.ScoringMethodForExternalNode
This calculates the coverage score for one external node.
calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
This returns a score between 0.0 (no binary domain combination in common) and 1.0 (all binary domain combinations in common) measuring the similarity between two genomes based on the number of shared binary domain combinations: t: sum of (distinct) binary domain combinations s: sum of shared (distinct) binary domain combinations 1 - ( ( t - s ) / t )
calculateSharedDomainsBasedGenomeSimilarityScore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
This returns a score between 0.0 (no domains in common) and 1.0 (all domains in common) measuring the similarity between two genomes based on the number of shared domains: t: sum of (distinct) domains s: sum of shared (distinct) domains 1 - ( ( t - s ) / t )
calculateSimilarities(PairwiseDomainSimilarityCalculator, List<GenomeWideCombinableDomains>, boolean, boolean) - Method in class org.forester.surfacing.BasicDomainSimilarityCalculator
 
calculateSimilarities(PairwiseDomainSimilarityCalculator, List<GenomeWideCombinableDomains>, boolean, boolean) - Method in interface org.forester.surfacing.DomainSimilarityCalculator
 
calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator
 
calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator
 
calculateSimilarity(CombinableDomains, CombinableDomains) - Method in interface org.forester.surfacing.PairwiseDomainSimilarityCalculator
 
calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator
 
calculateSubtreeHeight(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
This calculates the height of the subtree emanating at n for rooted, tree-shaped phylogenies
calculateSumOfDistinctTaxonomies(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Returns the sum of different taxonomies of all external nodes of node.
calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
calculateZScoreForSpecies(Species) - Method in class org.forester.surfacing.DomainLengths
Note.
calculator - Variable in class org.biojava.bio.structure.align.ce.CeMain
 
call() - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
call() - Method in class org.biojava3.alignment.template.CallablePairwiseSequenceAligner
 
call() - Method in class org.biojava3.alignment.template.CallablePairwiseSequenceScorer
 
call() - Method in class org.biojava3.alignment.template.CallableProfileProfileAligner
 
call() - Method in class org.biojava3.ronn.ORonn
 
CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
Implements a concurrency wrapper for a PairwiseSequenceAligner.
CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava3.alignment.template.CallablePairwiseSequenceAligner
Creates a pairwise sequence alignment task for simplified parallel execution.
CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
Implements a concurrency wrapper for a PairwiseSequenceScorer.
CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava3.alignment.template.CallablePairwiseSequenceScorer
Creates a pairwise sequence scoring task for simplified parallel execution.
CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.template
Implements a concurrency wrapper for a ProfileProfileAligner.
CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava3.alignment.template.CallableProfileProfileAligner
Creates a profile-profile alignment task for simplified parallel execution.
CallableStructureAlignment - Class in org.biojava.bio.structure.align
 
CallableStructureAlignment() - Constructor for class org.biojava.bio.structure.align.CallableStructureAlignment
 
calNS(FatCatParameters, AFPChain) - Method in class org.biojava.bio.structure.align.fatcat.calc.SigEva
 
calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.bio.structure.align.fatcat.calc.SigEva
 
cancel() - Method in class org.biojava3.phylo.TreeConstructor
 
canceled(Object) - Method in interface org.biojava3.phylo.NJTreeProgressListener
 
canceled(Object) - Method in class org.biojava3.phylo.ProgessListenerStub
 
canComplement(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement
CaseFreeAminoAcidCompoundSet - Class in org.biojava3.aaproperties.xml
Set of proteinogenic amino acids.
CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
CaseInsensitiveCompound - Class in org.biojava3.core.sequence.transcription
Attempts to wrap compounds so it is possible to view them in a case insensitive manner
CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
CasePreservingProteinSequenceCreator - Class in org.biojava3.core.sequence.io
A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
 
cbAtomName - Static variable in class org.biojava.bio.structure.StructureTools
 
CDSComparator - Class in org.biojava3.core.sequence
 
CDSComparator() - Constructor for class org.biojava3.core.sequence.CDSComparator
 
CDSSequence - Class in org.biojava3.core.sequence
Represents a exon or coding sequence in a gene.
CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava3.core.sequence.CDSSequence
 
CECalculator - Class in org.biojava.bio.structure.align.ce
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CECalculator(CeParameters) - Constructor for class org.biojava.bio.structure.align.ce.CECalculator
 
CeCalculatorEnhanced - Class in org.biojava.bio.structure.align.ce
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
ceColumnNames - Static variable in class org.biojava.bio.structure.align.gui.DBResultTable
 
CeCPMain - Class in org.biojava.bio.structure.align.ce
A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
CeCPMain() - Constructor for class org.biojava.bio.structure.align.ce.CeCPMain
 
CeCPMain.CPRange - Class in org.biojava.bio.structure.align.ce
Tiny wrapper for the disallowed regions of an alignment.
CeCPMain.CPRange() - Constructor for class org.biojava.bio.structure.align.ce.CeCPMain.CPRange
 
CeCPUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
 
CeCPUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.CeCPUserArgumentProcessor
 
CELLULAR_COMPONENT_STR - Variable in class org.forester.go.GoNameSpace
 
CeMain - Class in org.biojava.bio.structure.align.ce
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeMain() - Constructor for class org.biojava.bio.structure.align.ce.CeMain
 
centerAtoms(Atom[]) - Static method in class org.biojava.bio.structure.Calc
Center the atoms at the Centroid.
centerAtoms(Atom[], Atom) - Static method in class org.biojava.bio.structure.Calc
Center the atoms at the Centroid, if the centroid is already know.
centerOfMass(Atom[]) - Static method in class org.biojava.bio.structure.Calc
 
CeParameters - Class in org.biojava.bio.structure.align.ce
Contains the parameters that can be sent to CE
CeParameters() - Constructor for class org.biojava.bio.structure.align.ce.CeParameters
 
CeSideChainMain - Class in org.biojava.bio.structure.align.ce
 
CeSideChainMain() - Constructor for class org.biojava.bio.structure.align.ce.CeSideChainMain
 
CeSideChainUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
 
CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor
 
CeUserArgumentProcessor - Class in org.biojava.bio.structure.align.ce
process the arguments from command line
CeUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.ce.CeUserArgumentProcessor
 
Chain - Interface in org.biojava.bio.structure
Defines the interface for a Chain.
CHAIN_NR_SYMBOL - Static variable in class org.biojava.bio.structure.align.util.AtomCache
 
CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.bio.structure.align.util.AtomCache
 
chainId - Variable in class org.biojava.bio.structure.align.client.StructureName
 
ChainImpl - Class in org.biojava.bio.structure
A Chain in a PDB file.
ChainImpl() - Constructor for class org.biojava.bio.structure.ChainImpl
Constructs a ChainImpl object.
characters(char[], int, int) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
 
characters(char[], int, int) - Method in class org.forester.io.parsers.tol.TolXmlHandler
 
CharacterStateMatrix<S> - Interface in org.forester.phylogenyinference
 
CharacterStateMatrix.BinaryStates - Enum in org.forester.phylogenyinference
It is crucial that the order ABSENT, UNKNOWN, PRESENT not be changes since this determines the sort order.
CharacterStateMatrix.Format - Enum in org.forester.phylogenyinference
 
CharacterStateMatrix.GainLossStates - Enum in org.forester.phylogenyinference
 
CharacterStateMatrix.NucleotideStates - Enum in org.forester.phylogenyinference
 
charged - Static variable in class org.biojava3.phylo.ResidueProperties
 
CHARSTATELABELS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
checkDoFirstInstall() - Method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
checks if the chemical components already have been installed into the PDB directory.
checkForOutputFileWriteability(File) - Static method in class org.forester.surfacing.SurfacingUtil
 
checkPath() - Static method in class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
make sure all paths are initialized correctly
checkPoint() - Method in class org.biojava3.ronn.Timer
 
checkSequence(String) - Static method in class org.biojava3.aaproperties.Utils
Checks if the sequence contains invalid characters.
checkSequence(String, Set<Character>) - Static method in class org.biojava3.aaproperties.Utils
Checks if the sequence contains invalid characters.
checksum(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Performs a simple CRC64 checksum on any given sequence.
CheckTreeAccuracy - Class in org.biojava3.phylo
 
CheckTreeAccuracy() - Constructor for class org.biojava3.phylo.CheckTreeAccuracy
 
CheckTreeAccuracy - Class in org.forester.application
 
CheckTreeAccuracy() - Constructor for class org.forester.application.CheckTreeAccuracy
 
CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
 
chem_comp_type - Variable in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
String value of the type
ChemComp - Class in org.biojava.bio.structure.io.mmcif.model
A definition for a Chemical Component, as maintained by the wwPDB.
ChemComp() - Constructor for class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
ChemCompConsumer - Class in org.biojava.bio.structure.io.mmcif
 
ChemCompConsumer() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
ChemCompDescriptor - Class in org.biojava.bio.structure.io.mmcif.model
Container object for _pdbx_chem_comp_descriptor
ChemCompDescriptor() - Constructor for class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
ChemCompGroupFactory - Class in org.biojava.bio.structure.io.mmcif
 
ChemCompGroupFactory() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
 
ChemCompProvider - Interface in org.biojava.bio.structure.io.mmcif
Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.bio.structure.io.mmcif.chem
Some tools for working with chemical compounds.
ChemCompTools() - Constructor for class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
ChemicalComponentDictionary - Class in org.biojava.bio.structure.io.mmcif
A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
ChildNodeIteratorForward - Class in org.forester.phylogeny.iterators
 
ChildNodeIteratorForward(PhylogenyNode) - Constructor for class org.forester.phylogeny.iterators.ChildNodeIteratorForward
Creates a new ChildNodeIteratorForward.
children() - Method in class org.biojava3.alignment.GuideTree.Node
 
chol() - Method in class org.biojava.bio.structure.jama.Matrix
Cholesky Decomposition
CholeskyDecomposition - Class in org.biojava.bio.structure.jama
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
ChooseDirAction - Class in org.biojava.bio.structure.align.gui
Ask the user to provide a directory containting PDB files.
ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.bio.structure.align.gui.ChooseDirAction
 
ChromosomeSequence - Class in org.biojava3.core.sequence
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
ChromosomeSequence() - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
ChromosomeSequence(String) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
String is king and assume DNA
ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
circularLocation(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
circularLocation(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
CLADE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
CLADE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
CLADE_DATE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
CLADE_DATE_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
CLADE_DATE_MAX - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
CLADE_DATE_MIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
CLADE_DATE_UNIT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
CLADE_DATE_VALUE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
claFileName - Static variable in class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
claFileName - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
classEqual(Object, Object) - Static method in class org.biojava3.core.util.Equals
This method should be called before beginning any equals methods.
ClasspathResource - Class in org.biojava3.core.sequence.io.util
This object represents a classpath resource on the local system.
ClasspathResource(String) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource
Basic constructor only allowing you to specify where to find the file.
ClasspathResource(String, boolean) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource
Advanced constructor which allows you to optionally pre-cache the data
ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource
Advanced constructor which lets you set the preCache variable and to force the type of file we are decompressing.
cleanSequence(String, Set<Character>) - Static method in class org.biojava3.aaproperties.Utils
Returns a new sequence with all invalid characters being replaced by '-'.
cleanSequence(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
Removes all whitespace chars in the sequence string
cleanup() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalc
 
cleanup() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
cleanup() - Method in interface org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable
 
cleanUp() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
cleanup(List<Domain>) - Static method in class org.biojava.bio.structure.domain.pdp.ShortSegmentRemover
 
cleanup() - Method in class org.biojava.bio.structure.gui.util.AlignmentCalc
 
clear() - Method in interface org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider
reset all suggestions
clear() - Method in class org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
clear() - Method in class org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
clear() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
Clears all finite endpoints
clear() - Method in class org.biojava3.core.util.FlatFileCache
 
clear() - Method in class org.biojava3.core.util.SoftHashMap
 
clear() - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
clear() - Method in interface org.biojava3.structure.gui.Selection
 
clear() - Method in class org.biojava3.structure.gui.SelectionImpl
 
clear() - Method in interface org.biojava3.structure.gui.StructureViewer
Clear the current display
clear() - Method in class org.forester.datastructures.Queue
Removes all elements from this queue.
clearAlgorithms() - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
Removes all algorithms from the list
clearAtoms() - Method in interface org.biojava.bio.structure.Group
Remove all atoms from this group.
clearAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
remove all atoms
clearCache() - Static method in class org.biojava.bio.structure.PDBStatus
The status of PDB IDs are cached to reduce server overload.
clearCache() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
clearCache() - Method in interface org.biojava3.alignment.template.AlignedSequence
Nullifies cached arrays/objects.
clearConsumers() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
Remove all consumers from the parser.
clearConsumers() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
clearExtensions() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
clearExtensions() - Method in class org.biojava.bio.structure.io.PDBFileReader
clear the supported file extensions
clearExtensions() - Method in interface org.biojava.bio.structure.io.StructureIOFile
clear all file extensions
clearFilters() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
clearFilters() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
clearFilters() - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
remove all filters, next time getAll is called, it will return all available PDBs
clearListeners() - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
clearListeners() - Method in class org.biojava.bio.structure.align.FarmJob
 
clearListeners() - Method in class org.biojava.bio.structure.align.StructurePairAligner
 
clearListeners() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
clearListeners() - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
clearListeners() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
Deprecated.
 
clearStructureListeners() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
clearStructureListeners() - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
CliTools - Class in org.biojava.bio.structure.align.util
Utilities for autoconfiguring javabeans based on command line arguments.
clone() - Method in class org.biojava.bio.structure.align.model.AFPChain
Creates and returns a copy of this object.
clone() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
clone() - Method in class org.biojava.bio.structure.AminoAcidImpl
returns and identical copy of this Group object .
clone() - Method in interface org.biojava.bio.structure.Atom
returns and identical copy of this object .
clone() - Method in class org.biojava.bio.structure.AtomImpl
returns and identical copy of this object .
clone() - Method in interface org.biojava.bio.structure.Chain
returns an identical copy of this Chain.
clone() - Method in class org.biojava.bio.structure.ChainImpl
Returns an identical copy of this Chain .
clone() - Method in class org.biojava.bio.structure.Compound
 
clone() - Method in interface org.biojava.bio.structure.Group
returns and identical copy of this Group object .
clone() - Method in class org.biojava.bio.structure.GroupIterator
Creates and returns a copy of this object.
clone() - Method in class org.biojava.bio.structure.HetatomImpl
returns and identical copy of this Group object .
clone() - Method in class org.biojava.bio.structure.jama.Matrix
Clone the Matrix object.
clone() - Method in class org.biojava.bio.structure.NucleotideImpl
 
clone() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
clone() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
clone() - Method in class org.biojava.bio.structure.secstruc.HBond
 
clone() - Method in class org.biojava.bio.structure.SSBond
 
clone() - Method in interface org.biojava.bio.structure.Structure
returns an identical copy of this Structure object
clone() - Method in class org.biojava.bio.structure.StructureImpl
returns an identical copy of this structure .
clone() - Method in class org.forester.archaeopteryx.webservices.WebservicesManager
 
clone() - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory
 
clone() - Method in class org.forester.phylogeny.PhylogenyMethods
 
cloneCAArray(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
Provides an equivalent copy of Atoms in a new array.
cloneGroups(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
Clone a set of CA Atoms, but returns the parent groups
clonePoint() - Method in class org.biojava3.core.sequence.location.SimplePoint
 
clonePoint() - Method in interface org.biojava3.core.sequence.location.template.Point
Returns a copy of this point
close() - Method in class org.biojava.bio.structure.align.util.SynchronizedOutFile
 
close() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
 
close(Closeable) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.
close() - Method in class org.biojava3.core.util.PrettyXMLWriter
 
close() - Method in interface org.biojava3.core.util.XMLWriter
Close this XMLWriter, and it's underlying stream.
closeTag(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
closeTag(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
closeTag(String, String) - Method in interface org.biojava3.core.util.XMLWriter
Closes an element
closeTag(String) - Method in interface org.biojava3.core.util.XMLWriter
Closes an un-qualified element.
cluster(AlternativeAlignment[]) - Static method in class org.biojava.bio.structure.align.ClusterAltAligs
 
cluster(AlternativeAlignment[], int) - Static method in class org.biojava.bio.structure.align.ClusterAltAligs
 
cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.bio.structure.domain.pdp.ClusterDomains
 
ClusterAltAligs - Class in org.biojava.bio.structure.align
A class that clusters alternative alignments according to their similarity.
ClusterAltAligs() - Constructor for class org.biojava.bio.structure.align.ClusterAltAligs
 
ClusterDomains - Class in org.biojava.bio.structure.domain.pdp
 
ClusterDomains() - Constructor for class org.biojava.bio.structure.domain.pdp.ClusterDomains
 
CodonCompound - Class in org.biojava3.core.sequence.compound
Define a codon
CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava3.core.sequence.compound.CodonCompound
 
codonHash - Static variable in class org.biojava3.phylo.ResidueProperties
 
codonHash2 - Static variable in class org.biojava3.phylo.ResidueProperties
 
codonTranslate(String) - Static method in class org.biojava3.phylo.ResidueProperties
 
coefficientOfVariation() - Method in class org.forester.util.BasicDescriptiveStatistics
 
coefficientOfVariation() - Method in interface org.forester.util.DescriptiveStatistics
Computes the coefficient of variation.
collapseWhiteSpace(String) - Static method in class org.forester.util.ForesterUtil
 
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, BinaryDomainCombination.DomainCombinationType, List<BinaryDomainCombination>, boolean) - Static method in class org.forester.surfacing.SurfacingUtil
 
CollectionTools - Class in org.biojava.bio.structure.align.util
Utilities for working with collections.
CollectionTools() - Constructor for class org.biojava.bio.structure.align.util.CollectionTools
 
COLOR - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
COLOR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
COLOR_BLUE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
COLOR_GREEN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
COLOR_RED - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
coloring - Variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
ColorInterpolator - Interface in org.biojava.bio.structure.gui.util.color
 
ColorParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
colorToHex(Color) - Static method in class org.forester.util.ForesterUtil
 
ColorUtils - Class in org.biojava.bio.structure.gui.util.color
 
ColorUtils() - Constructor for class org.biojava.bio.structure.gui.util.color.ColorUtils
 
colorWheel - Static variable in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
CombinableDomains - Interface in org.forester.surfacing
 
CombinationsBasedPairwiseDomainSimilarity - Class in org.forester.surfacing
 
CombinationsBasedPairwiseDomainSimilarity(int, int, int) - Constructor for class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
 
CombinationsBasedPairwiseDomainSimilarityCalculator - Class in org.forester.surfacing
 
CombinationsBasedPairwiseDomainSimilarityCalculator() - Constructor for class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator
 
COMMAND_LINE_HELP - Static variable in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
CommandLineArguments - Class in org.forester.util
 
CommandLineArguments(String[]) - Constructor for class org.forester.util.CommandLineArguments
 
CommandPrompt - Class in org.biojava3.aaproperties
 
CommandPrompt() - Constructor for class org.biojava3.aaproperties.CommandPrompt
 
CommandPrompt.PropertyName - Enum in org.biojava3.aaproperties
 
compare(int[], int[]) - Method in class org.biojava.bio.structure.align.helper.IdxComparator
 
compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.bio.structure.align.pairwise.AltAligComparator
 
compare(Segment, Segment) - Method in class org.biojava.bio.structure.domain.pdp.SegmentComparator
 
compare(CDSSequence, CDSSequence) - Method in class org.biojava3.core.sequence.CDSComparator
Used to sort two CDSSequences where Negative Strand makes it tough
compare(ExonSequence, ExonSequence) - Method in class org.biojava3.core.sequence.ExonComparator
 
compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava3.core.sequence.SequenceComparator
 
compare(Phylogeny, Phylogeny, boolean, boolean, boolean) - Static method in class org.forester.development.SupportCount
 
compareTo(PdbPair) - Method in class org.biojava.bio.structure.align.client.PdbPair
 
compareTo(StructureName) - Method in class org.biojava.bio.structure.align.client.StructureName
 
compareTo(Domain) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
compareTo(Segment) - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
compareTo(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
compareTo(ResidueNumber) - Method in class org.biojava.bio.structure.ResidueNumber
 
compareTo(Site) - Method in class org.biojava.bio.structure.Site
 
compareTo(Point) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
compareTo(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
compareTo(FastaSequence) - Method in class org.biojava3.data.sequence.FastaSequence
 
compareTo(ProteinModification) - Method in class org.biojava3.protmod.ProteinModificationImpl
 
compareTo(ModifiedCompound) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
compareTo(StructureGroup) - Method in class org.biojava3.protmod.structure.StructureGroup
 
compareTo(HmmerDomain) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
compareTo(HmmerResult) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
compareTo(GoRelationship) - Method in class org.forester.go.BasicGoRelationship
 
compareTo(GoSubset) - Method in class org.forester.go.BasicGoSubset
 
compareTo(GoTerm) - Method in class org.forester.go.BasicGoTerm
Compares based on GO id.
compareTo(GoXRef) - Method in class org.forester.go.BasicGoXRef
 
compareTo(OntologizerResult) - Method in class org.forester.go.etc.OntologizerResult
 
compareTo(GoId) - Method in class org.forester.go.GoId
 
compareTo(Mapping) - Method in class org.forester.go.PfamToGoMapping
 
compareTo(Confidence) - Method in class org.forester.phylogeny.data.Confidence
 
compareTo(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
 
compareTo(DiscreteState) - Method in class org.forester.phylogenyinference.DiscreteState
 
compareTo(BinaryDomainCombination) - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
compareTo(Domain) - Method in class org.forester.surfacing.BasicDomain
Basic domains are compared/sorted based upon their identifiers (case insensitive) and their numbers.
compareTo(Species) - Method in class org.forester.surfacing.BasicSpecies
 
compareTo(DomainId) - Method in class org.forester.surfacing.DomainId
 
compareTo(DomainSimilarity) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
compareTo(ProteinId) - Method in class org.forester.surfacing.ProteinId
 
compareTo(Domain) - Method in class org.forester.surfacing.SimpleDomain
 
Comparison - Class in org.biojava3.phylo
 
Comparison() - Constructor for class org.biojava3.phylo.Comparison
 
ComplementCompound - Interface in org.biojava3.core.sequence.template
 
ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava3.core.sequence.views
For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g.
ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava3.core.sequence.views.ComplementSequenceView
 
complete(Object) - Method in interface org.biojava3.phylo.NJTreeProgressListener
 
complete(Object) - Method in class org.biojava3.phylo.ProgessListenerStub
 
complete() - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this listener the FASTQ formatted sequence is complete.
completeCircularPasses(int, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.
completeCircularPasses(int, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.
Component - Class in org.biojava3.protmod
contains information about a certain Component.
componentHidden(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel
 
componentMoved(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel
 
componentResized(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel
 
componentShown(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel
 
ComponentXMLConverter - Class in org.biojava3.protmod.io
 
ComponentXMLConverter() - Constructor for class org.biojava3.protmod.io.ComponentXMLConverter
 
Compound - Class in org.biojava.bio.structure
Created by IntelliJ IDEA.
Compound() - Constructor for class org.biojava.bio.structure.Compound
 
Compound - Interface in org.biojava3.core.sequence.template
 
CompoundNotFoundError - Error in org.biojava3.core.exceptions
 
CompoundNotFoundError(CharSequence) - Constructor for error org.biojava3.core.exceptions.CompoundNotFoundError
 
compoundsEqual(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
compoundsEquivalent(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
compoundsEquivalent(C, C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
CompoundSet<C extends Compound> - Interface in org.biojava3.core.sequence.template
 
compoundsPerDatatype() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Should return the maximum amount of compounds we can encode per int
compoundsPerDatatype() - Method in class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
compoundsPerDatatype() - Method in class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
compoundToInt(NucleotideCompound) - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava3.core.sequence.template
 
computeMappingCostL() - Method in class org.forester.sdi.SDI
Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.
computeMolecularWeight(ElementTable) - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
ConcurrencyTools - Class in org.biojava3.core.util
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
cond() - Method in class org.biojava.bio.structure.jama.Matrix
Matrix condition (2 norm)
cond() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Two norm condition number
confadd - Class in org.forester.application
 
confadd() - Constructor for class org.forester.application.confadd
 
CONFIDENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Confidence - Class in org.forester.phylogeny.data
 
Confidence() - Constructor for class org.forester.phylogeny.data.Confidence
 
Confidence(double, String) - Constructor for class org.forester.phylogeny.data.Confidence
 
CONFIDENCE_DEFAULT - Static variable in class org.forester.phylogeny.data.ProteinDomain
 
CONFIDENCE_DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.Confidence
 
CONFIDENCE_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
ConfidenceAssessor - Class in org.forester.tools
 
ConfidenceParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
ConfigPDBInstallPanel - Class in org.biojava.bio.structure.align.gui
 
ConfigStrucAligParams - Interface in org.biojava.bio.structure.align.ce
 
ConfigurationException - Exception in org.biojava.bio.structure.align.util
 
ConfigurationException(String) - Constructor for exception org.biojava.bio.structure.align.util.ConfigurationException
Constructs a ConfigurationException object.
ConfigurationException(Throwable) - Constructor for exception org.biojava.bio.structure.align.util.ConfigurationException
Constructs a ConfigurationException object.
configureBean(Object, String[]) - Static method in class org.biojava.bio.structure.align.util.CliTools
Configure a JavaBean based on a set of command line arguments.
configureParameters() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
ConfigXMLHandler - Class in org.biojava.bio.structure.align.webstart
XML content handler for serialisation of RegistryConfiguration class
ConfigXMLHandler() - Constructor for class org.biojava.bio.structure.align.webstart.ConfigXMLHandler
 
consistentAccessions(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Scans a list of locations and returns true if all the given locations are linked to the same sequence.
Constants - Class in org.forester.archaeopteryx
 
Constants() - Constructor for class org.forester.archaeopteryx.Constants
 
Constraints - Class in org.biojava3.aaproperties
This class is used to support the implementation of properties stated in IPeptideProperties.
Constraints() - Constructor for class org.biojava3.aaproperties.Constraints
 
constructWithCopy(double[][]) - Static method in class org.biojava.bio.structure.jama.Matrix
Construct a matrix from a copy of a 2-D array.
contains(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location contains the other.
contains(DomainId) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
contains(List<DomainId>, boolean) - Method in class org.forester.surfacing.BasicProtein
 
contains(DomainId) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
contains(List<DomainId>, boolean) - Method in interface org.forester.surfacing.Protein
If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored).
containsCharacter(String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
containsCharacter(String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
containsIdentifier(String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
containsIdentifier(String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
containsKey(Object) - Method in class org.biojava.bio.structure.align.util.AlignmentTools.IdentityMap
 
containsKey(Object) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
containsValue(Object) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
ContinuousColorMapper - Interface in org.biojava.bio.structure.gui.util.color
Provides a mapping between real numbers and Colors.
ContinuousColorMapperTransform - Class in org.biojava.bio.structure.gui.util.color
Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.
ContinuousColorMapperTransform(ContinuousColorMapper) - Constructor for class org.biojava.bio.structure.gui.util.color.ContinuousColorMapperTransform
Creates a transform.
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Charge
Class for the conversion of protein sequence into charge
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
Class for the conversion of protein sequence into hydrophobicity
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
Class for the conversion of protein sequence into normalized van der waals volume
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
Class for the conversion of protein sequence into polarity
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
Class for the conversion of protein sequence into polarizability
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
Class for the conversion of protein sequence into secondary structure
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
Class for the conversion of protein sequence into solvent accessibility
convert(char) - Method in class org.biojava3.aaproperties.profeat.convertor.Convertor
Returns the grouping of the amino acid character.
convert(ProteinSequence) - Method in class org.biojava3.aaproperties.profeat.convertor.Convertor
Returns the converted sequence.
Convert2Charge - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2Charge() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Charge
 
Convert2Hydrophobicity - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2Hydrophobicity() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
 
Convert2NormalizedVanDerWaalsVolume - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2NormalizedVanDerWaalsVolume() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
 
Convert2Polarity - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2Polarity() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
 
Convert2Polarizability - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2Polarizability() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
 
Convert2SecondaryStructure - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2SecondaryStructure() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
 
Convert2SolventAccessibility - Class in org.biojava3.aaproperties.profeat.convertor
 
Convert2SolventAccessibility() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
 
convert_3code_1code(String) - Static method in class org.biojava.bio.structure.StructureTools
convert three character amino acid codes into single character e.g.
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
copy data from this class into AFPChain container object.
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
copy data from this class into AFPChain container object.
convertAtomsToSeq(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
 
Convertor - Class in org.biojava3.aaproperties.profeat.convertor
 
Convertor() - Constructor for class org.biojava3.aaproperties.profeat.convertor.Convertor
 
convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.bio.structure.align.xml.PdbPairXMLConverter
 
convertStreamToString(InputStream) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
convertStreamToString(InputStream) - Static method in class org.biojava3.core.util.StringManipulationHelper
 
convertXMLtoPairs(String) - Static method in class org.biojava.bio.structure.align.xml.PdbPairXMLConverter
 
CoordManager - Class in org.biojava.bio.structure.gui.util
a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates
CoordManager() - Constructor for class org.biojava.bio.structure.gui.util.CoordManager
 
copy(File, File) - Static method in class org.biojava.bio.structure.io.util.FileDownloadUtils
Copy the content of file A to B
copy() - Method in class org.biojava.bio.structure.jama.Matrix
Make a deep copy of a matrix
copy(InputStream, OutputStream) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Moves the bytes from input to output using a 4KB byte array.
copy() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
copy() - Method in class org.forester.development.AminoAcidSequence
 
copy() - Method in class org.forester.development.BasicMsa
 
copy() - Method in class org.forester.go.BasicGoTerm
Makes a shallow copy.
copy() - Method in class org.forester.phylogeny.data.Accession
 
copy() - Method in class org.forester.phylogeny.data.Annotation
 
copy() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
copy() - Method in class org.forester.phylogeny.data.BranchColor
 
copy() - Method in class org.forester.phylogeny.data.BranchData
 
copy() - Method in class org.forester.phylogeny.data.BranchWidth
 
copy() - Method in class org.forester.phylogeny.data.Confidence
 
copy() - Method in class org.forester.phylogeny.data.Date
 
copy() - Method in class org.forester.phylogeny.data.Distribution
 
copy() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
copy() - Method in class org.forester.phylogeny.data.Event
 
copy() - Method in class org.forester.phylogeny.data.Identifier
 
copy() - Method in class org.forester.phylogeny.data.NodeData
 
copy() - Method in interface org.forester.phylogeny.data.PhylogenyData
Creates a new PhylogenyData object with identical values as this PhylogenyData.
copy(ArrayList<PhylogenyData>) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
Creates a deep copy of ArrayList of PhylogenyData objects.
copy() - Method in class org.forester.phylogeny.data.Point
 
copy() - Method in class org.forester.phylogeny.data.PropertiesMap
 
copy() - Method in class org.forester.phylogeny.data.Property
 
copy() - Method in class org.forester.phylogeny.data.ProteinDomain
 
copy() - Method in class org.forester.phylogeny.data.Reference
 
copy() - Method in class org.forester.phylogeny.data.Sequence
Not a deep copy.
copy() - Method in class org.forester.phylogeny.data.SequenceRelation
 
copy() - Method in class org.forester.phylogeny.data.Taxonomy
 
copy() - Method in class org.forester.phylogeny.data.Uri
 
copy() - Method in class org.forester.phylogeny.Phylogeny
Returns a deep copy of this Phylogeny.
copy() - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
copy() - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
copyMatrix(DistanceMatrix) - Static method in class org.biojava3.phylo.CheckTreeAccuracy
 
copyNodeData() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a new PhylogenyNode which has its data copied from this PhylogenyNode.
count(Phylogeny, Phylogeny[], boolean, boolean) - Static method in class org.forester.development.SupportCount
 
count(Phylogeny, Phylogeny[], boolean, double, boolean) - Static method in class org.forester.development.SupportCount
This counts the support of topology phylogeny by the topologies in phylogenies.
COUNT_DEFAULT - Static variable in class org.forester.phylogeny.data.BinaryCharacters
 
count_support - Class in org.forester.application
 
count_support() - Constructor for class org.forester.application.count_support
 
countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Returns the count of AT in the given sequence
countCategories(List<GoTerm>, List<GoTerm>, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.
countCategoriesId(List<GoId>, List<GoId>, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
 
countChars(String, char) - Static method in class org.forester.util.ForesterUtil
 
countCompounds(C...) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Counts the number of times a compound appears in this sequence store
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Delegates to SequenceMixin#countCompounds(org.biojava3.core.sequence.template.Sequence, C[])
countCompounds(C...) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
countCompounds(C...) - Method in interface org.biojava3.core.sequence.template.Sequence
Returns the number of times we found a compound in the Sequence
countCompounds(Sequence<C>, C...) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
countCompounds(C...) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Returns the count of GC in the given sequence
countMatchesInSequence(String, String) - Static method in class org.biojava3.data.sequence.FastaSequence
 
CountProgressListener - Class in org.biojava.bio.structure.align.client
 
CountProgressListener() - Constructor for class org.biojava.bio.structure.align.client.CountProgressListener
 
CountsBasedPairwiseDomainSimilarity - Class in org.forester.surfacing
 
CountsBasedPairwiseDomainSimilarity(int, int) - Constructor for class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity
counts_difference: (counts for domain 1) minus (counts for domain 2).
countSharedAncestralClades(Phylogeny, int, String[], String[]) - Method in class org.forester.sdi.ORcount
 
countSharedAncestralClades(Phylogeny[], int) - Method in class org.forester.sdi.ORcount
 
countSuperOrthologousRelations(int) - Method in class org.forester.sdi.ORcount
 
Coverage - Interface in org.forester.pccx
 
CoverageCalculationMethod - Interface in org.forester.pccx
 
CoverageCalculationOptions - Interface in org.forester.pccx
 
CoverageCalculator - Class in org.forester.pccx
 
CoverageExtender - Interface in org.forester.pccx
 
cpPoint - Variable in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
The CP point, specified as a residue index
CRC64Checksum - Class in org.biojava3.core.util
Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojava3.core.util.CRC64Checksum
 
create(Object) - Method in interface org.forester.development.Factory
 
create(Object) - Method in interface org.forester.development.MsaFactory
 
create(InputStream) - Method in interface org.forester.development.StreamBasedMsaFactory
 
create() - Method in class org.forester.phylogeny.factories.BasicPhylogenyFactory
 
create(Object, Object) - Method in class org.forester.phylogeny.factories.BasicPhylogenyFactory
 
create(Object, Object, List<Object>) - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory
 
create(Object, Object, String, List<Object>) - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory
 
create() - Method in interface org.forester.phylogeny.factories.PhylogenyFactory
This must be implemented in such a way that it returns an empty Phylogeny.
create(Object, Object) - Method in interface org.forester.phylogeny.factories.PhylogenyFactory
This must create a Phylogeny from source (e.g.
create(Object, Object, List<Object>) - Method in interface org.forester.phylogeny.factories.PhylogenyFactory
This must create a Phylogeny from source (e.g.
createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Fundimentally, an alignment is just a list of aligned residues in each protein.
createApplication(Phylogeny) - Static method in class org.forester.archaeopteryx.Archaeopteryx
 
createApplication(Phylogeny[]) - Static method in class org.forester.archaeopteryx.Archaeopteryx
 
createApplication(Phylogeny[], String, String) - Static method in class org.forester.archaeopteryx.Archaeopteryx
 
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
createBalancedPhylogeny(int, int) - Static method in class org.forester.development.DevelopmentTools
Creates a completely balanced rooted phylogeny with a given number of levels and children per node.
createBiologicalProcess() - Static method in class org.forester.go.GoNameSpace
 
createBufferedWriter(File) - Static method in class org.forester.util.ForesterUtil
 
createBufferedWriter(String) - Static method in class org.forester.util.ForesterUtil
 
createCellularComponent() - Static method in class org.forester.go.GoNameSpace
 
createDefaultClients() - Static method in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
createDNASequence(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Create and return a new DNASequence from the specified FASTQ formatted sequence.
createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.
createDomainIdToGoIdMap(List<PfamToGoMapping>) - Static method in class org.forester.surfacing.SurfacingUtil
 
createDomainIdToSecondaryFeaturesMap(File) - Static method in class org.forester.surfacing.SurfacingUtil
 
createErrorProbabilities(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
createFileForWriting(String) - Static method in class org.forester.util.ForesterUtil
 
createFromNhxString(String) - Static method in class org.forester.phylogeny.data.Property
 
createGoIdToGoTermMap(List<GoTerm>) - Static method in class org.forester.go.GoUtils
 
createGradients() - Static method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
createImage(String, String, Object, int) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
createImageIcon(String) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
Returns an ImageIcon, or null if the path was invalid.
createInstance() - Static method in class org.forester.phylogenyinference.DolloParsimony
 
createInstance() - Static method in class org.forester.phylogenyinference.NeighborJoining
 
createInstance() - Static method in class org.forester.phylogenyinference.SymmetricalDistanceMatrixParser
 
createInstance(String) - Static method in class org.forester.surfacing.AdjactantDirectedBinaryDomainCombination
 
createInstance(String) - Static method in class org.forester.surfacing.BasicBinaryDomainCombination
 
createInstance(List<Protein>, boolean, Species) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
createInstance(List<Protein>, boolean, Species, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
createInstance(List<Protein>, boolean, Species, Map<DomainId, List<GoId>>, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
createInstance(String) - Static method in class org.forester.surfacing.DirectedBinaryDomainCombination
 
createInstance(Phylogeny) - Static method in class org.forester.surfacing.DomainParsimonyCalculator
 
createInstance(Phylogeny, List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator
 
createInstance(Phylogeny, List<GenomeWideCombinableDomains>, Map<DomainId, Set<String>>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator
 
createIterator(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.
createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator
 
createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains>, SortedSet<DomainId>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator
 
createMeanBasedStatisticsPerSpeciesTable() - Method in class org.forester.surfacing.DomainLengthsTable
 
createMMcifInfoList(File[], File, File) - Method in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
parses a set of PDB files and writes info into a file the file is tab separated and has the following columns: name length resolution depositionDate modificationDate technique title classification filename binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup This method needs to be run, before a DBSearch can be performed, since the files created by this method are required for the DBSearch
createMolecularFunction() - Static method in class org.forester.go.GoNameSpace
 
createNjTreeBasedOnMatrixToFile(File, DistanceMatrix) - Static method in class org.forester.surfacing.SurfacingUtil
 
createOutput(String, String) - Method in class org.biojava3.aaproperties.xml.SchemaGenerator
 
createParserDependingFileContents(File, boolean) - Static method in class org.forester.util.ForesterUtil
 
createParserDependingOnFileType(File, boolean) - Static method in class org.forester.util.ForesterUtil
 
createParserDependingOnSuffix(String, boolean) - Static method in class org.forester.util.ForesterUtil
Return null if it can not guess the parser to use based on name suffix.
createParserDependingOnUrlContents(URL, boolean) - Static method in class org.forester.util.ForesterUtil
 
createPDBInfoList(File[], File, File) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
parses a set of PDB files and writes info into a file the file is tab separated and has the following columns: name length resolution depositionDate modificationDate technique title classification filename binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup This method needs to be run, before a DBSearch can be performed, since the files created by this method are required for the DBSearch
createPhylogenyWriter() - Static method in class org.forester.io.writers.PhylogenyWriter
 
createPhyloXmlParserXsdValidating() - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
createQualityScores(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.
createReader(Object) - Static method in class org.forester.io.parsers.ParserUtils
 
createSequence(Sequence<F>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
createSequence(Sequence<F>) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
 
createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
 
createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
 
createSequences(Sequence<F>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
createSequences(Sequence<F>) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
 
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
Overloaded local version which delegates to an optional translator when told to (specified during construction).
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
Performs the core conversion of RNA to Peptide.
createSingleDuplicationEvent() - Static method in class org.forester.phylogeny.data.Event
 
createSingleSpeciationEvent() - Static method in class org.forester.phylogeny.data.Event
 
createSingleSpeciationOrDuplicationEvent() - Static method in class org.forester.phylogeny.data.Event
 
createSubAlignment(int[], int[]) - Method in class org.forester.development.BasicMsa
 
createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Creates a simple sub sequence view delimited by the given start and end.
createUnassigned() - Static method in class org.forester.go.GoNameSpace
 
createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.bio.structure.Calc
creates a virtual C-beta atom.
crossChains() - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
crossChains() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
CS_HSV - Static variable in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
The HSV color space
CUSTOM_DATA_ON_NODE - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
Cut - Class in org.biojava.bio.structure.domain.pdp
 
Cut() - Constructor for class org.biojava.bio.structure.domain.pdp.Cut
 
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.bio.structure.domain.pdp.Cut
 
CUT_OFF_VALUE - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE1 - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE1M - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE1S - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
CUT_OFF_VALUE2 - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
CutDomain - Class in org.biojava.bio.structure.domain.pdp
 
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.bio.structure.domain.pdp.CutDomain
 
cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.bio.structure.domain.pdp.CutDomain
 
CutSites - Class in org.biojava.bio.structure.domain.pdp
 
CutSites() - Constructor for class org.biojava.bio.structure.domain.pdp.CutSites
 
cutsPerSection - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
CutValues - Class in org.biojava.bio.structure.domain.pdp
 
CutValues() - Constructor for class org.biojava.bio.structure.domain.pdp.CutValues
 
cyan - Static variable in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
Cys - Static variable in class org.biojava3.phylo.ResidueProperties
 

D

D - Static variable in class org.biojava3.aaproperties.Constraints
 
D_PROMISCUITY_FILE_SUFFIX - Static variable in class org.forester.application.surfacing
 
D_PROMISCUITY_FILE_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
darker(Color, double) - Static method in class org.biojava.bio.structure.gui.util.color.ColorUtils
Make a color darker.
DatabasePDBremark - Class in org.biojava.bio.structure.io.mmcif.model
 
DatabasePDBremark() - Constructor for class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
 
DatabasePDBrev - Class in org.biojava.bio.structure.io.mmcif.model
 
DatabasePDBrev() - Constructor for class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
DatabaseReferenceInterface - Interface in org.biojava3.core.sequence.features
If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)
DataSource - Enum in org.biojava3.core.sequence
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
DATATYPE - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
Date - Class in org.forester.phylogeny.data
 
Date() - Constructor for class org.forester.phylogeny.data.Date
 
Date(String) - Constructor for class org.forester.phylogeny.data.Date
 
Date(String, BigDecimal, BigDecimal, BigDecimal, String) - Constructor for class org.forester.phylogeny.data.Date
 
dateFormat - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
DateParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
DBL - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
DBRef - Class in org.biojava.bio.structure
A class to represent database cross references.
DBRef() - Constructor for class org.biojava.bio.structure.DBRef
 
DBReferenceInfo - Class in org.biojava3.core.sequence.features
If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.
DBReferenceInfo(String, String) - Constructor for class org.biojava3.core.sequence.features.DBReferenceInfo
The source database and id
DBResultTable - Class in org.biojava.bio.structure.align.gui
 
DBResultTable() - Constructor for class org.biojava.bio.structure.align.gui.DBResultTable
 
DBSearchGUI - Class in org.biojava.bio.structure.align.gui
 
DBSearchGUI() - Constructor for class org.biojava.bio.structure.align.gui.DBSearchGUI
 
debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
 
debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
 
debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
 
debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
 
debug - Static variable in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
debug - Static variable in class org.biojava.bio.structure.align.gui.DisplayAFP
 
DEBUG - Static variable in class org.biojava3.core.util.SoftHashMap
 
DEBUG - Static variable in class org.forester.io.parsers.phyloxml.XmlElement
 
declareNamespace(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
declareNamespace(String, String) - Method in interface org.biojava3.core.util.XMLWriter
Hints that a namespace is going to be used in a sub-tree.
decorate(Phylogeny, Map<String, Map<String, String>>, boolean, int) - Static method in class org.forester.tools.PhylogenyDecorator
 
decorate(Phylogeny, Map<String, String>, PhylogenyDecorator.FIELD, boolean, boolean, boolean, boolean, boolean, int, boolean) - Static method in class org.forester.tools.PhylogenyDecorator
 
decorate(Phylogeny, Map<String, String>, PhylogenyDecorator.FIELD, boolean, boolean, Map<String, String>, boolean, boolean, boolean, int, boolean) - Static method in class org.forester.tools.PhylogenyDecorator
 
decorate(Phylogeny[], Map<String, Map<String, String>>, boolean, int) - Static method in class org.forester.tools.PhylogenyDecorator
 
decorate(Phylogeny[], Map<String, String>, PhylogenyDecorator.FIELD, boolean, boolean, boolean, boolean, boolean, int, boolean) - Static method in class org.forester.tools.PhylogenyDecorator
 
decorate(Phylogeny[], Map<String, String>, PhylogenyDecorator.FIELD, boolean, boolean, Map<String, String>, boolean, boolean, boolean, int, boolean) - Static method in class org.forester.tools.PhylogenyDecorator
 
decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity>, DomainSimilarityCalculator.Detailedness, DomainSimilarityCalculator.GoAnnotationOutput, Map<GoId, GoTerm>, GoNameSpace) - Static method in class org.forester.surfacing.SurfacingUtil
 
decorateRna(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
Performs an optimisation where RNASequences are not translated into their own objects but are views onto the base DNA sequence.
decorator - Class in org.forester.application
 
decorator() - Constructor for class org.forester.application.decorator
 
deepCleanSequence(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
Removes all special characters and digits as well as whitespace chars from the sequence
DEFAUL_CHAIN_FILE - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
DEFAULT - Static variable in class org.forester.sdi.DistanceCalculator
 
DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.bio.structure.align.model.AFPChain
the default algorithm used in the RCSB PDB all vs.
DEFAULT_BATCH_SIZE - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_CHAIN_ID - Static variable in class org.biojava.bio.structure.ChainImpl
The default chain identifier is an empty space.
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
size per character
DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.bio.structure.align.ClusterAltAligs
 
DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.bio.structure.align.util.HTTPConnectionTools
 
DEFAULT_DIR_SPLIT - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_DISORDER - Static variable in class org.biojava3.ronn.RonnConstraint
 
DEFAULT_FRAGLEN - Static variable in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
DEFAULT_GAP_OPEN - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
DEFAULT_INDEX_FILE - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
DEFAULT_JOB_TIME - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_LIMIT - Static variable in class org.biojava3.core.util.SoftHashMap
 
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
number of chars per line
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
separation of line 1 and 2 in alignment
DEFAULT_MAX_ITERATIONS - Static variable in class org.biojava.bio.structure.secstruc.BigSqrt
 
DEFAULT_METHOD_NAME - Static variable in class org.biojava.bio.structure.align.xml.PdbPairXMLConverter
 
DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.bio.structure.align.ce.CeCPMain
 
DEFAULT_NR_ALIGNMENTS - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_NR_THREADS - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_ORDER - Static variable in class org.biojava3.ronn.RonnConstraint
 
DEFAULT_oRmsdThr - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.bio.structure.io.PDBFileReader
 
DEFAULT_PDB_PATH - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_PDB_SERVER - Static variable in class org.biojava.bio.structure.PDBStatus
 
DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava3.ronn.RonnConstraint
 
DEFAULT_RESOLUTION - Static variable in class org.biojava.bio.structure.PDBHeader
 
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
Space on the right side between sequence and legend.
DEFAULT_SCALE - Static variable in class org.biojava.bio.structure.secstruc.BigSqrt
we take 3 aftercomma
DEFAULT_SCORING_STRATEGY - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
DEFAULT_SCRIPT - Static variable in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
DEFAULT_SEARCH_CUT_GA - Variable in class org.biojava3.ws.hmmer.RemoteHmmerScan
 
DEFAULT_SERVER - Static variable in class org.biojava.bio.structure.domain.RemotePDPProvider
 
DEFAULT_SERVER - Static variable in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
DEFAULT_SERVER_URL - Static variable in class org.biojava.bio.structure.align.client.FarmJobParameters
 
DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.Event
 
DEFAULT_VARIANT - Static variable in class org.biojava3.sequencing.io.fastq.FastqBuilder
Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.
DEFAULT_VERSION - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
DEFAULT_X_SPACE - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
left boundary
DEFAULT_X_START - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_BOTTOM - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_HEIGHT - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_SPACE - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
top boundary
DEFAULT_Y_START - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
DEFAULT_Y_STEP - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
size of space between rows
DEFAULT_Y_STEP - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
DefaultAAIndexProvider - Class in org.biojava3.alignment.aaindex
The default provider for AAINDEX loads substituion matrices from the AAINDEX file in the resources directory
DefaultAAIndexProvider() - Constructor for class org.biojava3.alignment.aaindex.DefaultAAIndexProvider
 
DefaultAutoSuggestProvider - Class in org.biojava.bio.structure.align.gui.autosuggest
 
DefaultAutoSuggestProvider() - Constructor for class org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
DefaultMatrixMapper - Class in org.biojava.bio.structure.gui.util.color
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
DefaultMatrixMapper(double, float) - Constructor for class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
 
defaultProperties - Static variable in class org.biojava.bio.structure.align.gui.SystemInfo
 
degreesPerRadian - Static variable in class org.biojava.bio.structure.Calc
Degrees per radian.
deleteAllDomainIdsToIgnore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
deleteExternalNodesNegativeSelection(Set<Integer>, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
deleteExternalNodesNegativeSelection(String[], Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
deleteExternalNodesPositiveSelection(Set<Taxonomy>, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
deleteExternalNodesPositiveSelection(String[], Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
deleteResidueAt(int, int) - Method in class org.forester.development.SimpleMutableMsa
 
deleteSubtree(PhylogenyNode, boolean) - Method in class org.forester.phylogeny.Phylogeny
Need the delete and/or rehash _idhash (not done automatically to allow client multiple deletions in linear time).
dequeue() - Method in class org.forester.datastructures.Queue
Dequeues one element from this queue.
description() - Method in enum org.biojava3.protmod.ModificationCategory
 
description(String) - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this parse listener of a description line.
DescriptiveStatistics - Interface in org.forester.util
 
deserialize(File) - Static method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
desFileName - Static variable in class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
desFileName - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
destroy() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
destroy() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
destroy() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
destroy() - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
destroy() - Static method in class org.biojava3.core.util.FlatFileCache
 
destroy() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
destroy() - Method in class org.forester.archaeopteryx.ArchaeopteryxA
 
destroy() - Method in class org.forester.archaeopteryx.ArchaeopteryxE
 
det() - Method in class org.biojava.bio.structure.jama.LUDecomposition
Determinant
det() - Method in class org.biojava.bio.structure.jama.Matrix
Matrix determinant
detectCicular(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Loops through the given list of locations and returns true if it looks like they represent a circular location.
detectEnd(List<Location>, boolean) - Static method in class org.biojava3.core.sequence.location.LocationHelper
This will attempt to find what the last point is and returns that position.
detectStart(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Assumes that the first element is the start & clones it
detectStrand(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Loops through the given list of locations and returns the consensus Strand class.
DevelopmentTools - Class in org.forester.development
 
diAA2Instability - Static variable in class org.biojava3.aaproperties.Constraints
 
dialogAsk(String, String) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
DIGIT - Static variable in class org.biojava3.data.sequence.SequenceUtil
A digit
DIMENSIONS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
DirectedBinaryDomainCombination - Class in org.forester.surfacing
 
DirectedBinaryDomainCombination(DomainId, DomainId) - Constructor for class org.forester.surfacing.DirectedBinaryDomainCombination
 
DirectedBinaryDomainCombination(String, String) - Constructor for class org.forester.surfacing.DirectedBinaryDomainCombination
 
DirectedCombinableDomains - Class in org.forester.surfacing
 
DirectedCombinableDomains(DomainId, Species) - Constructor for class org.forester.surfacing.DirectedCombinableDomains
 
disableCache() - Method in class org.biojava.bio.structure.domain.SerializableCache
 
DiscreteState - Class in org.forester.phylogenyinference
 
DiscreteState(String) - Constructor for class org.forester.phylogenyinference.DiscreteState
 
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>, List<Group>, List<Group>) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
Display the alignment
DisplayAFP - Class in org.biojava.bio.structure.align.gui
A utility class for visualistion of structure alignments
DisplayAFP() - Constructor for class org.biojava.bio.structure.align.gui.DisplayAFP
 
distance(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Return distance between this location and the other location.
DISTANCE_DEFAULT - Static variable in class org.forester.phylogeny.PhylogenyNode
Value of -99.0 is used as default value.
DISTANCE_INCREMENT - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
DistanceCalculator - Class in org.forester.sdi
 
DistanceCalculator() - Constructor for class org.forester.sdi.DistanceCalculator
Default constructor.
DistanceCalculator(Phylogeny) - Constructor for class org.forester.sdi.DistanceCalculator
Constructor.
DistanceCalculator(Phylogeny, Vector<PhylogenyNode>) - Constructor for class org.forester.sdi.DistanceCalculator
Constructor.
distanceIncrement - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
DistanceMatrix - Interface in org.forester.phylogenyinference
 
DistanceMatrix.Format - Enum in org.forester.phylogenyinference
 
DistanceMatrixParser - Interface in org.forester.phylogenyinference
 
DistanceMethod - Interface in org.forester.phylogenyinference
 
DistEn - Class in org.biojava.bio.structure.secstruc
 
DistEn() - Constructor for class org.biojava.bio.structure.secstruc.DistEn
 
DISTRIBUTION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Distribution - Class in org.forester.phylogeny.data
 
Distribution(String) - Constructor for class org.forester.phylogeny.data.Distribution
 
Distribution(String, BigDecimal, BigDecimal, BigDecimal, String) - Constructor for class org.forester.phylogeny.data.Distribution
 
DISTRIBUTION_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
DistributionParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
DNA_ONLY - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Convenience Set of polymer types classified as DNA.
dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
DNACompoundSet - Class in org.biojava3.core.sequence.compound
 
DNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.DNACompoundSet
 
dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
DNASequence - Class in org.biojava3.core.sequence
This is class should model the attributes associated with a DNA sequence
DNASequence() - Constructor for class org.biojava3.core.sequence.DNASequence
Shouldn't be used but makes it bean happy
DNASequence(String) - Constructor for class org.biojava3.core.sequence.DNASequence
String is king and create a sequence from DNA with default DNA compound set
DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.DNASequence
Create a sequence where the actual storage of the sequence data is somewhere else
DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.DNASequence
Create a sequence from a string with user defined compound set
DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.DNASequence
Create a sequence from a ProxySequencereader and user defined compound set
DNASequence.DNAType - Enum in org.biojava3.core.sequence
The type of DNA sequence
DNASequenceCreator - Class in org.biojava3.core.sequence.io
A helper class that allows different ways to read a string and create a DNA sequence.
DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.io.DNASequenceCreator
 
DNAToRNATranslator - Class in org.biojava3.core.sequence.transcription
Performs the first stage of transcription by going from DNA to RNA.
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava3.core.sequence.transcription.DNAToRNATranslator
 
doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPChainer
// Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
documentEnd() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
documentEnd() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
called at end of document
documentEnd() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
documentStart() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
documentStart() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
called at start of document
documentStart() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
Start the parsing
doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava3.aaproperties.Utils
Checks if given sequence contains invalid characters.
doIter0(int, double, double) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
doIter0(int, double, double) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
DolloParsimony - Class in org.forester.phylogenyinference
 
Domain - Class in org.biojava.bio.structure.domain.pdp
 
Domain() - Constructor for class org.biojava.bio.structure.domain.pdp.Domain
 
Domain - Interface in org.forester.surfacing
 
DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX - Static variable in class org.forester.application.surfacing
 
DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing
 
DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing_old
 
DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing
 
DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing_old
 
DOMAIN_STRUCTURE - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
DOMAIN_STRUCTURE_COLOR_1 - Static variable in class org.forester.archaeopteryx.Constants
 
DOMAIN_STRUCTURE_FONT_COLOR - Static variable in class org.forester.archaeopteryx.Constants
 
DomainArchitecture - Class in org.forester.phylogeny.data
 
DomainArchitecture() - Constructor for class org.forester.phylogeny.data.DomainArchitecture
 
DomainArchitecture(List<PhylogenyData>, int) - Constructor for class org.forester.phylogeny.data.DomainArchitecture
 
DomainArchitecture(String) - Constructor for class org.forester.phylogeny.data.DomainArchitecture
 
DomainArchitectureBasedGenomeSimilarityCalculator - Class in org.forester.surfacing
 
DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains, GenomeWideCombinableDomains) - Constructor for class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
DomainArchitectureParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
DomainCountsBasedPairwiseSimilarityCalculator - Class in org.forester.surfacing
 
DomainCountsBasedPairwiseSimilarityCalculator() - Constructor for class org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator
 
DomainCountsDifferenceUtil - Class in org.forester.surfacing
 
DomainCountsDifferenceUtil() - Constructor for class org.forester.surfacing.DomainCountsDifferenceUtil
 
DomainCountsDifferenceUtil.COPY_CALCULATION_MODE - Enum in org.forester.surfacing
 
DomainId - Class in org.forester.surfacing
 
DomainId(String) - Constructor for class org.forester.surfacing.DomainId
 
DomainLengths - Class in org.forester.surfacing
 
DomainLengths(DomainId) - Constructor for class org.forester.surfacing.DomainLengths
 
DomainLengthsTable - Class in org.forester.surfacing
 
DomainLengthsTable() - Constructor for class org.forester.surfacing.DomainLengthsTable
 
DomainParsimonyCalculator - Class in org.forester.surfacing
 
DomainProvider - Interface in org.biojava.bio.structure.domain
 
DomainProviderFactory - Class in org.biojava.bio.structure.domain
A simple factory object that returns the system wide default DomainProvider
DOMAINS - Static variable in class org.forester.io.parsers.nhx.NHXtags
Deprecated.
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing
 
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing_old
 
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing
 
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing_old
 
DOMAINS_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing
 
DOMAINS_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing_old
 
DOMAINS_SEPARATOR - Static variable in class org.forester.io.parsers.nhx.NHXtags
Deprecated.
DomainSimilarity - Interface in org.forester.surfacing
 
DomainSimilarity.DomainSimilarityScoring - Enum in org.forester.surfacing
 
DomainSimilarity.DomainSimilaritySortField - Enum in org.forester.surfacing
 
DomainSimilarityCalculator - Interface in org.forester.surfacing
 
DomainSimilarityCalculator.Detailedness - Enum in org.forester.surfacing
 
DomainSimilarityCalculator.GoAnnotationOutput - Enum in org.forester.surfacing
 
doPOST(URL, String) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
do a POST to a URL and return the response stream for further processing elsewhere.
doPOST(URL, String, int) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
do a POST to a URL and return the response stream for further processing elsewhere.
doPrintConnections() - Method in class org.biojava.bio.structure.io.FileConvert
returns if the Connections should be added default is true;
DotPlotPanel - Class in org.biojava.bio.structure.align.gui
Displays the dot plot trace for an alignment.
DotPlotPanel(AFPChain) - Constructor for class org.biojava.bio.structure.align.gui.DotPlotPanel
 
DownloadChemCompProvider - Class in org.biojava.bio.structure.io.mmcif
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
DownloadChemCompProvider() - Constructor for class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
 
downloadCIF(String) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
downloadClaFile() - Method in class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
downloadClaFile() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
downloadDesFile() - Method in class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
downloadDesFile() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
downloadFile() - Static method in class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
Downloads the components.cif.gz file from the wwPDB site.
downloadFileFromRemote(URL, File) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
downloadFileIfAvailable(URL, File) - Static method in class org.biojava.bio.structure.io.util.FileDownloadUtils
 
downloadGzipCompressedFile(URL, File) - Static method in class org.biojava.bio.structure.io.util.FileDownloadUtils
Download the content provided at URL url and stores the result to a local file
downloadHieFile() - Method in class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
downloadHieFile() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
downloadingStructures(String) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
downloadingStructures(String) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
 
downloadingStructures(String) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
downloadPDB(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
downstream(int) - Method in class org.biojava3.genome.parsers.gff.Location
Return the adjacent location of specified length directly downstream of this location.
drawBoxes(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
draw high scoring fragments that are used for the initial alignment seed selection
drawDistances(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
For each element in matrix, draw it as a colored square or pixel.
drawIdx(Graphics2D, int) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
drawLine(double, double, double, double, Graphics) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
drawPairs(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
draw alternative alignments
drawScale(Graphics2D, int) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
draw the Scale
drawSequence(Graphics2D, int) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
draw the Amino acid sequence
drawString(String, double, double, Graphics) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
duplicateCA2(Atom[]) - Static method in class org.biojava.bio.structure.StructureTools
Utility method for working with circular permutations.

E

E - Static variable in class org.biojava3.aaproperties.Constraints
 
EC_NUMBER - Static variable in class org.forester.io.parsers.nhx.NHXtags
Deprecated.
EC_STR - Static variable in interface org.forester.go.GoXRef
 
Edge - Interface in org.forester.phylogeny
 
Edit<C extends Compound> - Interface in org.biojava3.core.sequence.edits
Interface for carrying out edit operations on a Sequence.
edit(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
edit(Sequence<C>) - Method in interface org.biojava3.core.sequence.edits.Edit
 
Edit.AbstractEdit<C extends Compound> - Class in org.biojava3.core.sequence.edits
Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.
Edit.AbstractEdit(int) - Constructor for class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
Edit.AbstractEdit(int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
Edit.Delete<C extends Compound> - Class in org.biojava3.core.sequence.edits
Implementation which allows for the deletion of bases from a Sequence
Edit.Delete(int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Delete
 
Edit.Delete(int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Delete
 
Edit.Insert<C extends Compound> - Class in org.biojava3.core.sequence.edits
Edit implementation which allows us to insert a base at any position in a Sequence.
Edit.Insert(String, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
 
Edit.Insert(Sequence<C>, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
 
Edit.Insert(String, int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
 
Edit.Insert(Sequence<C>, int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
 
Edit.Substitute<C extends Compound> - Class in org.biojava3.core.sequence.edits
Allows for the substitution of bases into an existing Sequence.
Edit.Substitute(String, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Substitute
 
Edit.Substitute(Sequence<C>, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Substitute
 
eig() - Method in class org.biojava.bio.structure.jama.Matrix
Eigenvalue Decomposition
EigenvalueDecomposition - Class in org.biojava.bio.structure.jama
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition provides a way to access D and V.
Element - Enum in org.biojava.bio.structure
Element is an enumeration of the elements of the periodic table.
Element - Class in org.biojava3.aaproperties.xml
One way to model the elements
Element() - Constructor for class org.biojava3.aaproperties.xml.Element
 
Element(String, String, int, List<Isotope>, double) - Constructor for class org.biojava3.aaproperties.xml.Element
 
ElementTable - Class in org.biojava3.aaproperties.xml
 
ElementTable() - Constructor for class org.biojava3.aaproperties.xml.ElementTable
 
ElementTable(List<Element>) - Constructor for class org.biojava3.aaproperties.xml.ElementTable
 
ElementType - Enum in org.biojava.bio.structure
ElementType is an enumeration of the types of elements found in the periodic table.
EMPTY - Static variable in interface org.biojava3.core.sequence.location.template.Location
Basic location which is set to the minimum and maximum bounds of Integer.
enableCache() - Method in class org.biojava.bio.structure.domain.SerializableCache
 
ENCOUNTERED_PFAMS_SUMMARY_SUFFIX - Static variable in class org.forester.application.surfacing
 
ENCOUNTERED_PFAMS_SUMMARY_SUFFIX - Static variable in class org.forester.application.surfacing_old
 
end() - Method in class org.biojava3.genome.parsers.gff.Location
Get the ending index.
END - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
endElement(String, String, String) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
 
endElement(String, String, String) - Method in class org.forester.io.parsers.tol.TolXmlHandler
 
ENDS - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
endsAfter(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location ends after other location ends.
endsBefore(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location ends before other location ends.
ENDSEND - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
enqueue(Object) - Method in class org.forester.datastructures.Queue
Adds Object element to thisqueue.
ensureClaInstalled() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
ensureDesInstalled() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
ensureHieInstalled() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
ensurePresenceOfDate(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil
 
ensurePresenceOfDistribution(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil
 
ensurePresenceOfSequence(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil
 
ensurePresenceOfTaxonomy(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil
 
Entity - Class in org.biojava.bio.structure.io.mmcif.model
A simple class to represent Entity records in mmCif files
Entity() - Constructor for class org.biojava.bio.structure.io.mmcif.model.Entity
 
entity_poly_type - Variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
 
EntityPolySeq - Class in org.biojava.bio.structure.io.mmcif.model
Container for _entity_poly_seq records
EntityPolySeq() - Constructor for class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
entrySet() - Method in class org.biojava.bio.structure.align.util.AlignmentTools.IdentityMap
Always returns the empty set
entrySet() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
entrySet() - Method in class org.biojava3.core.util.SoftHashMap
 
EOL_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
EQR_COLOR - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
equal(int, int) - Static method in class org.biojava3.core.util.Equals
 
equal(long, long) - Static method in class org.biojava3.core.util.Equals
 
equal(boolean, boolean) - Static method in class org.biojava3.core.util.Equals
 
equal(Object, Object) - Static method in class org.biojava3.core.util.Equals
 
equals(Object) - Method in class org.biojava.bio.structure.align.client.PdbPair
 
equals(Object) - Method in class org.biojava.bio.structure.align.client.StructureName
 
equals(Object) - Method in class org.biojava.bio.structure.align.model.AFPChain
A week equality metric.
equals(Object) - Method in class org.biojava.bio.structure.Author
 
equals(Object) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
equals(Object) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
equals(Object) - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
equals(Object) - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
equals(PDBHeader) - Method in class org.biojava.bio.structure.PDBHeader
Compare two PDBHeader objects
equals(Object) - Method in class org.biojava.bio.structure.ResidueNumber
Require chainId, insCode, and seqNum to be equal
equals(Object) - Method in class org.biojava.bio.structure.scop.ScopDescription
Compares the fields sunID, category, classificationId, and name for equality
equals(Object) - Method in class org.biojava.bio.structure.Site
 
equals(Object) - Method in class org.biojava3.core.sequence.AccessionID
 
equals(Object) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
 
equals(Object) - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
equals(Object) - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
equals(Object) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
equals(Object) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
equals(Object) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
equals(Object) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
equals(Object) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
equals(Object) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
 
equals(Object) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
 
equals(Object) - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
equals(Object) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
equals(Object) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
equals(Object) - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
equals(Object) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
Equals - Class in org.biojava3.core.util
A set of helper methods which return true if the two parameters are equal to each other.
Equals() - Constructor for class org.biojava3.core.util.Equals
 
equals(Object) - Method in class org.biojava3.data.sequence.FastaSequence
 
equals(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Compare locations for equality.
equals(Object) - Method in class org.biojava3.protmod.ProteinModificationImpl
 
equals(Object) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
equals(Object) - Method in class org.biojava3.protmod.structure.StructureAtom
 
equals(Object) - Method in class org.biojava3.protmod.structure.StructureAtomLinkage
 
equals(Object) - Method in class org.biojava3.protmod.structure.StructureGroup
 
equals(Object) - Method in class org.biojava3.ronn.Jronn.Range
 
equals(Object) - Method in class org.biojava3.ronn.ModelLoader.Model
 
equals(Object) - Method in class org.forester.go.BasicGoRelationship
Based on value and type.
equals(Object) - Method in class org.forester.go.BasicGoSubset
 
equals(Object) - Method in class org.forester.go.BasicGoTerm
Return true if both GO id and namespace are equal.
equals(Object) - Method in class org.forester.go.BasicGoXRef
Based on value and type.
equals(Object) - Method in class org.forester.go.GoId
 
equals(Object) - Method in class org.forester.go.GoNameSpace
 
equals(Object) - Method in class org.forester.go.PfamToGoMapping
Based on key and value.
equals(Object) - Method in class org.forester.phylogeny.data.Accession
 
equals(Object) - Method in class org.forester.phylogeny.data.Identifier
 
equals(Object) - Method in class org.forester.phylogeny.data.Sequence
 
equals(Object) - Method in class org.forester.phylogeny.data.Taxonomy
 
equals(Object) - Method in class org.forester.phylogeny.PhylogenyBranch
 
equals(Object) - Method in class org.forester.phylogeny.PhylogenyNode
 
equals(Object) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
equals(Object) - Method in class org.forester.phylogenyinference.DiscreteState
 
equals(Object) - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
equals(Object) - Method in class org.forester.surfacing.BasicDomain
Basic domains are considered equal if they have the same identifier (case sensitive).
equals(Object) - Method in class org.forester.surfacing.BasicSpecies
 
equals(Object) - Method in class org.forester.surfacing.DomainId
 
equals(Object) - Method in class org.forester.surfacing.ProteinId
 
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
equalsIgnoreCase(Compound) - Method in interface org.biojava3.core.sequence.template.Compound
 
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
equalsToIgnoreEndline(String, String) - Static method in class org.biojava3.core.util.StringManipulationHelper
compares two strings for equality, line by line, ignoring any difference of end line delimiters contained within the 2 Strings.
equalsToXml(String, String) - Static method in class org.biojava3.core.util.StringManipulationHelper
 
EQUIVALENT - Static variable in class org.biojava.bio.structure.gui.util.AlignedPosition
flag if this position is equivalent
errorProbabilities(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Return the error probabilities from the specified FASTQ formatted sequence.
errorProbabilities(Fastq, double[]) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
errorProbability(char) - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Convert the specified quality in ASCII format to an error probability.
errorProbability(int) - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Calculate the error probability given the specified quality score.
eval(String) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
evalString(String) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
evalString(String) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
evalString(String) - Method in class org.biojava.bio.structure.gui.BiojavaJmol
 
evaluate(String, Phylogeny[], Phylogeny, boolean, double) - Static method in class org.forester.tools.ConfidenceAssessor
 
evaluate(String, Phylogeny[], Phylogeny, boolean, double, int, int) - Static method in class org.forester.tools.ConfidenceAssessor
 
Event - Class in org.forester.phylogeny.data
 
Event() - Constructor for class org.forester.phylogeny.data.Event
 
Event(Event.EventType) - Constructor for class org.forester.phylogeny.data.Event
 
Event(int, int, int) - Constructor for class org.forester.phylogeny.data.Event
 
Event(int, int, int, String) - Constructor for class org.forester.phylogeny.data.Event
 
Event(String) - Constructor for class org.forester.phylogeny.data.Event
 
Event.EventType - Enum in org.forester.phylogeny.data
 
EVENT_DUPLICATIONS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
EVENT_LOSSES - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
EVENT_SPECIATIONS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
EVENT_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
EventParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
EVENTS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
execute(Msa) - Method in interface org.forester.phylogenyinference.DistanceMethod
 
execute(Phylogeny, CharacterStateMatrix<CharacterStateMatrix.BinaryStates>) - Method in class org.forester.phylogenyinference.DolloParsimony
 
execute(Phylogeny, CharacterStateMatrix<STATE_TYPE>) - Method in class org.forester.phylogenyinference.FitchParsimony
 
execute(DistanceMatrix) - Method in class org.forester.phylogenyinference.NeighborJoining
 
execute(List<DistanceMatrix>) - Method in class org.forester.phylogenyinference.NeighborJoining
 
execute(Phylogeny, CharacterStateMatrix<STATE_TYPE>) - Method in class org.forester.phylogenyinference.SankoffParsimony
 
execute(Phylogeny, Phylogeny) - Static method in class org.forester.sdi.TaxonomyAssigner
 
executeCmd(String) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
executeDolloParsimonyOnBinaryDomainCombintionPresence() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeDolloParsimonyOnDomainPresence() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeDolloParsimonyOnDomainPresence(SortedSet<DomainId>) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeDolloParsimonyOnSecondaryFeatures(Map<Species, MappingResults>) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeDomainLengthAnalysis(String[][], int, DomainLengthsTable, File) - Static method in class org.forester.surfacing.SurfacingUtil
 
executeFitchParsimonyOnBinaryDomainCombintion(boolean) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeFitchParsimonyOnBinaryDomainCombintion(long) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeFitchParsimonyOnDomainPresence(boolean) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeFitchParsimonyOnDomainPresence(long) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates>, String[]) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
executeParsimonyAnalysis(long, boolean, String, DomainParsimonyCalculator, Phylogeny, Map<DomainId, List<GoId>>, Map<GoId, GoTerm>, GoNameSpace, String, Map<DomainId, Set<String>>[], SortedSet<DomainId>, boolean, List<BinaryDomainCombination>, List<BinaryDomainCombination>, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.SurfacingUtil
 
executeParsimonyAnalysisForSecondaryFeatures(String, DomainParsimonyCalculator, Phylogeny, String, Map<Species, MappingResults>) - Static method in class org.forester.surfacing.SurfacingUtil
 
ExonComparator - Class in org.biojava3.core.sequence
Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.
ExonComparator() - Constructor for class org.biojava3.core.sequence.ExonComparator
 
ExonSequence - Class in org.biojava3.core.sequence
A gene contains a collection of Exon sequences
ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava3.core.sequence.ExonSequence
Need a parent gene sequence and the bioBegin and bioEnd.
Exptl - Class in org.biojava.bio.structure.io.mmcif.model
 
Exptl() - Constructor for class org.biojava.bio.structure.io.mmcif.model.Exptl
 
extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
 
extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
 
ExternalForwardIterator - Class in org.forester.phylogeny.iterators
 
ExternalForwardIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.ExternalForwardIterator
Constructor for ExternalForwardIterator.
ExternalNodeBasedCoverage - Class in org.forester.pccx
 
ExternalNodeBasedCoverage(DescriptiveStatistics, double, CoverageCalculationOptions) - Constructor for class org.forester.pccx.ExternalNodeBasedCoverage
 
ExternalNodeBasedCoverageMethod - Class in org.forester.pccx
 
ExternalNodeBasedCoverageMethod() - Constructor for class org.forester.pccx.ExternalNodeBasedCoverageMethod
 
ExternalNodeBasedCoverageMethodOptions - Class in org.forester.pccx
 
ExternalNodeBasedCoverageMethodOptions(String) - Constructor for class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions
This constructor sets the class name for the scoring method e.g.
externalNodesHaveChanged() - Method in class org.forester.phylogeny.Phylogeny
 
extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
 
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
extractProteinNames(List<Protein>, List<DomainId>, Writer, String) - Static method in class org.forester.surfacing.SurfacingUtil
 
extractProteinNames(SortedMap<Species, List<Protein>>, DomainId, Writer, String) - Static method in class org.forester.surfacing.SurfacingUtil
 

F

F - Static variable in class org.biojava3.aaproperties.Constraints
 
Factory - Interface in org.forester.development
 
FarmJob - Class in org.biojava.bio.structure.align
A job as it can be run on the farm.
FarmJob() - Constructor for class org.biojava.bio.structure.align.FarmJob
 
FarmJobParameters - Class in org.biojava.bio.structure.align.client
 
FarmJobParameters() - Constructor for class org.biojava.bio.structure.align.client.FarmJobParameters
 
FarmJobRunnable - Class in org.biojava.bio.structure.align.client
Contains the single thread for a job that can run multiple alignments.
FarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.bio.structure.align.client.FarmJobRunnable
 
FastaGeneWriter - Class in org.biojava3.core.sequence.io
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava3.core.sequence.io.FastaGeneWriter
 
FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava3.core.sequence.io.FastaGeneWriter
 
FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava3.core.sequence.io.template
 
FastaHeaderParserInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava3.core.sequence.io.template
 
FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
FastaReader(InputStream, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava3.core.sequence.io.FastaReader
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.
FastaReader(File, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava3.core.sequence.io.FastaReader
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
FastaReaderHelper - Class in org.biojava3.core.sequence.io
 
FastaReaderHelper() - Constructor for class org.biojava3.core.sequence.io.FastaReaderHelper
 
FastaSequence - Class in org.biojava3.data.sequence
A FASTA formatted sequence.
FastaSequence(String, String) - Constructor for class org.biojava3.data.sequence.FastaSequence
Upon construction the any whitespace characters are removed from the sequence
FastaSequenceParser - Class in org.biojava3.core.sequence.io
Used to parse a stream of a fasta file to get the sequence
FastaSequenceParser() - Constructor for class org.biojava3.core.sequence.io.FastaSequenceParser
 
FastaStructureParser - Class in org.biojava.bio.structure.io
Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.
FastaStructureParser(InputStream, FastaHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.bio.structure.io.FastaStructureParser
 
FastaStructureParser(File, FastaHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.bio.structure.io.FastaStructureParser
 
FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.bio.structure.io.FastaStructureParser
 
FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io
The FastaWriter writes a collection of sequences to an outputStream.
FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava3.core.sequence.io.FastaWriter
Use default line length of 60
FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava3.core.sequence.io.FastaWriter
Set custom lineLength
FastaWriterHelper - Class in org.biojava3.core.sequence.io
The class that should be used to write out fasta file of a sequence collection
FastaWriterHelper() - Constructor for class org.biojava3.core.sequence.io.FastaWriterHelper
 
Fastq - Class in org.biojava3.sequencing.io.fastq
FASTQ formatted sequence.
fastq(Fastq) - Method in interface org.biojava3.sequencing.io.fastq.StreamListener
Notify this listener of a FASTQ formatted sequence.
FastqBuilder - Class in org.biojava3.sequencing.io.fastq
Fluent builder API for creating FASTQ formatted sequences.
FastqBuilder() - Constructor for class org.biojava3.sequencing.io.fastq.FastqBuilder
Create a new FASTQ formatted sequence builder.
FastqReader - Interface in org.biojava3.sequencing.io.fastq
Reader for FASTQ formatted sequences.
FastqTools - Class in org.biojava3.sequencing.io.fastq
Utility methods for FASTQ formatted sequences.
FastqVariant - Enum in org.biojava3.sequencing.io.fastq
FASTQ sequence format variant.
FastqWriter - Interface in org.biojava3.sequencing.io.fastq
Writer for FASTQ formatted sequences.
fatalError(String, String) - Static method in class org.forester.util.ForesterUtil
 
FatCat - Class in org.biojava.bio.structure.align.fatcat
 
FatCat() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCat
 
FATCAT_BLOCK - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
FATCAT_TEXT - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
FatCatAligner - Class in org.biojava.bio.structure.align.fatcat.calc
A class that does calculations on an AFPChain
FatCatAligner() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
FatCatFlexible - Class in org.biojava.bio.structure.align.fatcat
 
FatCatFlexible() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
FatCatParameters - Class in org.biojava.bio.structure.align.fatcat.calc
 
FatCatParameters() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
FatCatRigid - Class in org.biojava.bio.structure.align.fatcat
 
FatCatRigid() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
FatCatUserArgumentProcessor - Class in org.biojava.bio.structure.align.fatcat
 
FatCatUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor
 
fatColumnNames - Static variable in class org.biojava.bio.structure.align.gui.DBResultTable
 
FCAlignHelper - Class in org.biojava.bio.structure.align.fatcat.calc
 
FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper
do an alignment given the provided matrix sij0
Feature - Class in org.biojava3.genome.parsers.gff
A Feature corresponds to a single row in a GFF file.
Feature(Feature) - Constructor for class org.biojava3.genome.parsers.gff.Feature
Make a copy of the specified feature.
Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava3.genome.parsers.gff.Feature
Construct a new Feature from raw data (usually a GFF row).
FeatureHelper - Class in org.biojava3.genome.parsers.gff
 
FeatureHelper() - Constructor for class org.biojava3.genome.parsers.gff.FeatureHelper
 
FeatureI - Interface in org.biojava3.genome.parsers.gff
A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava3.core.sequence.features
Interface class to handle describing arbitrary features.
FeatureList - Class in org.biojava3.genome.parsers.gff
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
FeatureList() - Constructor for class org.biojava3.genome.parsers.gff.FeatureList
Construct an empty list.
FeatureList(Collection<FeatureI>) - Constructor for class org.biojava3.genome.parsers.gff.FeatureList
Construct a new list containing the same features as the specified list.
FeaturesKeyWordInterface - Interface in org.biojava3.core.sequence.features
Models the keywords that are annotated for a protein sequence at Uniprot.
FIELD_LINE - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
file2array(File) - Static method in class org.forester.util.ForesterUtil
 
file2list(File) - Static method in class org.forester.util.ForesterUtil
 
file2set(File) - Static method in class org.forester.util.ForesterUtil
 
FILE_SEPARATOR - Static variable in class org.forester.util.ForesterUtil
 
FileAccessError - Error in org.biojava3.core.exceptions
Thrown from SequenceFileProxyLoader if error opening file using RandomnAccessFile
FileAccessError(String) - Constructor for error org.biojava3.core.exceptions.FileAccessError
 
FileConvert - Class in org.biojava.bio.structure.io
Methods to convert a structure object into different file formats.
FileConvert(Structure) - Constructor for class org.biojava.bio.structure.io.FileConvert
Constructs a FileConvert object.
FileDownloadUtils - Class in org.biojava.bio.structure.io.util
 
FileDownloadUtils() - Constructor for class org.biojava.bio.structure.io.util.FileDownloadUtils
 
FileParsingParameters - Class in org.biojava.bio.structure.io
A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
FileParsingParameters() - Constructor for class org.biojava.bio.structure.io.FileParsingParameters
 
FileProxyDNASequenceCreator - Class in org.biojava3.core.sequence.io
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
FileProxyProteinSequenceCreator - Class in org.biojava3.core.sequence.io
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
fileSeparator - Static variable in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
 
FILESPLIT - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
filterByClassificationId(String) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
filterByClassificationId(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
filterByClassificationId(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Get all scop descriptions that start with a classifcation ID, e.g.
filterByClassificationId(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
filterByDescription(String) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
filterByDescription(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
filterByDescription(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Get all scop descriptions that start with a certain name.
filterByDescription(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
filterByDomainName(String) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
filterByDomainName(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
filterByDomainName(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
search through SCOP and filter based on domain name
filterByDomainName(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.ce.CeCPMain
Takes as input an AFPChain where ca2 has been artificially duplicated.
filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], int) - Static method in class org.biojava.bio.structure.align.ce.CeCPMain
 
find(List<Phylogeny>, List<String>, int, CoverageCalculationOptions, PrintStream) - Method in class org.forester.pccx.BasicExternalNodeBasedCoverageExtender
 
find(List<Phylogeny>, List<String>, int, CoverageCalculationOptions, PrintStream) - Method in interface org.forester.pccx.CoverageExtender
 
findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
Find linkages between two groups within tolerance of bond length, from potential atoms.
findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
Find linkages between two groups within tolerance of bond length, from potential atoms.
findBonds(Group, List<Group>) - Static method in class org.biojava.bio.structure.StructureTools
 
findChain(String) - Method in interface org.biojava.bio.structure.Structure
request a particular chain from a structure.
findChain(String, int) - Method in interface org.biojava.bio.structure.Structure
request a particular chain from a particular model
findChain(String, int) - Method in class org.biojava.bio.structure.StructureImpl
 
findChain(String) - Method in class org.biojava.bio.structure.StructureImpl
 
findCommonParent(PhylogenyNode) - Method in class org.biojava3.phylo.CheckTreeAccuracy
 
findCommonParent(PhylogenyNode) - Method in class org.forester.application.CheckTreeAccuracy
 
findGroup(String, String) - Method in interface org.biojava.bio.structure.Structure
request a particular group from a structure.
findGroup(String, String, int) - Method in interface org.biojava.bio.structure.Structure
request a particular group from a structure.
findGroup(String, String, int) - Method in class org.biojava.bio.structure.StructureImpl
 
findGroup(String, String) - Method in class org.biojava.bio.structure.StructureImpl
 
findLinkage(Group, Group, String, String, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
Find a linkage between two groups within tolerance of bond length.
findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava3.protmod.structure.StructureUtil
Find a linkage between two groups within tolerance of bond length, from potential atoms.
findSequence(String, boolean, boolean) - Method in class org.forester.development.BasicMsa
 
finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
first_cut - Variable in class org.biojava.bio.structure.domain.pdp.CutValues
 
FitchParsimony<STATE_TYPE> - Class in org.forester.phylogenyinference
 
FitchParsimony() - Constructor for class org.forester.phylogenyinference.FitchParsimony
 
FlatFileCache - Class in org.biojava3.core.util
Provides a cache for storing multiple small files in memory.
FlatFileInstallation - Class in org.biojava.bio.structure.server
Deprecated. 
FlatFileInstallation(File) - Constructor for class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
create a new FlatFile Installation and point it to the directory that contains all PDB files
flipAlignment(String) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
Takes an XML representation of the alignment and flips the positions of name1 and name2
flipChain(AFPChain) - Static method in class org.biojava.bio.structure.align.xml.AFPChainFlipper
Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
flushCache() - Method in class org.biojava.bio.structure.domain.RemoteDomainProvider
 
flushCache() - Method in class org.biojava.bio.structure.domain.SerializableCache
 
flushCache() - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
FontChooser - Class in org.forester.archaeopteryx
 
FontChooser() - Constructor for class org.forester.archaeopteryx.FontChooser
 
FontChooser(Font) - Constructor for class org.forester.archaeopteryx.FontChooser
 
FontChooser(String, int, int) - Constructor for class org.forester.archaeopteryx.FontChooser
 
ForesterConstants - Class in org.forester.util
 
ForesterConstants() - Constructor for class org.forester.util.ForesterConstants
 
ForesterUtil - Class in org.forester.util
 
ForesterUtil.PhylogenyNodeField - Enum in org.forester.util
 
FORMAT - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
FORMATTER_06 - Static variable in class org.forester.util.ForesterUtil
 
FORMATTER_3 - Static variable in class org.forester.util.ForesterUtil
 
FORMATTER_6 - Static variable in class org.forester.util.ForesterUtil
 
FORMATTER_9 - Static variable in class org.forester.util.ForesterUtil
 
FourBitSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
Four bit encoding of the bit formats.
FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader
 
FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava3.core.sequence.storage
A four bit per compound implementation of the bit array worker code.
FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitSequenceReader.FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FourBitSequenceReader.FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
 
FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava3.alignment.FractionalIdentityInProfileScorer
Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements an algorithm which computes a score for a sequence alignment pair.
FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava3.alignment.FractionalIdentityScorer
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava3.alignment.FractionalIdentityScorer
Creates a fractional identity scorer for an aligned pair of sequences.
FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava3.alignment.FractionalSimilarityInProfileScorer
Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava3.alignment.FractionalSimilarityScorer
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava3.alignment.FractionalSimilarityScorer
Creates a fractional similarity scorer for an aligned pair of sequences.
frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
Calculate the pairwise compatibility of fpairs.
FragmentJoiner - Class in org.biojava.bio.structure.align.pairwise
Joins the initial Fragments together to larger Fragments
FragmentJoiner() - Constructor for class org.biojava.bio.structure.align.pairwise.FragmentJoiner
 
FragmentPair - Class in org.biojava.bio.structure.align.pairwise
a pair of fragments of two protein structures
FragmentPair(int, int, int) - Constructor for class org.biojava.bio.structure.align.pairwise.FragmentPair
 
Frame - Enum in org.biojava3.core.sequence.transcription
Indicates a way of translating a sequence.
frame() - Method in class org.biojava3.genome.parsers.gff.Feature
Get frame (aka phase).
fromBio(int, int, char) - Static method in class org.biojava3.genome.parsers.gff.Location
Create location from "biocoordinates", as in GFF file.
fromBioExt(int, int, char, int) - Static method in class org.biojava3.genome.parsers.gff.Location
Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.
fromCIEXYZ(float[]) - Method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
fromRGB(float[]) - Method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
fromStartupParams(StartupParameters) - Static method in class org.biojava.bio.structure.align.util.UserConfiguration
 
fromString(String) - Static method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
fromString(String) - Static method in enum org.biojava.bio.structure.PDBStatus.Status
 
fromString(String) - Static method in class org.biojava.bio.structure.ResidueNumber
Convert a string representation of a residue number to a residue number object.
fromString(String) - Static method in enum org.biojava.bio.structure.scop.ScopCategory
 
fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
 
fromXML(String) - Method in class org.biojava.bio.structure.align.xml.HasResultXMLConverter
 
fromXML(String) - Method in class org.biojava.bio.structure.align.xml.PositionInQueueXMLConverter
 
fromXML(String) - Static method in class org.biojava.bio.structure.align.xml.RepresentativeXMLConverter
 
fromXML(String) - Static method in class org.biojava.bio.structure.domain.AssignmentXMLSerializer
 
fromXML(String) - Static method in class org.biojava.bio.structure.scop.server.ScopDescriptions
 
fromXML(String) - Static method in class org.biojava.bio.structure.scop.server.ScopDomains
 
fromXML(String) - Static method in class org.biojava.bio.structure.scop.server.ScopNodes
 
fromXML(String) - Static method in class org.biojava.bio.structure.scop.server.TreeSetStringWrapper
 
fromXML(String) - Static method in class org.biojava3.protmod.io.ComponentXMLConverter
 
fromXML(Node) - Static method in class org.biojava3.protmod.io.ComponentXMLConverter
 
fromXML(String) - Static method in class org.biojava3.protmod.io.ModifiedCompoundXMLConverter
 
fromXML(Node) - Static method in class org.biojava3.protmod.io.StructureAtomXMLConverter
 
fromXML(Node) - Static method in class org.biojava3.protmod.io.StructureGroupXMLConverter
 
functionXY(String, int, int) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
functionXYZ(String, int, int, int) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
FuzzyPoint - Class in org.biojava3.core.sequence.location
Implementation for resolving fuzzy locations.
FuzzyPoint(int, int) - Constructor for class org.biojava3.core.sequence.location.FuzzyPoint
 
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava3.core.sequence.location.FuzzyPoint
 
FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava3.core.sequence.location.FuzzyPoint
 

G

G - Static variable in class org.biojava3.aaproperties.Constraints
 
GAP - Static variable in class org.forester.development.AminoAcid
 
GAP_CODE - Static variable in class org.forester.development.AminoAcid
 
GAP_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
GapArray - Class in org.biojava.bio.structure.align.helper
 
GapArray() - Constructor for class org.biojava.bio.structure.align.helper.GapArray
 
gapExtension - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
gapOpen - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
gapPenalty - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
GapPenalty - Interface in org.biojava3.alignment.template
Defines a data structure for the gap penalties used during a sequence alignment routine.
GapPenalty.Type - Enum in org.biojava3.alignment.template
Defines the possible types of gap penalties.
GCStats - Class in org.biojava3.genome.parsers.gff
 
GCStats() - Constructor for class org.biojava3.genome.parsers.gff.GCStats
 
GENE_NAME - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
GENE_NAME_SYNONYM - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
GeneFeatureHelper - Class in org.biojava3.genome
 
GeneFeatureHelper() - Constructor for class org.biojava3.genome.GeneFeatureHelper
 
GeneIDGFF2Reader - Class in org.biojava3.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDGFF2Reader() - Constructor for class org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
 
GeneIDXMLReader - Class in org.biojava3.genome.parsers.geneid
 
GeneIDXMLReader(String) - Constructor for class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
 
GeneMarkGTFReader - Class in org.biojava3.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneMarkGTFReader() - Constructor for class org.biojava3.genome.parsers.gff.GeneMarkGTFReader
 
GeneralTable<IDENTIFIER_TYPE,VALUE_TYPE> - Class in org.forester.util
 
GeneralTable() - Constructor for class org.forester.util.GeneralTable
 
generateCompoundsToIndex() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns what the value of a compound is in the backing bit storage i.e.
generateCompoundsToIndex() - Method in class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
Returns a Map which encodes the contents of CompoundSet.
generateCompoundsToIndex() - Method in class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
Returns a Map which encodes TCAG into positions 0,1,2,3.
generateIndexToCompounds() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Should return the inverse information that BitSequenceReader.BitArrayWorker.generateCompoundsToIndex() returns i.e.
generateIndexToCompounds() - Method in class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
Returns a List which reverse encodes the Compound, Integer map
generateIndexToCompounds() - Method in class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
Returns a List which encodes TCAG into positions 0,1,2,3.
generatePoint(String, String) - Method in class org.biojava3.core.sequence.location.InsdcParser
 
GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io
We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
GenericFastaHeaderFormat() - Constructor for class org.biojava3.core.sequence.io.GenericFastaHeaderFormat
 
GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.io
The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE PDB EBI PDB:1ECY_A mol:protein length:142 ECOTIN Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
GenericFastaHeaderParser() - Constructor for class org.biojava3.core.sequence.io.GenericFastaHeaderParser
 
GeneSequence - Class in org.biojava3.core.sequence
 
GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava3.core.sequence.GeneSequence
A class that keeps track of the details of a GeneSequence which is difficult to properly model.
GenomeWideCombinableDomains - Interface in org.forester.surfacing
 
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder - Enum in org.forester.surfacing
 
get(Object) - Method in class org.biojava.bio.structure.align.util.AlignmentTools.IdentityMap
 
get(K) - Method in class org.biojava.bio.structure.domain.SerializableCache
 
get(Object) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
get(int, int) - Method in class org.biojava.bio.structure.jama.Matrix
Get a single element.
get(int) - Method in class org.biojava3.core.sequence.views.WindowedSequence
Returns the window specified at the given index in offsets i.e.
get(Object) - Method in class org.biojava3.core.util.SoftHashMap
 
get(DomainId) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
get(DomainId) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
get1LetterCode(String) - Static method in class org.biojava.bio.structure.StructureTools
convert a three letter code into single character.
get_distances - Class in org.forester.application
 
get_distances() - Constructor for class org.forester.application.get_distances
 
getA() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getAA3Hash() - Static method in class org.biojava3.phylo.ResidueProperties
 
getAAComposition(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the composition of the 20 standard amino acid in the sequence.
getAAComposition(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAComposition(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getAACompositionChar(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAACompositionString(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
getAAIndexProvider() - Static method in class org.biojava3.alignment.aaindex.AAindexFactory
 
getAboutMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the absorbance (optical density) of sequence.
getAbsorbance(String, boolean) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to returns the absorbance (optical density) of sequence.
getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getAbsorpt_coefficient_mu() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getAbsorpt_correction_T_max() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getAbsorpt_correction_T_min() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getAbsorpt_correction_type() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getAbsorpt_process_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getAcc() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getAcceptedAtomNames() - Method in class org.biojava.bio.structure.io.FileParsingParameters
by default the parser will read in all atoms (unless using the CAonly switch).
getAccession() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getAccession() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getAccession() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getAccession() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getAccession(String) - Method in class org.biojava3.core.sequence.location.InsdcParser
 
getAccession() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getAccession() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getAccession() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
 
getAccession() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getAccession() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Unsupoorted
getAccession() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getAccession() - Method in interface org.biojava3.core.sequence.template.Accessioned
Returns the AccessionID this location is currently bound with
getAccession() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getAccession() - Method in class org.forester.phylogeny.data.Sequence
 
getAccession() - Method in class org.forester.surfacing.BasicProtein
 
getAccession() - Method in interface org.forester.surfacing.Protein
 
getAccessions() - Method in class org.biojava.bio.structure.io.FastaStructureParser
Gets the protein accessions mapped from the Fasta file.
getAdapter() - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
getAfpAftIndex() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpBefIndex() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpChain() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
getAFPChain() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
getAfpChain() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
getAFPChainFromServer(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getAFPChainFromServer(String, String, String, String, Atom[], Atom[], int) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getAfpChainLen() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpChainList() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpChainTwiBin() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpChainTwiList() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpChainTwiNum() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpDisCut() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getAfpDisCut0() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getAfpIndex() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAfpSet() - Method in class org.biojava.bio.structure.align.model.AFPChain
Get the set of AFPs for this alignment.
getAlgorithm() - Method in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
getAlgorithm() - Method in class org.biojava.bio.structure.align.ce.CeCPUserArgumentProcessor
 
getAlgorithm() - Method in class org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor
 
getAlgorithm() - Method in class org.biojava.bio.structure.align.ce.CeUserArgumentProcessor
 
getAlgorithm() - Method in class org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor
 
getAlgorithm() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
getAlgorithm() - Method in class org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
getAlgorithm(String) - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.ce.CeCPMain
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.ce.CeMain
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.ce.CeSideChainMain
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlgorithmName() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
getAlgorithmName() - Method in interface org.biojava.bio.structure.align.StructureAlignment
Get the name of the Algorithm
getAligMap() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
getAligMat() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getAligMat(int, int) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getAligMat() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getAlign(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
Extract the alignment output
getAlign(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen
getAlign_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getAlign_se1() - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getAlign_se1() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getAlign_se2() - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getAlign_se2() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getAlignedAtoms1(AFPChain, Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
getAlignedAtoms2(AFPChain, Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
getAlignedSequence(int) - Method in class org.biojava3.alignment.SimpleProfile
 
getAlignedSequence(S) - Method in class org.biojava3.alignment.SimpleProfile
 
getAlignedSequence(int) - Method in interface org.biojava3.alignment.template.Profile
Returns AlignedSequence at given index.
getAlignedSequence(S) - Method in interface org.biojava3.alignment.template.Profile
Searches for the given Sequence within this alignment profile.
getAlignedSequence(int) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Uses bioIndex starting at 1 instead of 0
getAlignedSequence(int) - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns Sequence at given index.
getAlignedSequences() - Method in class org.biojava3.alignment.SimpleProfile
 
getAlignedSequences(int...) - Method in class org.biojava3.alignment.SimpleProfile
 
getAlignedSequences(S...) - Method in class org.biojava3.alignment.SimpleProfile
 
getAlignedSequences() - Method in interface org.biojava3.alignment.template.Profile
Returns a List containing the individual AlignedSequences of this alignment.
getAlignedSequences(int...) - Method in interface org.biojava3.alignment.template.Profile
Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignedSequences(S...) - Method in interface org.biojava3.alignment.template.Profile
Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignedSequences() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Get the list of sequences
getAlignedSequences() - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns a List containing the individual Sequences of this alignment.
getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
Get an artifical Structure containing both chains.
getAlignedStructure(Structure, Structure) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
create an artifical Structure object that contains the two structures superimposed onto each other.
getAlignmentAtoms(Structure) - Method in class org.biojava.bio.structure.align.StructurePairAligner
Returns the atoms that are being used for the alignment.
getAlignmentIndexAt(int) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getAlignmentIndexAt(int) - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the column index within an alignment corresponding to the given index in the original Sequence.
getAlignmentNumber() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
 
getAlignmentOption(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
This method forwards to NCBIQBlastAlignmentProperties.getAlignmentOption(BlastAlignmentParameterEnum).
getAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Gets the value of specified parameter or null if it is not set.
getAlignmentOption(String) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties
Method that returns the value associated with the key given in parameter.
getAlignmentOptions() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Gets parameters, which are currently set
getAlignmentOptions() - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties
Method to get all keys to the information stored in this object.
getAlignmentOutputFormat() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
 
getAlignmentPairsFromServer() - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
talk to centralized server and fetch all alignments to run.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Extracts the actual Blast report for given request id according to options provided in outputProperties argument.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentService
Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
getAlignments() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getAlignments() - Method in class org.biojava.bio.structure.align.StructurePairAligner
return the alternative alignments that can be found for the two structures
getAlignmentString() - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
getAlignmentTextMenu(JFrame, ActionListener, AFPChain) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
Create the menu for the "Text Only" representation of alignments
getAlignPairs() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getAlignPos(int[][]) - Method in class org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper
record the aligned pairs in alignList[][0], alignList[][1]; return the number of aligned pairs
getAlignScore() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlignScoreUpdate() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAligSeq(Point) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.
getAliLenth() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getAll() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
getAll() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
getAll() - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
getAllAlgorithmNames() - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
 
getAllAlgorithms() - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
 
getAllBinaryDomainCombinations() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.
getAllCombinableDomainsIds() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getAllCombinableDomainsIds() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
getAllCompounds() - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getAllCompounds() - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
getAllCompounds() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
getAllCompounds() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
getAllCompounds() - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
getAllDescendants(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
getAllDomainIds() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getAllDomainIds() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
This should return all domains ids present in the genome.
getAllDomainIds(List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.SurfacingUtil
 
getAllDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getAllDomains() - Method in interface org.forester.surfacing.CombinableDomains
This must return all domains in this set of combinable domains (i.e.
getAllDomains() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
Does not return domains which are to be ignored -- if ignoring is allowed.
getAllExternalDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a List containing references to all external children of this PhylogenyNode.
getAllExternalDescendantsNames() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a List containing references to all names of the external children of this PhylogenyNode.
getAllExternalNodeNames() - Method in class org.forester.phylogeny.Phylogeny
 
getAllFrames() - Static method in enum org.biojava3.core.sequence.transcription.Frame
Delegates to Frame.values()
getAllMMcif(File) - Method in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
 
getAllowsChildren() - Method in class org.biojava3.alignment.GuideTree.Node
 
getAllPairsAlignments(List<S>, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava3.alignment.Alignments
Factory method which computes a sequence alignment for all Sequence pairs in the given List.
getAllPairsScorers(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava3.alignment.Alignments
Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
getAllPairsScores(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava3.alignment.Alignments
Factory method which computes a sequence pair score for all Sequence pairs in the given List.
getAllPairsScores() - Method in class org.biojava3.alignment.GuideTree
Returns a sequence pair score for all Sequence pairs in the given List.
getAllPDB(File) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
get all PDBfiles from a directory
getAllPDBIDs() - Method in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
Returns a list of all PDB IDs that are available in this installation
getAllSuperGoIds(GoId, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
 
getAllSuperGoTerms(GoId, List<GoTerm>) - Static method in class org.forester.go.GoUtils
 
getAllSuperGoTerms(GoId, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
 
getAllSuperGoTerms(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
 
getAlnbeg1() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlnbeg2() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlnLength() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlnseq1() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlnseq2() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlnsymb() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getAlpha() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getAlt() - Method in class org.forester.phylogeny.data.Point
 
getAltAligNumber() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
returns the sequential number of this alternative alignment
getAlternativeAligs() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
getAlternativeAligs() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
getAltIds() - Method in class org.forester.go.BasicGoTerm
 
getAltIds() - Method in interface org.forester.go.GoTerm
 
getAltitude() - Method in class org.forester.phylogeny.data.Distribution
 
getAltLoc() - Method in interface org.biojava.bio.structure.Atom
get set alternate Location.
getAltLoc() - Method in class org.biojava.bio.structure.AtomImpl
get alternate Location.
getAltLocs() - Method in interface org.biojava.bio.structure.Group
Get the list of alternate locations.
getAltLocs() - Method in class org.biojava.bio.structure.HetatomImpl
 
getAltUnit() - Method in class org.forester.phylogeny.data.Point
 
getAmbiguity(NucleotideCompound...) - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
Calculates the best symbol for a collection of compounds.
getAminoAcid(String) - Static method in class org.biojava.bio.structure.StandardAminoAcid
get a standard amino acid.
getAminoacid() - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
getAminoAcid() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getAminoAcidCompounds() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getAminoAcidCompoundSet() - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
getAminoAcidCompoundSet() - Static method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getAminoAcidCompoundSet() - Static method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
getAminoAcids(Chain) - Static method in class org.biojava3.protmod.structure.StructureUtil
Get all amino acids in a chain.
getAminoOneLetter(String) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
getAminoThreeLetter(Character) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
getAminoType() - Method in interface org.biojava.bio.structure.AminoAcid
returns the name of the AA, in single letter code.
getAminoType() - Method in class org.biojava.bio.structure.AminoAcidImpl
returns the name of the AA, in single letter code.
getAnchors() - Method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Returns the list of anchors.
getAngleDiff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getAniso_B() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getAnnotation(int) - Method in class org.forester.phylogeny.data.Sequence
 
getAnnotations() - Method in class org.forester.phylogeny.data.Sequence
 
getAnnotationType() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getApliphaticIndex(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the apliphatic index of sequence.
getApliphaticIndex(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the apliphatic index of sequence.
getApliphaticIndex(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getAppliesTo() - Method in class org.forester.phylogeny.data.Property
 
getArray() - Method in class org.biojava.bio.structure.jama.Matrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class org.biojava.bio.structure.jama.Matrix
Copy the internal two-dimensional array.
getAsList() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getAsList() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getAsList() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getAsList() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getAsList() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getAsList() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns this Sequence store as a List
getAsList() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getAsList() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Delegates to SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
getAsList() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getAsList() - Method in interface org.biojava3.core.sequence.template.Sequence
Returns the Sequence as a List of compounds
getAsList() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getAssignments() - Method in class org.biojava.bio.structure.domain.AssignmentXMLSerializer
 
getAsym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getAsym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getAtcc() - Method in class org.biojava.bio.structure.Compound
 
getAtom(String) - Method in interface org.biojava.bio.structure.Group
Get an atom.
getAtom(int) - Method in interface org.biojava.bio.structure.Group
Get at atom by position.
getAtom(String) - Method in class org.biojava.bio.structure.HetatomImpl
get an atom throws StructureException if atom not found.
getAtom(int) - Method in class org.biojava.bio.structure.HetatomImpl
return an atom by its position in the internal List.
getAtom1() - Method in class org.biojava3.protmod.structure.StructureAtomLinkage
 
getAtom2() - Method in class org.biojava3.protmod.structure.StructureAtomLinkage
 
getAtomA() - Method in class org.biojava.bio.structure.Bond
 
getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
 
getAtomArray(Structure, String[]) - Static method in class org.biojava.bio.structure.StructureTools
Returns an array of the requested Atoms from the Structure object.
getAtomArray(Chain, String[]) - Static method in class org.biojava.bio.structure.StructureTools
Returns an array of the requested Atoms from the Structure object.
getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.bio.structure.StructureTools
Returns an array of the requested Atoms from the Structure object.
getAtomB() - Method in class org.biojava.bio.structure.Bond
 
getAtomByPDBname(String) - Method in interface org.biojava.bio.structure.Group
Get an atom by the full PDB name e.g.
getAtomByPDBname(String) - Method in class org.biojava.bio.structure.HetatomImpl
Get an atom by the full PDB name e.g.
getAtomCAArray(Chain) - Static method in class org.biojava.bio.structure.StructureTools
Returns an Atom array of the CA atoms.
getAtomCAArray(Structure) - Static method in class org.biojava.bio.structure.StructureTools
Returns an Atom array of the CA atoms.
getAtomCaThreshold() - Method in class org.biojava.bio.structure.io.FileParsingParameters
the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
getAtomDistance(Atom, Atom) - Static method in class org.biojava3.protmod.structure.StructureUtil
 
getAtomForAligPos(AFPChain, int, int, Atom[], boolean) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
return the atom at alignment position aligPos.
getAtomGroup(int) - Method in interface org.biojava.bio.structure.Chain
return the Group at position X.
getAtomGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
return the group at position .
getAtomGroups() - Method in interface org.biojava.bio.structure.Chain
Return all groups that have been specified in the ATOM section of this chain .
getAtomGroups(String) - Method in interface org.biojava.bio.structure.Chain
Return a List of all groups of a special type (e.g.
getAtomGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
getAtomGroups() - Method in class org.biojava.bio.structure.ChainImpl
Return all groups that have been specified in the ATOM section of this chain .
getAtomicMass() - Method in enum org.biojava.bio.structure.Element
Returns the atomic mass for this Element.
getAtomicNumber() - Method in enum org.biojava.bio.structure.Element
Returns the atomic number of this Element.
getAtomLength() - Method in interface org.biojava.bio.structure.Chain
Return the number of Groups in the ATOM records of the chain.
getAtomLength() - Method in class org.biojava.bio.structure.ChainImpl
Return the number of Groups in the ATOM records of the chain.
getAtomLigands() - Method in interface org.biojava.bio.structure.Chain
Get all groups that are not polymer groups and that are not solvent groups.
getAtomLigands() - Method in class org.biojava.bio.structure.ChainImpl
Get all groups that are not polymer groups and that are not solvent groups.
getAtomLinkages() - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
getAtomLinkages() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
getAtomName() - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
getAtomName() - Method in class org.biojava3.protmod.structure.StructureAtom
 
getAtomNames(Group) - Static method in class org.biojava3.protmod.structure.StructureUtil
 
getAtoms(String) - Method in class org.biojava.bio.structure.align.util.AtomCache
Returns the CA atoms for the provided name.
getAtoms(String, boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
Deprecated.
does the same as AtomCache.getAtoms(String) ;
getAtoms() - Method in interface org.biojava.bio.structure.Group
Get list of atoms.
getAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
get all atoms of this group .
getAtomSequence() - Method in interface org.biojava.bio.structure.Chain
Return the sequence of amino acids as it has been provided in the ATOM records.
getAtomSequence() - Method in class org.biojava.bio.structure.ChainImpl
Return the sequence of amino acids as it has been provided in the ATOM records.
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Charge
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
 
getAttribute() - Method in class org.biojava3.aaproperties.profeat.convertor.Convertor
Return the attribute of the grouping
getAttribute(String) - Method in class org.biojava3.genome.parsers.gff.Feature
Get value of specified attribute key.
getAttribute(String) - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get the attribute value for this key.
getAttribute(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getAttributeOld(String) - Method in class org.biojava3.genome.parsers.gff.Feature
 
getAttributes() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getAtttributeValue(XmlElement, String) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
 
getAtttributeValue(XmlElement, String) - Static method in class org.forester.io.parsers.tol.TolXmlHandler
 
getAuth_asym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getAuth_atom_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getAuth_comp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getAuth_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getAuth_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getAuth_seq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getAuth_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getAuth_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getAuthority() - Method in class org.forester.phylogeny.data.Taxonomy
 
getAuthorList() - Method in class org.biojava.bio.structure.JournalArticle
Get the list of Authors of the JournalArticle
getAuthors() - Method in class org.biojava.bio.structure.PDBHeader
Returns the names of the authors as listed in the AUTHORS section of a PDB file.
getAutoFetch() - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
getAutoSuggestProvider() - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
getAvailablePhylogeniesWebserviceClient(int) - Method in class org.forester.archaeopteryx.webservices.WebservicesManager
 
getAvailablePhylogeniesWebserviceClients() - Method in class org.forester.archaeopteryx.webservices.WebservicesManager
 
getAvarageNormalizedScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getAvarageRawScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getAvgHydropathy(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the average hydropathy value of sequence.
getAvgHydropathy(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the average hydropathy value of sequence.
getAvgHydropathy(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getB() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getB_iso_max() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getB_iso_mean() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getB_iso_min() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getB_iso_or_equiv() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getB_iso_or_equiv_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getBackboneAtomArray(Structure) - Static method in class org.biojava.bio.structure.StructureTools
Returns an Atom array of the MainChain atoms.
getBackingSequence() - Method in class org.biojava3.core.sequence.views.WindowedSequence
Access the sequence which backs this window
getBadRmsd() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getBase() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
getBegin() - Method in class org.biojava3.genome.parsers.gff.Location
 
getBeta() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getBinaryCharacters() - Method in class org.forester.phylogeny.data.NodeData
 
getBinaryDomainCombinationsSpecificToGenome0() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
getBinaryDomainCombinationsSpecificToGenome1() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
getBioBegin() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getBioEnd() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getBioEnd() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getBioEnd() - Method in interface org.biojava3.core.sequence.template.SequenceView
1-indexed, inclusive.
getBiol_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
Loads the biological assembly for a given PDB ID and bioAssemblyId.
getBiologicalUnit(String) - Method in class org.biojava.bio.structure.align.util.AtomCache
Loads the default biological unit (*.pdb1.gz) file.
getBiologicalUnit() - Method in class org.biojava.bio.structure.Compound
 
getBiologicalUnit(String) - Method in class org.biojava.bio.structure.io.LocalCacheStructureProvider
Returns the first available biological unit for the PDB ID.
getBiologicalUnit(String) - Method in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
 
getBiologicalUnit(String) - Method in interface org.biojava.bio.structure.io.StructureProvider
get the biological unit for a file
getBioStart() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getBioStart() - Method in interface org.biojava3.core.sequence.template.SequenceView
1-indexed, inclusive.
getBJSequence() - Method in interface org.biojava.bio.structure.Chain
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
getBJSequence() - Method in class org.biojava.bio.structure.ChainImpl
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
getBlastAdvancedOptions() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastDatabase() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastExpect() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastFromPosition() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastGapCosts() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the actual string for the GAPCOSTS parameter which is used to build the URL
getBlastGapCreation() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
getBlastGapExtension() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
getBlastMatrix() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value of the specified substitution matrix
getBlastProgram() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastToPosition() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
getBlastWordSize() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Returns the value of the WORD_SIZE parameter used for this blast run
getBlock2Afp() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockGap() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
Deprecated.
use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
get the block number for an aligned position
getBlockNum() - Method in class org.biojava.bio.structure.align.model.AFPChain
The number of blocks in the alignment
getBlockNumClu() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockNumIni() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockNumSpt() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockResList() - Method in class org.biojava.bio.structure.align.model.AFPChain
tracks the residues of the initial blocks (before optimization)
getBlockResSize() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockRmsd() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockRotationMatrix() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockScore() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockShiftVector() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlockSize() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getBlosum100() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 100 matrix by Henikoff & Henikoff
getBlosum30() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 30 matrix by Henikoff & Henikoff
getBlosum35() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 35 matrix by Henikoff & Henikoff
getBlosum40() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 40 matrix by Henikoff & Henikoff
getBlosum45() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 45 matrix by Henikoff & Henikoff
getBlosum50() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 50 matrix by Henikoff & Henikoff
getBlosum55() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 55 matrix by Henikoff & Henikoff
getBlosum60() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 60 matrix by Henikoff & Henikoff
getBlosum62() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 62 matrix by Henikoff & Henikoff
getBLOSUM62() - Static method in class org.biojava3.phylo.ResidueProperties
 
getBLOSUM62(char, char) - Static method in class org.biojava3.phylo.ResidueProperties
 
getBlosum65() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 65 matrix by Henikoff & Henikoff
getBlosum70() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 70 matrix by Henikoff & Henikoff
getBlosum75() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 75 matrix by Henikoff & Henikoff
getBlosum80() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 80 matrix by Henikoff & Henikoff
getBlosum85() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 85 matrix by Henikoff & Henikoff
getBlosum90() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Blosum 90 matrix by Henikoff & Henikoff
getBootstraps() - Method in class org.forester.sdi.RIO
Returns the numbers of trees analyzed.
getBranchColor() - Method in class org.forester.phylogeny.data.BranchData
 
getBranchColorValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method
getBranchData() - Method in class org.forester.phylogeny.PhylogenyNode
 
getBranchesInPreorder(Phylogeny) - Static method in class org.forester.sdi.SDIR
 
getBranchWidth() - Method in class org.forester.phylogeny.data.BranchData
 
getBranchWidthValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method
getBufferedReader() - Method in class org.biojava3.core.sequence.io.util.ClasspathResource
Returns the reader representation of this classpath resource
getByCategory(ScopCategory) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getByCategory(ScopCategory) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getByCategory(ScopCategory) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Get all records of a particular classification.
getByCategory(ScopCategory) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getByCategory(ModificationCategory) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getByComponent(Component, Component...) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
Get ProteinModifications that involves one or more components.
getById(String) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getByKeyword(String) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getByLabel(String) - Static method in enum org.biojava3.protmod.ModificationCategory
 
getByLabel(String) - Static method in enum org.biojava3.protmod.ModificationOccurrenceType
 
getByOccurrenceType(ModificationOccurrenceType) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getByPdbccId(String) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getByPsimodId(String) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getByResidId(String) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
 
getBytesRead() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Keep track of bytesread via ReadLine to account for CR-LF in the stream.
getC() - Method in interface org.biojava.bio.structure.AminoAcid
get C atom.
getC() - Method in class org.biojava.bio.structure.AminoAcidImpl
get C atom.
getC() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getC() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
getCA() - Method in interface org.biojava.bio.structure.AminoAcid
get CA atom.
getCA() - Method in class org.biojava.bio.structure.AminoAcidImpl
get CA atom.
getCA() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
getCa1() - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
getCa1() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
getCa1() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
getCa1Length() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getCa2() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
getCa2() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
getCa2Length() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getCache() - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
getCache() - Static method in class org.biojava.bio.structure.align.util.CacheFactory
 
getCacheLocation() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getCacheSize() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
getCacheSize() - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
getCalculationTime() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getCalculationTime() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getCAOnly(List<Chain>) - Static method in class org.biojava.bio.structure.io.CAConverter
Convert a List of chain objects to another List of chains, containing C-alpha atoms only.
getCAOnly(Chain) - Static method in class org.biojava.bio.structure.io.CAConverter
Convert a Chain to a new Chain containing C-alpha atoms only.
getCartn_x() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getCartn_x_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getCartn_y() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getCartn_y_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getCartn_z() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getCartn_z_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getCategory() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
getCategory() - Method in interface org.biojava3.protmod.ProteinModification
 
getCategory() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getCB() - Method in interface org.biojava.bio.structure.AminoAcid
get CB atom.
getCB() - Method in class org.biojava.bio.structure.AminoAcidImpl
get CB atom.
getCDSSequences() - Method in class org.biojava3.core.sequence.TranscriptSequence
Get the CDS sequences that have been added to the TranscriptSequences
getCECalculator() - Method in class org.biojava.bio.structure.align.ce.CeMain
 
getCell() - Method in class org.biojava.bio.structure.Compound
 
getCellColor() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
getCellColor() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
getCellLine() - Method in class org.biojava.bio.structure.Compound
 
getCellularLocation() - Method in class org.biojava.bio.structure.Compound
 
getCenter(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
getCenter1() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getCenter2() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getCenterVector(Atom[]) - Static method in class org.biojava.bio.structure.Calc
Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
getCenterVector(Atom[], Atom) - Static method in class org.biojava.bio.structure.Calc
Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
getCentroid(Atom[]) - Static method in class org.biojava.bio.structure.Calc
Returns the center of mass of the set of atoms.
getChain() - Method in interface org.biojava.bio.structure.Group
Returns the parent Chain of the Group.
getChain() - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
getChain() - Method in class org.biojava.bio.structure.HetatomImpl
Returns the parent Chain of the Group.
getChain(int) - Method in interface org.biojava.bio.structure.Structure
retrieve a chain by it's position within the Structure .
getChain(int, int) - Method in interface org.biojava.bio.structure.Structure
retrieve a chain by it's position within the Structure and model number.
getChain(int) - Method in class org.biojava.bio.structure.StructureImpl
retrieve a chain by it's position within the Structure.
getChain(int, int) - Method in class org.biojava.bio.structure.StructureImpl
retrieve a chain by it's position within the Structure and model number.
getChain1() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getChain1() - Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
getChain2() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getChainByPDB(String) - Method in interface org.biojava.bio.structure.Structure
request a chain by it's PDB code by default takes only the first model
getChainByPDB(String, int) - Method in interface org.biojava.bio.structure.Structure
request a chain by it's PDB code by default takes only the first model
getChainByPDB(String, int) - Method in class org.biojava.bio.structure.StructureImpl
 
getChainByPDB(String) - Method in class org.biojava.bio.structure.StructureImpl
 
getChainId() - Method in class org.biojava.bio.structure.align.client.StructureName
 
getChainId() - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
getChainID() - Method in interface org.biojava.bio.structure.Chain
get and set the name of this chain (Chain id in PDB file ).
getChainID() - Method in class org.biojava.bio.structure.ChainImpl
get and set the name of this chain (Chain id in PDB file ).
getChainId() - Method in class org.biojava.bio.structure.Compound
Returns the chain id value.
getChainId() - Method in class org.biojava.bio.structure.DBRef
The chain ID of the corresponding chain.
getChainId() - Method in interface org.biojava.bio.structure.Group
Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.bio.structure.HetatomImpl
Utility method for returning the chainId of the Group or null if no Chain has been set.
getChainId() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getChainId() - Method in class org.biojava.bio.structure.ResidueNumber
 
getChainId() - Method in class org.biojava3.protmod.structure.StructureGroup
 
getChainId1() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getChainID1() - Method in class org.biojava.bio.structure.SSBond
 
getChainId2() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getChainID2() - Method in class org.biojava.bio.structure.SSBond
 
getChainInfoFile() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
getChainLen() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getChainRmsd() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getChains() - Method in class org.biojava.bio.structure.Compound
get the chains that are part of this Compound
getChains() - Method in interface org.biojava.bio.structure.Structure
retrieve all chains - if it is a NMR structure will return the chains of the first model.
getChains(int) - Method in interface org.biojava.bio.structure.Structure
retrieve all chains of a model.
getChains(int) - Method in class org.biojava.bio.structure.StructureImpl
retrieve all chains of a model.
getChains() - Method in class org.biojava.bio.structure.StructureImpl
 
getCharacter(int) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getCharacter(int) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getCharacterIndex(String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getCharacterIndex(String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getCharStateLabels() - Method in class org.forester.io.parsers.nexus.NexusCharactersParser
 
getChemComp() - Method in interface org.biojava.bio.structure.Group
Get the chemical component that closer describes this group.
getChemComp() - Method in class org.biojava.bio.structure.HetatomImpl
 
getChemComp(String) - Method in class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
Returns a new instance of a chemical component definition.
getChemComp(String) - Static method in class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
 
getChemComp(String) - Method in interface org.biojava.bio.structure.io.mmcif.ChemCompProvider
Returns a new instance of a chemical component definition.
getChemComp(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
getChemComp(String) - Method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
Loads the definitions for this ChemComp from a local file and instantiates a new object.
getChemComp(String) - Method in class org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider
 
getChemCompProvider() - Static method in class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
 
getChild1() - Method in class org.biojava3.alignment.GuideTree.Node
 
getChild1() - Method in interface org.biojava3.alignment.template.GuideTreeNode
Returns the first child node of this node.
getChild2() - Method in class org.biojava3.alignment.GuideTree.Node
 
getChild2() - Method in interface org.biojava3.alignment.template.GuideTreeNode
Returns the second child node of this node.
getChildAt(int) - Method in class org.biojava3.alignment.GuideTree.Node
 
getChildCount() - Method in class org.biojava3.alignment.GuideTree.Node
 
getChildElement(int) - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getChildNode(int) - Method in class org.forester.phylogeny.PhylogenyNode
This return child node n of this node.
getChildNode(int) - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
getChildNode1() - Method in class org.forester.phylogeny.PhylogenyNode
Convenience method.
getChildNode2() - Method in class org.forester.phylogeny.PhylogenyNode
Convenience method.
getChildNodeIndex() - Method in class org.forester.phylogeny.PhylogenyNode
This gets the child node index of this node.
getChildNodeIndex(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
This gets the child node index of this node, given that parent is its parent
getChildren() - Method in class org.biojava.bio.structure.scop.ScopNode
 
getChildrenFeatures() - Method in class org.biojava3.core.sequence.features.AbstractFeature
Get the children features
getChildrenFeatures() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Get the features contained by this feature
getChromosomeNumber() - Method in class org.biojava3.core.sequence.ChromosomeSequence
 
getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
getClaFilename() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getClassId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getClassification() - Method in class org.biojava.bio.structure.PDBHeader
 
getClassificationId() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
getClassificationId(ScopCategory) - Method in class org.biojava.bio.structure.scop.ScopDescription
Return a portion of the classificationID corresponding to the specified category (class, fold, superfamily, family).
getClassificationId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getCloseMenuItem(JFrame) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getCluster() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
get the number of the cluster this alignment belongs to
getCluster() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getCodingSequence() - Method in class org.biojava3.core.sequence.CDSSequence
A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence.
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
Returns the compound set of codons
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava3.core.sequence.transcription.Table
 
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
Returns a list of codons where the source and target compounds are the same as those given by the parameters.
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava3.core.sequence.transcription.Table
 
getCodons(String) - Static method in class org.biojava3.phylo.ResidueProperties
 
getCol() - Method in class org.biojava.bio.structure.align.helper.IndexPair
 
getColor(double) - Method in interface org.biojava.bio.structure.gui.util.color.ContinuousColorMapper
 
getColor(double) - Method in class org.biojava.bio.structure.gui.util.color.ContinuousColorMapperTransform
Return the color corresponding to submapper.getColor(transform(value)).
getColor(double) - Method in class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
 
getColor(double) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
getColor() - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
getColor() - Method in interface org.biojava3.structure.gui.StructureViewer
 
getCols() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getCols() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getCols() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getColumnDimension() - Method in class org.biojava.bio.structure.jama.Matrix
Get column dimension.
getColumnIdentifiers() - Method in class org.forester.util.GeneralTable
 
getColumnPackedCopy() - Method in class org.biojava.bio.structure.jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getColumnsAsMap(int, int) - Method in class org.forester.util.BasicTable
 
getColumnsAsMapDouble(int, int) - Method in class org.forester.util.BasicTable
 
getCombinableDomainIds(Species) - Method in interface org.forester.surfacing.DomainSimilarity
 
getCombinableDomainIds(Species) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getCombinableDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getCombinableDomains() - Method in interface org.forester.surfacing.CombinableDomains
 
getCombinableDomainsIds() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getCombinableDomainsIds() - Method in interface org.forester.surfacing.CombinableDomains
Returns the combinable domain identifiers sorted in alphabetical manner: - keys are the combinable domain identifiers - values are the counts of proteins exhibiting a particular combination
getCombiningDomainIdsAsStringBuilder() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getCombiningDomainIdsAsStringBuilder() - Method in interface org.forester.surfacing.CombinableDomains
 
getCombiningDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getCommandLineArgsAsString() - Method in class org.forester.util.CommandLineArguments
 
getComment() - Static method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getComment() - Method in class org.forester.go.BasicGoTerm
 
getComment() - Method in interface org.forester.go.GoTerm
 
getCommonName() - Method in class org.forester.phylogeny.data.Taxonomy
 
getCommonValence() - Method in enum org.biojava.bio.structure.Element
Returns the common valence for this Element.
getComp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
getComp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
getComparator(int) - Method in class org.biojava.bio.structure.align.gui.MyTableRowSorter
 
getComplement() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
getComplement() - Method in class org.biojava3.core.sequence.DNASequence
Returns a Sequence which will complement every base
getComplement() - Method in class org.biojava3.core.sequence.RNASequence
Get the complement view of the RNA sequence
getComplement() - Method in interface org.biojava3.core.sequence.template.ComplementCompound
 
getComponent1() - Method in class org.biojava3.protmod.ModificationLinkage
 
getComponent2() - Method in class org.biojava3.protmod.ModificationLinkage
 
getComponents() - Method in interface org.biojava3.protmod.ModificationCondition
 
getComponents() - Method in class org.biojava3.protmod.ModificationConditionImpl
}
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
Returns the composition of the specific grouping for the given attribute.
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getComposition(ProteinSequence) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
An adaptor method which returns the composition of the specific grouping for the given attribute.
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getComposition(ProteinSequence) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getComposition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getComposition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getComposition(String) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getComposition(ProteinSequence) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getComposition(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Does a linear scan over the given Sequence and records the number of times each base appears.
getCompoundAt(int) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getCompoundAt(int, int) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundAt(S, int) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundAt(int, int) - Method in interface org.biojava3.alignment.template.Profile
Returns the Compound at row of given sequence and column of alignment index.
getCompoundAt(S, int) - Method in interface org.biojava3.alignment.template.Profile
Returns the Compound at row of given sequence and column of alignment index.
getCompoundAt(int) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns the compound at the specified biological index
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns the compound at the specified biological index
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Always returns the compound given at construction
getCompoundAt(int) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getCompoundAt(int) - Method in interface org.biojava3.core.sequence.template.Sequence
Returns the Compound at the given biological index
getCompoundAt(int) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.views.ReversedSequenceView
 
getCompoundAt(int) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
getCompoundById(String) - Method in interface org.biojava.bio.structure.Structure
request a particular compound by its id
getCompoundById(String) - Method in class org.biojava.bio.structure.StructureImpl
 
getCompoundCountsAt(int) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundCountsAt(int, List<C>) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundCountsAt(int) - Method in interface org.biojava3.alignment.template.Profile
Returns the number of each Compound in the given column for all compounds in CompoundSet.
getCompoundCountsAt(int, List<C>) - Method in interface org.biojava3.alignment.template.Profile
Returns the number of each Compound in the given column only for compounds in the given list.
getCompoundForString(String) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getCompoundForString(String) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
getCompoundForString(String) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
getCompoundForString(String) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
getCompoundForString(String) - Method in interface org.biojava3.core.sequence.template.CompoundSet
Return null if not recognised.
getCompoundInQueryAt(int) - Method in class org.biojava3.alignment.SimpleSequencePair
 
getCompoundInQueryAt(int) - Method in interface org.biojava3.alignment.template.SequencePair
Returns the Compound in query sequence at given column index in alignment.
getCompoundInTargetAt(int) - Method in class org.biojava3.alignment.SimpleSequencePair
 
getCompoundInTargetAt(int) - Method in interface org.biojava3.alignment.template.SequencePair
Returns the Compound in target sequence at given column index in alignment.
getCompounds() - Method in interface org.biojava.bio.structure.Structure
get all the Compounds that are defined in the PDB Header
getCompounds() - Method in class org.biojava.bio.structure.StructureImpl
 
getCompounds(int) - Method in class org.biojava3.core.sequence.views.WindowedSequence
For a given position into the windowed view this will return those compounds we can see in the window.
getCompoundsAt(int) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundsAt(int) - Method in interface org.biojava3.alignment.template.Profile
Returns the Compound elements of the original Sequences at the given column.
getCompoundsAt(int) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Get a list of compounds at a sequence position
getCompoundsAt(int) - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns the Compound elements of the original Sequences at the given column.
getCompoundSet() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getCompoundSet() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getCompoundSet() - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundSet() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getCompoundSet() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getCompoundSet() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getCompoundSet() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getCompoundSet() - Method in interface org.biojava3.alignment.template.Profile
Returns CompoundSet of all AlignedSequences
getCompoundSet() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns the CompoundSet on which the matrix is defined.
getCompoundSet() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
 
getCompoundSet() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getCompoundSet() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getCompoundSet() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getCompoundSet() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Get the Compounds defined in the first sequence
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns the compound set backing this store
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns the compound set backing this store
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Returns the compound set given at construction
getCompoundSet() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getCompoundSet() - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns CompoundSet of all Sequences
getCompoundSet() - Method in interface org.biojava3.core.sequence.template.Sequence
Gets the compound set used to back this Sequence
getCompoundSet() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getCompoundsOfQuery() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getCompoundsOfQuery() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getCompoundsOfQuery() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getCompoundsOfTarget() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getCompoundsOfTarget() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getCompoundsOfTarget() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getCompoundsToIndexLookup() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns a map which converts from compound to an integer representation
getCompoundWeightsAt(int) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundWeightsAt(int, List<C>) - Method in class org.biojava3.alignment.SimpleProfile
 
getCompoundWeightsAt(int) - Method in interface org.biojava3.alignment.template.Profile
Returns the fraction of each Compound in the given column for all compounds in CompoundSet.
getCompoundWeightsAt(int, List<C>) - Method in interface org.biojava3.alignment.template.Profile
Returns the fraction of each Compound in the given column only for compounds in the given list.
getComputationTime() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getComputationTime() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getComputationTime() - Method in interface org.biojava3.alignment.template.Aligner
Returns the computation time needed for an alignment computed in nanoseconds.
getCondition() - Method in interface org.biojava3.protmod.ProteinModification
 
getCondition() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getConfidence() - Method in class org.forester.phylogeny.data.Annotation
 
getConfidence(int) - Method in class org.forester.phylogeny.data.BranchData
 
getConfidence() - Method in class org.forester.phylogeny.data.Event
 
getConfidence() - Method in class org.forester.phylogeny.data.ProteinDomain
 
getConfidence() - Method in class org.forester.phylogeny.Phylogeny
 
getConfidences() - Method in class org.forester.phylogeny.data.BranchData
 
getConfidenceValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method
getConfidenceValuesAsArray(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method
getConfig() - Method in class org.biojava.bio.structure.align.webstart.ConfigXMLHandler
 
getConn() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getConnectedNode(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch
 
getConnections() - Method in interface org.biojava.bio.structure.Structure
Returns the connections value.
getConnections() - Method in class org.biojava.bio.structure.StructureImpl
Returns the connections value.
getConsituents() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
getContacts() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getContig() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
 
getCoordManager() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
getCoords() - Method in interface org.biojava.bio.structure.Atom
get the coordinates.
getCoords() - Method in class org.biojava.bio.structure.AtomImpl
get the coordinates as a double[3] array .
getCopiedAndPastedNodes() - Method in class org.forester.archaeopteryx.MainPanel
 
getCoreElectronCount() - Method in enum org.biojava.bio.structure.Element
Returns the number of core electrons for this Element.
getCorrelation_coeff_Fo_to_Fc() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getCorrelation_coeff_Fo_to_Fc_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getCost() - Method in class org.forester.phylogenyinference.DolloParsimony
 
getCost() - Method in class org.forester.phylogenyinference.FitchParsimony
 
getCost() - Method in class org.forester.phylogenyinference.SankoffParsimony
 
getCost() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getCount() - Method in class org.biojava3.aaproperties.xml.Name2Count
 
getCount() - Method in class org.forester.sdi.SDIR
Returns the number of differently rooted trees which minimize the (rooting) "criterion" - as determined by method "infer".
getCovalentRadius() - Method in enum org.biojava.bio.structure.Element
Returns the covalent radius of this Element.
getCoverage1() - Method in class org.biojava.bio.structure.align.model.AFPChain
Get the coverage of protein 1 with the alignment
getCoverage2() - Method in class org.biojava.bio.structure.align.model.AFPChain
Get the coverage of protein 2 with the alignment
getCovered() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getCPPoint() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
getCreate_co() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getCreator() - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
getCrystallographicInfo() - Method in interface org.biojava.bio.structure.Structure
Gets crystallographic information for this structure
getCrystallographicInfo() - Method in class org.biojava.bio.structure.StructureImpl
Gets crystallographic information for this structure
getCrystals_number() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getCurrent(String) - Static method in class org.biojava.bio.structure.PDBStatus
Gets the current version of a PDB ID.
getCurrentChain() - Method in class org.biojava.bio.structure.AtomIterator
Get the chain that contains the current atom.
getCurrentChain() - Method in class org.biojava.bio.structure.GroupIterator
Get the current Chain.
getCurrentDateTime() - Static method in class org.forester.util.ForesterUtil
 
getCurrentModel() - Method in class org.biojava.bio.structure.AtomIterator
Get the model number of the model containing the current atom.
getCurrentModel() - Method in class org.biojava.bio.structure.GroupIterator
Get the model number of the current model.
getCurrentUserDesktopPath() - Static method in class org.forester.util.WindowsUtils
 
getCut_sites() - Method in class org.biojava.bio.structure.domain.pdp.CutSites
 
getCuts(int, int[], int[], boolean) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
getCutsPerSection() - Method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Returns the number of cuts added to each section during each pass.
getD() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getData() - Method in class org.biojava.bio.structure.scop.server.TreeSetStringWrapper
 
getData() - Method in interface org.forester.phylogeny.Edge
 
getData() - Method in class org.forester.phylogeny.PhylogenyBranch
 
getDataAsDoubleArray() - Method in class org.forester.util.BasicDescriptiveStatistics
 
getDataAsDoubleArray() - Method in interface org.forester.util.DescriptiveStatistics
 
getDatabase() - Method in class org.biojava.bio.structure.DBRef
The database of the db-ref.
getDatabase() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
 
getDatabaseReferences() - Method in interface org.biojava3.core.sequence.features.DatabaseReferenceInterface
 
getDatabaseReferences() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
The Uniprot mappings to other database identifiers for this sequence
getDatabaseReferences() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getDataSource() - Method in class org.biojava3.core.sequence.AccessionID
 
getDataSource() - Method in class org.biojava3.core.sequence.location.InsdcParser
 
getDataSource() - Method in class org.biojava3.core.sequence.TaxonomyID
 
getDataType() - Method in class org.forester.phylogeny.data.Property
 
getDate() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
getDate() - Method in class org.forester.phylogeny.data.NodeData
 
getDate_original() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
getDb_align_beg() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getDb_align_end() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getDb_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getDb_name() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getDbAccession() - Method in class org.biojava.bio.structure.DBRef
Sequence database accession code.
getDbIdCode() - Method in class org.biojava.bio.structure.DBRef
Sequence database identification code.
getDBRefs() - Method in interface org.biojava.bio.structure.Structure
get the list of database references
getDBRefs() - Method in class org.biojava.bio.structure.StructureImpl
 
getDBResultMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getDBSearch() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
getDbSearchLegend() - Method in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.bio.structure.align.ce.CeUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor
 
getDbSearchLegend() - Method in class org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
getDBSearchParameters() - Static method in class org.biojava.bio.structure.align.StrucAligParameters
 
getDbSearchResult(AFPChain) - Method in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
getDbSeqBegin() - Method in class org.biojava.bio.structure.DBRef
Initial sequence number of the database seqment.
getDbSeqEnd() - Method in class org.biojava.bio.structure.DBRef
Ending sequence position of the database segment.
getDcl() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getDefault() - Static method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
Default instance to use when Transcribing from DNA -> RNA -> Protein.
getDefaultConfig() - Static method in class org.biojava.bio.structure.align.webstart.WebStartMain
 
getDefaultDnaMatrix() - Static method in class org.biojava3.phylo.ResidueProperties
 
getDefaultFrame() - Static method in enum org.biojava3.core.sequence.transcription.Frame
 
getDefaultParameters() - Static method in class org.biojava.bio.structure.align.StrucAligParameters
 
getDefaultPeptideMatrix() - Static method in class org.biojava3.phylo.ResidueProperties
 
getDefaultText() - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
getDefinition() - Method in class org.forester.go.BasicGoTerm
 
getDefinition() - Method in interface org.forester.go.GoTerm
 
getDensityCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getDepDate() - Method in class org.biojava.bio.structure.PDBHeader
 
getDesc() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getDesc() - Method in class org.forester.phylogeny.data.Annotation
 
getDesc() - Method in class org.forester.phylogeny.data.Date
 
getDesc() - Method in class org.forester.phylogeny.data.Distribution
 
getDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
 
getDesciption() - Method in class org.forester.pccx.BranchCountingBasedScoringMethod
 
getDesciption() - Method in class org.forester.pccx.BranchLengthBasedScoringMethod
 
getDesciption() - Method in class org.forester.pccx.LogBranchLengthBasedScoringMethod
 
getDesciption() - Method in interface org.forester.pccx.ScoringMethodForExternalNode
This returns a short description of this scoring method
getDescription() - Method in class org.biojava.bio.structure.PDBHeader
 
getDescription() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
getDescription() - Method in class org.biojava.bio.structure.Site
gets the REMARK 800 description of the site
getDescription() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getDescription() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getDescription() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns the description of this matrix.
getDescription() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getDescription() - Method in class org.biojava3.core.sequence.features.AbstractFeature
 
getDescription() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Get the description that can be used to describe the feature
getDescription() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
getDescription() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getDescription() - Method in interface org.biojava3.core.sequence.template.Compound
 
getDescription() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
getDescription() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getDescription() - Method in interface org.biojava3.protmod.ProteinModification
 
getDescription() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getDescription() - Method in interface org.biojava3.protmod.structure.ModifiedCompound
return a description of this compound
getDescription() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
getDescription() - Method in class org.biojava3.sequencing.io.fastq.Fastq
Return the description of this FASTQ formatted sequence.
getDescription() - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return the description for this FASTQ formatted sequence builder.
getDescription() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return the description of this FASTQ sequence format variant.
getDescription() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getDescription() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
A short description of the webservice (~20 characters).
getDescription() - Method in class org.forester.phylogeny.data.Uri
 
getDescription() - Method in class org.forester.phylogeny.Phylogeny
 
getDescription() - Method in class org.forester.surfacing.BasicProtein
 
getDescription() - Method in class org.forester.surfacing.MappingResults
 
getDescription() - Method in interface org.forester.surfacing.Protein
 
getDescription2() - Method in class org.biojava.bio.structure.align.model.AFPChain
Get a textual description for the protein 2 of the alignment.
getDescriptionNumber() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
 
getDescriptor() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
getDescriptors() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getDesFilename() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getDetails() - Method in class org.biojava.bio.structure.Compound
 
getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getDiagonalAtK(Atom[], int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
 
getDiagonalDistance() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getDiagonalDistance2() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getDictionary() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
getDifferenceInCounts() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
 
getDifferenceInCounts() - Method in class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity
Returns (counts for domain 1) minus (counts for domain 2).
getDifferenceInCounts() - Method in interface org.forester.surfacing.PairwiseDomainSimilarity
This should return the -- not normalized, not absolute -- difference in counts (for example domain counts) for the two domains.
getDisCut() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
Get the distance cutoff used during AFP chain connectivity checks
getDisFilter() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getDisorder(FastaSequence) - Static method in class org.biojava3.ronn.Jronn
Calculates the disordered regions of the sequence.
getDisorder(List<FastaSequence>) - Static method in class org.biojava3.ronn.Jronn
Calculates the disordered regions of the sequence for many sequences in the input.
getDisorder(String) - Static method in class org.biojava3.ronn.Jronn
Calculates the disordered regions of the protein sequence.
getDisorderScores(FastaSequence) - Static method in class org.biojava3.ronn.Jronn
Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.
getDisorderScores(List<FastaSequence>) - Static method in class org.biojava3.ronn.Jronn
Calculates the probability of disorder scores for each residue in the sequence for many sequences in the input.
getDisSmooth() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getDist() - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
getDist1() - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getDist1() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getDist2() - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getDist2() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getDisTable1() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getDisTable2() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getDistance(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
calculate distance between two atoms.
getDistance() - Method in class org.biojava.bio.structure.secstruc.DistEn
 
getDistance() - Method in class org.biojava3.alignment.template.AbstractScorer
 
getDistance(double) - Method in class org.biojava3.alignment.template.AbstractScorer
 
getDistance() - Method in interface org.biojava3.alignment.template.Scorer
Returns score as a distance between 0.0 and 1.0.
getDistance(double) - Method in interface org.biojava3.alignment.template.Scorer
Returns score as a distance between 0.0 and scale.
getDistance() - Method in class org.biojava3.protmod.structure.StructureAtomLinkage
 
getDistance(String) - Method in class org.forester.sdi.RIO
Returns the distance to a sequences/taxa after a distance list file has been read in with readDistanceList(File).
getDistance(String, String) - Method in class org.forester.sdi.RIO
 
getDistanceFast(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
Will calculate the *square* of distances between two atoms.
getDistanceIncrement() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
matrix of all distances between two sets of 3d coords"
getDistanceMatrix() - Method in class org.biojava.bio.structure.align.model.AFPChain
A matrix with ca1length rows and ca2length columns.
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
getDistanceMatrix() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
The distance matrix this alignment is based on
GetDistanceMatrix - Class in org.biojava.bio.structure.domain.pdp
 
GetDistanceMatrix() - Constructor for class org.biojava.bio.structure.domain.pdp.GetDistanceMatrix
 
getDistanceMatrix(Atom[]) - Method in class org.biojava.bio.structure.domain.pdp.GetDistanceMatrix
A set of Calpha atoms that are representing the protein
getDistanceMatrix() - Method in class org.biojava3.alignment.GuideTree
Returns the distance matrix used to construct this guide tree.
getDistanceMatrix() - Method in interface org.biojava3.alignment.template.HierarchicalClusterer
Returns the distance matrix used in clustering.
getDistanceMatrix() - Method in class org.biojava3.phylo.TreeConstructor
 
getDistanceToLCA(String) - Method in class org.forester.sdi.DistanceCalculator
Calculates the distance of the PhylogenyNode with seq name seq_name to the LCA of ext_nodes, which has been set either with constructor DistanceCalculator(Phylogeny,Vector) or method setTreeAndExtNodes(Phylogeny,Vector).
getDistanceToNode(PhylogenyNode, PhylogenyNode) - Method in class org.forester.sdi.DistanceCalculator
Calculates the distance of PhylogenyNode outer to PhylogenyNode inner.
getDistanceToNode(String, PhylogenyNode) - Method in class org.forester.sdi.DistanceCalculator
Calculates the distance of the PhylogenyNode with seq name seq_name to PhylogenyNode inner.
getDistanceToParent() - Method in class org.biojava3.alignment.GuideTree.Node
 
getDistanceToParent() - Method in interface org.biojava3.alignment.template.GuideTreeNode
Returns the difference in height of this node and it's parent node.
getDistanceToParent() - Method in class org.forester.phylogeny.PhylogenyNode
Returns the length of the branch leading to the _parent of this PhylogenyNode (double).
getDistanceToParent() - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
getDistanceToRoot(PhylogenyNode) - Method in class org.forester.sdi.DistanceCalculator
Calculates the distance of PhylogenyNode n to the root of Phylogeny t which has been set either with a constructor, setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector).
getDistanceToRoot(String) - Method in class org.forester.sdi.DistanceCalculator
Calculates the distance of the PhylogenyNode with seq name seq_name to the root of Phylogeny t, which has been set either with a constructor, setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector).
getDistanceUnit() - Method in class org.forester.phylogeny.Phylogeny
 
getDistMat() - Method in class org.biojava.bio.structure.align.StructurePairAligner
return the difference of distance matrix between the two structures
getDistribution(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Analogous to SequenceMixin.getComposition(Sequence) but returns the distribution of that Compound over the given sequence.
getDistribution() - Method in class org.forester.phylogeny.data.NodeData
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getDistributionPosition(ProteinSequence) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(ProteinSequence) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(String) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getDistributionPosition(ProteinSequence) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getDNA() - Static method in class org.biojava3.phylo.ResidueProperties
 
getDNACodingSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence
Get the stitched together CDS sequences then maps to the cDNA
getDNACodingSequences() - Method in class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
 
getDnaCompounds() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getDNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
 
getDNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
 
getDNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.DNACompoundSet
 
getDNAOneLetter(String) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
getDnaRnaTranslator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getDnaToRna() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
getDNATwoLetter(Character) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
getDNAType() - Method in class org.biojava3.core.sequence.DNASequence
 
getDoi() - Method in class org.biojava.bio.structure.JournalArticle
Get the value of DOI field.
getDoi() - Method in class org.forester.phylogeny.data.Reference
 
getDomain(String, AtomCache) - Method in interface org.biojava.bio.structure.domain.PDPProvider
 
getDomain(String, AtomCache) - Method in class org.biojava.bio.structure.domain.RemotePDPProvider
 
getDomain(int) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getDomain(int) - Method in class org.forester.phylogeny.data.DomainArchitecture
 
getDomainArchitecture() - Method in class org.forester.phylogeny.data.Sequence
 
getDomainByScopID(String) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getDomainByScopID(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getDomainByScopID(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
getDomainByScopID(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getDomainCombinationType() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getDomainCombinationType() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
getDomainCounts(List<Protein>) - Static method in class org.forester.surfacing.SurfacingUtil
 
getDomainDistanceScoresMeans() - Method in class org.forester.surfacing.PairwiseGenomeComparator
 
getDomainId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getDomainId() - Method in class org.forester.surfacing.BasicDomain
 
getDomainId() - Method in interface org.forester.surfacing.Domain
 
getDomainId() - Method in class org.forester.surfacing.DomainLengths
 
getDomainId() - Method in interface org.forester.surfacing.DomainSimilarity
 
getDomainId() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getDomainId() - Method in class org.forester.surfacing.SimpleDomain
 
getDomainLengths(DomainId) - Method in class org.forester.surfacing.DomainLengthsTable
 
getDomainLengthsList() - Method in class org.forester.surfacing.DomainLengthsTable
 
getDomainNames(String) - Method in interface org.biojava.bio.structure.domain.DomainProvider
 
getDomainNames(String) - Method in class org.biojava.bio.structure.domain.RemoteDomainProvider
 
getDomainProvider() - Static method in class org.biojava.bio.structure.domain.DomainProviderFactory
 
getDomainRangesFromXML(String) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getDomainRangesXML(SortedSet<String>) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getDomains() - Method in class org.biojava.bio.structure.domain.pdp.CutDomain
 
getDomains() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getDomains() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getDomains() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
getDomainsEncountered() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsEncountered() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsForPDB(String) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getDomainsForPDB(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getDomainsForPDB(String) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Get a list of ScopDomains that have been assigned to a PDB ID
getDomainsForPDB(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getDomainsFromXML(String) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getDomainsIgnoredDueToDuf() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToDuf() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToEval() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToEval() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToIndividualScoreCutoff() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToIndividualScoreCutoff() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToNegativeDomainFilter() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToNegativeDomainFilter() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToNegativeDomainFilterCountsMap() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToNegativeDomainFilterCountsMap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToOverlap() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToOverlap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToVirusLikeIdCountsMap() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToVirusLikeIdCountsMap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsIgnoredDueToVirusLikeIds() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsIgnoredDueToVirusLikeIds() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsSpecificToGenome0() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
getDomainsSpecificToGenome1() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
getDomainsStored() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsStored() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsStoredSet() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getDomainsStoredSet() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getDomainsXML(SortedSet<Domain>) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getDoublePivot() - Method in class org.biojava.bio.structure.jama.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getDssp3state(String) - Static method in class org.biojava3.phylo.ResidueProperties
translate from other dssp secondary structure alphabets to 3-state
getDuplicationsSum() - Method in class org.forester.sdi.SDI
Returns the number of duplications.
getDVar() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getEcNums() - Method in class org.biojava.bio.structure.Compound
 
getEditorList() - Method in class org.biojava.bio.structure.JournalArticle
Get the list of editors of the JournalArticle
getElement() - Method in interface org.biojava.bio.structure.Atom
get element of the atom, e.g.
getElement() - Method in class org.biojava.bio.structure.AtomImpl
 
getElement() - Method in class org.biojava3.aaproperties.xml.ElementTable
 
getElement(String) - Method in class org.biojava3.aaproperties.xml.ElementTable
 
getElementFromHillIndex(int) - Static method in enum org.biojava.bio.structure.Element
Returns the Element that corresponds to the specified Hill Order.
getElementList() - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
getElementType() - Method in enum org.biojava.bio.structure.Element
Returns the Element Type for this Element.
getEmail() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Get the email for QBlast.
getEmptyChemComp() - Method in class org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider
 
getEmptySequence(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
Returns an empty sequence with the given compound set of the editing sequence
getEnd() - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
getEnd() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getEnd() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the Point within an alignment of the last element of the original Sequence.
getEnd() - Method in interface org.biojava3.alignment.template.ProfileView
Returns the column index of the viewed Profile corresponding to the final element in this view
getEnd() - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
getEnd(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Substitute
Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.
getEnd() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getEnd() - Method in interface org.biojava3.core.sequence.location.template.Location
End of the location
getEnd() - Method in class org.biojava3.genome.parsers.gff.Location
 
getEndLegendPosition(int, int) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
 
getEnergy() - Method in class org.biojava.bio.structure.secstruc.DistEn
 
getEnergy() - Method in class org.biojava.bio.structure.secstruc.HBond
 
getEngineered() - Method in class org.biojava.bio.structure.Compound
 
getEnrichment(ProteinSequence, AminoAcidCompound) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the composition of specified amino acid in the sequence.
getEnrichment(String, PeptideProperties.SingleLetterAACode) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(String, char) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(String, String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the composition of specified amino acid in the sequence.
getEnrichment(ProteinSequence, AminoAcidCompound) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getEntities() - Method in class org.biojava.bio.structure.io.sifts.SiftsXMLParser
 
getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getEntityId() - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
getEqr() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
returns the number of euqivalent residues in this alignment
getEQRAlignmentPos(AFPChain) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
 
getEquivalent() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
getEquivalentCompounds(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
getEquivalentCompounds(C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
getError() - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
getErrorCount() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
getErrorCount() - Method in class org.forester.io.parsers.tol.TolParser
 
getErrorMessages() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
getErrorMessages() - Method in class org.forester.io.parsers.tol.TolParser
 
getEvalCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getEvalue() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getEvCode() - Method in class org.biojava.bio.structure.Site
gets the REMARK 800 EVIDENCE CODE for the site.
getEvent() - Method in class org.forester.phylogeny.data.NodeData
 
getEventType() - Method in class org.forester.phylogeny.data.Event
 
getEvidence() - Method in class org.forester.phylogeny.data.Annotation
 
getExitMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getExonSequences() - Method in class org.biojava3.core.sequence.GeneSequence
Get the exons as an ArrayList
getExpectedExecutionTime() - Method in class org.biojava3.ws.alignment.qblast.BlastJob
 
getExportPDBMenuItem(StructureAlignmentJmol) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getExpressionSystem() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemAtccNumber() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemCell() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemCellLine() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemCellularLocation() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemGene() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemOrgan() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemOrganelle() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemOtherDetails() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemPlasmid() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemStrain() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemTaxId() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemTissue() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemVariant() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemVector() - Method in class org.biojava.bio.structure.Compound
 
getExpressionSystemVectorType() - Method in class org.biojava.bio.structure.Compound
 
getExtensionPenalty() - Method in class org.biojava3.alignment.SimpleGapPenalty
 
getExtensionPenalty() - Method in interface org.biojava3.alignment.template.GapPenalty
Returns penalty given when an already open gap elongates by a single element
getExternalDescendantsTaxonomy(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Returns taxonomy t if all external descendants have the same taxonomy t, null otherwise.
getExternalNodes() - Method in class org.forester.phylogeny.Phylogeny
Warning.
getExtinctionCoefficient(ProteinSequence, boolean) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the extinction coefficient of sequence.
getExtinctionCoefficient(String, boolean) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the extinction coefficient of sequence.
getExtinctionCoefficient(ProteinSequence, boolean) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getExtNodesOfAnalyzedGeneTrees() - Method in class org.forester.sdi.RIO
Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).
getFamilyId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getFarmJob() - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
getFarthestNode1() - Method in class org.forester.phylogeny.PhylogenyMethods
 
getFarthestNode2() - Method in class org.forester.phylogeny.PhylogenyMethods
 
getFatCatAligner() - Method in class org.biojava.bio.structure.align.fatcat.FatCat
 
getFeatures(String, int) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Return features at a sequence position by type
getFeatures(int) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Return features at a sequence position
getFeatures() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getFeaturesByType(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getFeaturesKeyWord() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getFile(int) - Method in class org.forester.util.CommandLineArguments
 
getFile1() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getFile2() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getFileExtension(File) - Static method in class org.biojava.bio.structure.io.util.FileDownloadUtils
 
getFileFormat() - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
getFileFormatSelect() - Static method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.LocalCacheStructureProvider
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
getFileParsingParameters() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.PDBFileParser
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.PDBFileReader
 
getFileParsingParameters() - Method in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
 
getFileParsingParameters() - Method in interface org.biojava.bio.structure.io.StructureIOFile
Get the parameters that should be used for file parsing
getFileParsingParameters() - Method in interface org.biojava.bio.structure.io.StructureProvider
Get the parameters that should be used for file parsing
getFileParsingParams() - Method in class org.biojava.bio.structure.align.util.AtomCache
 
getFilePath() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
getFilePath1() - Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
getFilePrefix(File) - Static method in class org.biojava.bio.structure.io.util.FileDownloadUtils
 
getFileSeparator() - Static method in class org.forester.util.ForesterUtil
 
getFirstChildNode() - Method in class org.forester.phylogeny.PhylogenyNode
Convenience method.
getFirstExternalNode() - Method in class org.forester.phylogeny.Phylogeny
Returns the first external PhylogenyNode.
getFirstLine(Object) - Static method in class org.forester.util.ForesterUtil
 
getFirstNode() - Method in interface org.forester.phylogeny.Edge
 
getFirstNode() - Method in class org.forester.phylogeny.PhylogenyBranch
 
getFivePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
Should return the 5-prime end of the given Sequence according to the edit.
getFivePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Delete
 
getFivePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Insert
 
getFivePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Substitute
 
getFocusAfpList() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getFocusAfpn() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getFocusRes1() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getFocusRes2() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getFocusResn() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getFoldId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getFont() - Method in class org.forester.archaeopteryx.FontChooser
 
getFontName() - Method in class org.forester.archaeopteryx.FontChooser
 
getFontSize() - Method in class org.forester.archaeopteryx.FontChooser
 
getFontStyle() - Method in class org.forester.archaeopteryx.FontChooser
 
getFormatedSequence(int) - Method in class org.biojava3.data.sequence.FastaSequence
Format sequence per width letter in one string.
getFormattedFasta() - Method in class org.biojava3.data.sequence.FastaSequence
 
getFormula() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getFormula() - Method in interface org.biojava3.protmod.ProteinModification
 
getFormula() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getFormula_weight() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getFormula_weight() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getForwardFrames() - Static method in enum org.biojava3.core.sequence.transcription.Frame
Returns all frames in the forward orientation
getFragCompat() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getFragLen() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getFragLen() - Method in class org.biojava.bio.structure.align.model.AFP
 
getFragLenSq() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getFragment(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
get a continue subset of Atoms based by the starting position and the length
getFragment() - Method in class org.biojava.bio.structure.Compound
 
getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
get a subset of Atoms based by their positions
getFragmentLength() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getFragmentMiniDistance() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
getFragmentPairs() - Method in class org.biojava.bio.structure.align.StructurePairAligner
get the results of step 1 - the FragmentPairs used for seeding the alignment
getFragmentPairs() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
getFragmentPairs() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
getFragScore() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getFrame() - Method in class org.biojava.bio.structure.gui.BiojavaJmol
 
getFrom() - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
getFrom() - Method in class org.forester.phylogeny.data.ProteinDomain
 
getFrom() - Method in class org.forester.surfacing.BasicDomain
 
getFrom() - Method in interface org.forester.surfacing.Domain
 
getFrom() - Method in class org.forester.surfacing.SimpleDomain
 
getFromCompoundSet() - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
getFromFtp() - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
getFullAtomSequence(List<Group>, Map<Integer, Integer>) - Static method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
getFullName() - Method in interface org.biojava.bio.structure.Atom
get full name of atom e.g.
getFullName() - Method in class org.biojava.bio.structure.AtomImpl
get full name of atom e.g.
getFurthestDescendant(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
getGainedCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getGainedCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getGainedCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getGainedCount() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getGainLossCountsMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getGainLossMatrix() - Method in class org.forester.phylogenyinference.DolloParsimony
 
getGainLossMatrix() - Method in class org.forester.phylogenyinference.FitchParsimony
 
getGainLossMatrix() - Method in class org.forester.phylogenyinference.SankoffParsimony
 
getGainLossMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getGamma() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getGapCreate() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getGapExtCol() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getGapExtCol() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getGapExtend() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getGapExtend() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
getGapExtension() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getGapExtension() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getGapExtRow() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getGapExtRow() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getGapLen() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getGapOpen() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getGapOpen() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
getGapOpen() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getGapOpenCol() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getGapOpenCol() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getGapOpenRow() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getGapOpenRow() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getGapPenalty() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Returns the gap penalties.
getGaps() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
return the number of gaps in this alignment
getGapScore() - Method in class org.forester.development.SimpleMutableMsa
 
getGC() - Method in class org.biojava3.core.sequence.RNASequence
 
getGCCount() - Method in class org.biojava3.core.sequence.DNASequence
Get the GC count in the DNA Sequence
getGCGChecksum(List<S>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Calculates GCG checksum for entire list of sequences
getGCGChecksum(S) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Calculates GCG checksum for a given sequence
getGCGHeader(List<S>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Assembles a GCG file header
getGCGType(CompoundSet<C>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Determines GCG type
getGCStats(Collection<DNASequence>) - Static method in class org.biojava3.genome.parsers.gff.GCStats
 
getGCStatsString(Collection<String>) - Static method in class org.biojava3.genome.parsers.gff.GCStats
 
getGene() - Method in class org.biojava.bio.structure.Compound
 
getGene(String) - Method in class org.biojava3.core.sequence.ChromosomeSequence
Get the gene based on accession.
getGeneName() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
Get the gene name associated with this sequence.
getGeneName() - Method in interface org.forester.development.Sequence
 
getGeneSequences() - Method in class org.biojava3.core.sequence.ChromosomeSequence
Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
getGeneTree() - Method in class org.forester.sdi.SDI
Returns the gene tree.
getGeodeticDatum() - Method in class org.forester.phylogeny.data.Distribution
 
getGeodeticDatum() - Method in class org.forester.phylogeny.data.Point
 
getGoId() - Method in class org.forester.go.BasicGoRelationship
 
getGoId() - Method in class org.forester.go.BasicGoTerm
 
getGoId() - Method in class org.forester.go.etc.OntologizerResult
 
getGoId() - Method in interface org.forester.go.GoRelationship
 
getGoId() - Method in interface org.forester.go.GoTerm
 
getGoId(int) - Method in class org.forester.surfacing.BasicDomain
 
getGoId(int) - Method in interface org.forester.surfacing.Domain
 
getGoId(int) - Method in class org.forester.surfacing.DomainId
 
getGoId(int) - Method in class org.forester.surfacing.SimpleDomain
 
getGoNameSpace() - Method in class org.forester.go.BasicGoTerm
 
getGoNameSpace() - Method in interface org.forester.go.GoTerm
 
getGoNamespaceLimit() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getGonnet250() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns PAM 250 matrix by Gonnet, Cohen & Benner
getGoRelationships() - Method in class org.forester.go.BasicGoTerm
 
getGoRelationships() - Method in interface org.forester.go.GoTerm
 
getGoSubsets() - Method in class org.forester.go.BasicGoTerm
 
getGoSubsets() - Method in interface org.forester.go.GoTerm
 
getGoTermCount() - Method in class org.forester.go.OBOparser
 
getGoXRefs() - Method in class org.forester.go.BasicGoTerm
 
getGoXRefs() - Method in interface org.forester.go.GoTerm
 
getGradientMapper(int, double, double) - Static method in class org.biojava.bio.structure.gui.util.color.GradientMapper
Constructs a gradientMapper to draw one of the pre-defined gradients For example, GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
getGroup() - Method in interface org.biojava.bio.structure.Atom
Returns the parent Group of the Atom.
getGroup() - Method in class org.biojava.bio.structure.AtomImpl
 
getGroup(int) - Method in interface org.biojava.bio.structure.Chain
Deprecated.
use getAtomGroup or getSeqResGroup instead
getGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
Deprecated.
use getAtomGroup or getSeqResGroup instead
getGroup() - Method in class org.biojava3.protmod.structure.StructureAtom
 
getGroup_PDB() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getGroupA() - Method in class org.biojava.bio.structure.Bond
 
getGroupB() - Method in class org.biojava.bio.structure.Bond
 
getGroupByPDB(String) - Method in interface org.biojava.bio.structure.Chain
Deprecated.
replaced by Chain.getGroupByPDB(ResidueNumber)
getGroupByPDB(ResidueNumber) - Method in interface org.biojava.bio.structure.Chain
Get a group by its PDB residue numbering.
getGroupByPDB(String) - Method in class org.biojava.bio.structure.ChainImpl
get a group by its PDB residue numbering.
getGroupByPDB(ResidueNumber) - Method in class org.biojava.bio.structure.ChainImpl
Get a group by its PDB residue numbering.
getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.bio.structure.StructureTools
Get a group represented by a ResidueNumber.
getGroupFromChemCompDictionary(String) - Static method in class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Charge
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
 
getGrouping() - Method in class org.biojava3.aaproperties.profeat.convertor.Convertor
Returns the groupings of the attribute
getGroups(String) - Method in interface org.biojava.bio.structure.Chain
Deprecated.
use getAtomGroups or getSeqResGroups instead
getGroups() - Method in interface org.biojava.bio.structure.Chain
Deprecated.
use getAtomGroups or getSeqResGroups instead
getGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
Deprecated.
use getAtomGroups instead
getGroups() - Method in class org.biojava.bio.structure.ChainImpl
Deprecated.
use getAtomGroups instead
getGroups() - Method in class org.biojava.bio.structure.Site
 
getGroups() - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
getGroups(boolean) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
getGroups() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
getGroups(boolean) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
getGroupsByPDB(String, String) - Method in interface org.biojava.bio.structure.Chain
Deprecated.
replaced by Chain.getGroupsByPDB(ResidueNumber, ResidueNumber)
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.bio.structure.Chain
Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(String, String, boolean) - Method in interface org.biojava.bio.structure.Chain
Deprecated.
replaced by #Chain.getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.bio.structure.Chain
Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(String, String, boolean) - Method in class org.biojava.bio.structure.ChainImpl
Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.bio.structure.ChainImpl
 
getGroupsByPDB(String, String) - Method in class org.biojava.bio.structure.ChainImpl
Get all groups that are located between two PDB residue numbers.
getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.bio.structure.ChainImpl
Get all groups that are located between two PDB residue numbers.
getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.bio.structure.StructureTools
 
getH() - Method in class org.biojava.bio.structure.jama.QRDecomposition
Return the Householder vectors
getH() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
getHeader() - Method in interface org.biojava.bio.structure.Chain
Returns the Header ( a Compound object) for this chain.
getHeader() - Method in class org.biojava.bio.structure.ChainImpl
Returns the Header ( a Compound object) for this chain.
getHeader() - Method in interface org.biojava.bio.structure.Structure
Deprecated.
use getPDBHeader instead
getHeader() - Method in class org.biojava.bio.structure.StructureImpl
get Header data.
getHeader(S) - Method in class org.biojava3.core.sequence.io.GenericFastaHeaderFormat
 
getHeader(S) - Method in interface org.biojava3.core.sequence.io.template.FastaHeaderFormatInterface
 
getHeaderVars() - Method in class org.biojava.bio.structure.Compound
 
getHeight() - Method in class org.forester.phylogeny.Phylogeny
This calculates the height for rooted, tree-shaped phylogenies.
getHelpMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getHetero() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
getHetero() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getHetGroups() - Method in interface org.biojava.bio.structure.Structure
 
getHetGroups() - Method in class org.biojava.bio.structure.StructureImpl
 
getHieFilename() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getHillOrder() - Method in enum org.biojava.bio.structure.Element
Returns the Hill Order of this Element.
getHitsQueryDef(double) - Method in class org.biojava3.genome.query.BlastXMLQuery
 
getHmmAcc() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getHmmDesc() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getHmmFrom() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getHmmName() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getHmmTo() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getHSVColorSpace() - Static method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
getHyd() - Static method in class org.biojava3.phylo.ResidueProperties
 
getHydmax() - Static method in class org.biojava3.phylo.ResidueProperties
 
getHydmin() - Static method in class org.biojava3.phylo.ResidueProperties
 
getIclose() - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
getId() - Method in class org.biojava.bio.structure.align.model.AFP
 
getId() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getId() - Method in class org.biojava.bio.structure.AtomImpl
Get the Hibernate database ID.
getId() - Method in interface org.biojava.bio.structure.Chain
Get the ID used by Hibernate.
getId() - Method in class org.biojava.bio.structure.ChainImpl
Get the ID used by Hibernate.
getId() - Method in class org.biojava.bio.structure.Compound
get the ID used by Hibernate
getId() - Method in class org.biojava.bio.structure.DBRef
Get the ID used by Hibernate.
getId() - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
getId() - Method in class org.biojava.bio.structure.HetatomImpl
the Hibernate database ID
getId() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getId() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getId() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
 
getId() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getId() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
getId() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getId() - Method in class org.biojava.bio.structure.PDBHeader
Get the ID used by Hibernate.
getId() - Method in interface org.biojava.bio.structure.Structure
get the ID used by Hibernate
getId() - Method in class org.biojava.bio.structure.StructureImpl
get the ID used by Hibernate
getID() - Method in class org.biojava3.core.sequence.AccessionID
 
getId() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
 
getId() - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
 
getID() - Method in class org.biojava3.core.sequence.TaxonomyID
 
getId() - Method in class org.biojava3.data.sequence.FastaSequence
Gets the value of id
getId() - Method in interface org.biojava3.protmod.ProteinModification
 
getId() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getId() - Method in class org.biojava3.ws.alignment.qblast.BlastJob
Request id (RID) as received from QBlast server
getId() - Method in class org.forester.go.GoId
 
getId() - Method in class org.forester.phylogeny.data.ProteinDomain
 
getId() - Method in class org.forester.phylogenyinference.DiscreteState
 
getId() - Method in class org.forester.surfacing.DomainId
 
getId() - Method in class org.forester.surfacing.ProteinId
 
getId0() - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
getId0() - Method in interface org.forester.surfacing.BinaryDomainCombination
 
getId1() - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
getId1() - Method in interface org.forester.surfacing.BinaryDomainCombination
 
getIdbnsBegin() - Method in class org.biojava.bio.structure.DBRef
Insertion code of initial residue of the segment, if PDB is the reference.
getIdbnsEnd() - Method in class org.biojava.bio.structure.DBRef
Insertion code of the ending residue of the segment, if PDB is the reference.
getIdCode() - Method in class org.biojava.bio.structure.DBRef
get the idCode for this entry
getIdCode() - Method in class org.biojava.bio.structure.PDBHeader
The PDB code for this protein structure.
getIdentifiedModifiedCompound() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
getIdentifier() - Method in class org.forester.phylogeny.data.Taxonomy
 
getIdentifier() - Method in class org.forester.phylogeny.Phylogeny
 
getIdentifier(int) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getIdentifier(int) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
getIdentifier(int) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getIdentifier(int) - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
getIdentifierIndex(String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getIdentifierIndex(String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getIdentity() - Method in class org.biojava.bio.structure.align.model.AFPChain
The percent of residues that are sequence-identical in the alignment.
getIDFormat(List<S>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Creates format String for accession IDs
getIdRef() - Method in class org.forester.phylogeny.data.Property
 
getIdx1() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
the positions of the structure equivalent positions in atom set 1
getIdx1() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
get the identical position in the alignment
getIdx2() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
the positions of the structure equivalent atoms in atom set 2
getIdx2() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
get the identical position in the alignment
getIdxlist() - Method in class org.biojava.bio.structure.align.helper.JointFragments
 
getImagEigenvalues() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getIndex() - Method in class org.biojava.bio.structure.align.helper.GapArray
 
getIndex(TreeNode) - Method in class org.biojava3.alignment.GuideTree.Node
 
getIndex(String) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
getIndex(String) - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
getIndexInQueryAt(int) - Method in class org.biojava3.alignment.SimpleSequencePair
 
getIndexInQueryAt(int) - Method in interface org.biojava3.alignment.template.SequencePair
Returns the query index corresponding to a given alignment column.
getIndexInQueryForTargetAt(int) - Method in class org.biojava3.alignment.SimpleSequencePair
 
getIndexInQueryForTargetAt(int) - Method in interface org.biojava3.alignment.template.SequencePair
Returns the query index corresponding to a given target index.
getIndexInTargetAt(int) - Method in class org.biojava3.alignment.SimpleSequencePair
 
getIndexInTargetAt(int) - Method in interface org.biojava3.alignment.template.SequencePair
Returns the target index corresponding to a given alignment column.
getIndexInTargetForQueryAt(int) - Method in class org.biojava3.alignment.SimpleSequencePair
 
getIndexInTargetForQueryAt(int) - Method in interface org.biojava3.alignment.template.SequencePair
Returns the target index corresponding to a given query index.
getIndexOf(C) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getIndexOf(C) - Method in class org.biojava3.alignment.SimpleProfile
 
getIndexOf(C) - Method in interface org.biojava3.alignment.template.Profile
Searches for the given Compound within this alignment profile.
getIndexOf(C) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getIndexOf(C) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getIndexOf(C) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns the first occurrence of the given compound in this store; performs a linear search
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Returns 1 if the given compound is equal to the one given during construction; otherwise will return -1.
getIndexOf(C) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getIndexOf(C) - Method in interface org.biojava3.core.sequence.template.Sequence
Scans through the Sequence looking for the first occurrence of the given compound
getIndexOf(C) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getIndexOf(C) - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
 
getIndexOf(NucleotideCompound) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
getIndexOfComponent1() - Method in class org.biojava3.protmod.ModificationLinkage
 
getIndexOfComponent2() - Method in class org.biojava3.protmod.ModificationLinkage
 
getIndexToCompoundsLookup() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Returns a list of compounds the index position of which is used to translate from the byte representation into a compound.
getIndicator() - Method in class org.forester.phylogeny.PhylogenyNode
Returns the _indicator value of this PhylogenyNode.
getIndicesAt(int) - Method in class org.biojava3.alignment.SimpleProfile
 
getIndicesAt(int) - Method in interface org.biojava3.alignment.template.Profile
Returns the indices in the original Sequences corresponding to the given column.
getIndividualCutoffAppliesTo() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getInferredOrthologs(String) - Method in class org.forester.sdi.RIO
Returns a HashMap containing the inferred orthologs of the external gene tree node with the sequence name seq_name.
getInferredSuperOrthologs(String) - Method in class org.forester.sdi.RIO
Returns a HashMap containing the inferred "super orthologs" of the external gene tree node with the sequence name seq_name.
getInferredUltraParalogs(String) - Method in class org.forester.sdi.RIO
Returns a HashMap containing the inferred "ultra paralogs" of the external gene tree node with the sequence name seq_name.
getInitialK() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getInitials() - Method in class org.biojava.bio.structure.Author
 
getInputStream(URL, int) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
connect to DAS server and return result as an InputStream.
getInputStream(URL) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
connect to DAS server and return result as an InputStream.
getInputStream(URL, boolean, int) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
open a URL and return an InputStream to it if acceptGzipEncoding == true, use GZIPEncoding to compress communication
getInputStream() - Method in class org.biojava3.core.sequence.io.util.ClasspathResource
Returns the InputStream instance of this classpath resource
getInputStream(String) - Static method in class org.biojava3.core.util.FlatFileCache
 
getInputStream(String) - Method in class org.biojava3.core.util.InputStreamProvider
get an InputStream for this file
getInputStream(URL) - Method in class org.biojava3.core.util.InputStreamProvider
 
getInputStream(File) - Method in class org.biojava3.core.util.InputStreamProvider
get an InputStream for the file
getInputStreamToAAindexFile() - Method in class org.biojava3.alignment.aaindex.DefaultAAIndexProvider
 
getInsCode() - Method in class org.biojava.bio.structure.ResidueNumber
 
getInsCode() - Method in class org.biojava3.protmod.structure.StructureGroup
 
getInsCode1() - Method in class org.biojava.bio.structure.SSBond
 
getInsCode2() - Method in class org.biojava.bio.structure.SSBond
 
getInsertBegin() - Method in class org.biojava.bio.structure.DBRef
Initial insertion code of the PDB sequence segment.
getInsertEnd() - Method in class org.biojava.bio.structure.DBRef
Ending insertion code of the PDB sequence segment.
getInstabilityIndex(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the instability index of sequence.
getInstabilityIndex(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the instability index of sequence.
getInstabilityIndex(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getInstance() - Static method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
getInstance(int) - Static method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
getInstance() - Static method in class org.biojava.bio.structure.gui.util.ScopInstallationInstance
 
getInstance() - Static method in class org.biojava3.core.sequence.io.IUPACParser
 
getInstance() - Static method in class org.biojava3.core.util.FlatFileCache
 
getInstance() - Static method in class org.forester.archaeopteryx.webservices.WebservicesManager
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.AccessionParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.AnnotationParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.BinaryCharactersParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.BranchWidthParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.ColorParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.ConfidenceParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.DateParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.DistributionParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.DomainArchitectureParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.EventParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.IdentifierParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.PointParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.PropertyParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.ProteinDomainParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.ReferenceParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.SequenceParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.SequenceRelationParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.TaxonomyParser
 
getInstance() - Static method in class org.forester.io.parsers.phyloxml.phylogenydata.UriParser
 
getInstance(CoverageCalculationMethod, CoverageCalculationOptions) - Static method in class org.forester.pccx.CoverageCalculator
 
getInstance() - Static method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory
 
getInstance() - Static method in class org.forester.phylogeny.PhylogenyMethods
 
getInstanceNoVisibilityChange() - Static method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
getInstructions() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getInstructions() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
Instructions (and examples) on how to use the webservice.
getIntermediate(Color, Color, int, int) - Static method in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
getInternalStatesMatrix() - Method in class org.forester.phylogenyinference.DolloParsimony
 
getInternalStatesMatrix() - Method in class org.forester.phylogenyinference.FitchParsimony
 
getInternalStatesMatrix() - Method in class org.forester.phylogenyinference.SankoffParsimony
 
getInternalStatesMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getInternalStatesMatrixPriorToTraceback() - Method in class org.forester.phylogenyinference.FitchParsimony
Returns a view of the internal states prior to trace-back.
getInternalStatesMatrixPriorToTraceback() - Method in class org.forester.phylogenyinference.SankoffParsimony
Returns a view of the internal states prior to trace-back.
getInterpolator() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
getIntronSequences() - Method in class org.biojava3.core.sequence.GeneSequence
Get the introns as an ArrayList
getInverse() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getInverse() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getInverse() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getInverse() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getInverse() - Method in class org.biojava3.core.sequence.RNASequence
Get the inverse view of the sequence.
getInverse() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getInverse() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
 
getInverse() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getInverse() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
 
getInverse() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getInverse() - Method in interface org.biojava3.core.sequence.template.Sequence
Does the right thing to get the inverse of the current Sequence.
getInverse() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getIoTime() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getIoTime() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getIsoelectricPoint(ProteinSequence, boolean) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the isoelectric point of sequence.
getIsoelectricPoint(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
 
getIsoelectricPoint(String, boolean) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the isoelectric point of sequence.
getIsoelectricPoint(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
 
getIsoelectricPoint(ProteinSequence, boolean) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getIsoelectricPoint(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getIsotope(String) - Method in class org.biojava3.aaproperties.xml.ElementTable
 
getIsotopeList() - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
getIsotopes() - Method in class org.biojava3.aaproperties.xml.Element
 
getIterations() - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
getJclose() - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
getJmolPanel() - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
getJmolScript4Block(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
getJmolString(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
getJoinRMSCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getJournalArticle() - Method in interface org.biojava.bio.structure.Structure
get the associated publication as defined by the JRNL records in a PDB file.
getJournalArticle() - Method in class org.biojava.bio.structure.StructureImpl
get the associated publication as defined by the JRNL records in a PDB file.
getJournalName() - Method in class org.biojava.bio.structure.JournalArticle
 
getKey() - Method in interface org.forester.go.Mapping
 
getKey() - Method in class org.forester.go.PfamToGoMapping
 
getKeyDomain() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getKeyDomain() - Method in interface org.forester.surfacing.CombinableDomains
Returns the domain whose combinable domains are in stored in this combinable domains.
getKeyDomainConfidenceDescriptiveStatistics() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getKeyDomainConfidenceDescriptiveStatistics() - Method in interface org.forester.surfacing.CombinableDomains
Gets descriptive statistics for the confidence (i.e.
getKeyDomainCount() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getKeyDomainCount() - Method in interface org.forester.surfacing.CombinableDomains
Returns how many times the key domain is present in a given species genome.
getKeyDomainProteinsCount() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getKeyDomainProteinsCount() - Method in interface org.forester.surfacing.CombinableDomains
Returns how many proteins with the key domain are present in a given species genome.
getKeyWords() - Method in interface org.biojava3.core.sequence.features.FeaturesKeyWordInterface
 
getKeyWords() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
Pull uniprot key words which is a mixed bag of words associated with this sequence
getKeywords() - Method in interface org.biojava3.protmod.ProteinModification
 
getKeywords() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getL() - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
Return triangular factor.
getL() - Method in class org.biojava.bio.structure.jama.LUDecomposition
Return lower triangular factor
getLabel_alt_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getLabel_asym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getLabel_atom_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getLabel_comp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getLabel_entity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getLabel_seq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getLabelOfAtomOnComponent1() - Method in class org.biojava3.protmod.ModificationLinkage
 
getLabelOfAtomOnComponent2() - Method in class org.biojava3.protmod.ModificationLinkage
 
getLastChildNode() - Method in class org.forester.phylogeny.PhylogenyNode
Convenience method.
getLastIndexOf(C) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getLastIndexOf(C) - Method in class org.biojava3.alignment.SimpleProfile
 
getLastIndexOf(C) - Method in interface org.biojava3.alignment.template.Profile
Searches for the given Compound within this alignment profile.
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns the last occurrence of the given compound in this store; performs a linear search
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Returns the length of the Sequence if the given compound was equal to the one given during construction.
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getLastIndexOf(C) - Method in interface org.biojava3.core.sequence.template.Sequence
Scans through the Sequence looking for the last occurrence of the given compound
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
 
getLastIndexOf(NucleotideCompound) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
getLat() - Method in class org.forester.phylogeny.data.Point
 
getLatitude() - Method in class org.forester.phylogeny.data.Distribution
 
getLCA(PhylogenyNode, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyMethods
Returns the LCA of PhylogenyNodes node1 and node2.
getLcmp() - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getLcmp() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getLegendPosition(int, int) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
getLength() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getLength() - Method in class org.biojava.bio.structure.Bond
 
getLength() - Method in interface org.biojava.bio.structure.Chain
Deprecated.
please use getAtomLength or getLengthSeqRes instead
getLength() - Method in class org.biojava.bio.structure.ChainImpl
Deprecated.
use getAtomLength instead
getLength() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getLength() - Method in class org.biojava3.alignment.SimpleProfile
 
getLength() - Method in interface org.biojava3.alignment.template.Profile
Returns the number of columns in the alignment profile.
getLength() - Method in class org.biojava3.core.sequence.CDSSequence
 
getLength() - Method in class org.biojava3.core.sequence.ExonSequence
 
getLength() - Method in class org.biojava3.core.sequence.GeneSequence
 
getLength() - Method in class org.biojava3.core.sequence.IntronSequence
 
getLength() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getLength() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getLength() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
The sequence length
getLength() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getLength() - Method in interface org.biojava3.core.sequence.location.template.Location
Returns the length of the outer bounds of this location
getLength() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Get the length of the MSA where it is assumed that all sequence position
getLength() - Method in class org.biojava3.core.sequence.StartCodonSequence
 
getLength() - Method in class org.biojava3.core.sequence.StopCodonSequence
 
getLength() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getLength() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
getLength() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns the length of the sequence
getLength() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getLength() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Returns the length given during construction
getLength() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getLength() - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns the number of columns in the alignment profile.
getLength() - Method in interface org.biojava3.core.sequence.template.Sequence
Returns the length of the Sequence
getLength() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getLength() - Method in class org.biojava3.core.sequence.TranscriptSequence
 
getLength() - Method in class org.biojava3.core.sequence.views.WindowedSequence
Returns the size of the windowed sequence which is the length by the window size.
getLength() - Method in class org.biojava3.data.sequence.FastaSequence
 
getLength() - Method in class org.forester.development.AminoAcidSequence
 
getLength() - Method in class org.forester.development.BasicMsa
 
getLength() - Method in interface org.forester.development.Msa
 
getLength() - Method in interface org.forester.development.Sequence
 
getLength() - Method in class org.forester.development.SimpleMutableMsa
 
getLength() - Method in class org.forester.phylogeny.data.ProteinDomain
 
getLength() - Method in class org.forester.surfacing.SimpleDomain
 
getLength1() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getLength2() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getLengthAminos() - Method in interface org.biojava.bio.structure.Chain
Deprecated.
use getAtomGroups("amino").size() instead.
getLengthAminos() - Method in class org.biojava.bio.structure.ChainImpl
returns the length of the AminoAcids in the ATOM records of this chain.
getLengthStatistic(Species) - Method in class org.forester.surfacing.DomainLengths
 
getLengthStatistic(DomainId, Species) - Method in class org.forester.surfacing.DomainLengthsTable
 
getLengthStatisticsList() - Method in class org.forester.surfacing.DomainLengths
 
getLineLength() - Method in class org.biojava3.core.sequence.io.FastaGeneWriter
 
getLineLength() - Method in class org.biojava3.core.sequence.io.FastaWriter
 
getLineSeparator() - Static method in class org.forester.util.ForesterUtil
 
getLink() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a refernce to the linked PhylogenyNode of this PhylogenyNode.
getLinkages() - Method in interface org.biojava3.protmod.ModificationCondition
 
getLinkages() - Method in class org.biojava3.protmod.ModificationConditionImpl
}
getList() - Method in class org.biojava3.core.sequence.io.util.ClasspathResource
Returns this resource as a list of Strings
getList(BufferedReader) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Returns the contents of a buffered reader as a list of strings
getList(InputStream) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Delegates to IOUtils.getList(BufferedReader) by wrapping the InputStream in a valid reader.
getList(File) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Delegates to IOUtils.getList(InputStream) by wrapping the File in a valid stream.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel.GradientRenderer
 
getLoadMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getLocalFileName(String) - Static method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
Returns the file name that contains the definition for this ChemComp
getLocation() - Method in class org.forester.phylogeny.data.Sequence
 
getLocationInAlignment() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getLocationInAlignment() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the Location of the original Sequence within an alignment.
getLocations() - Method in class org.biojava3.core.sequence.features.AbstractFeature
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
getLocations() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
The location(s) of this feature where the location should contain a reference to parent and sequence etc.
getLong() - Method in class org.forester.phylogeny.data.Point
 
getLongitude() - Method in class org.forester.phylogeny.data.Distribution
 
getLongName() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getLongName() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
getLongName() - Method in interface org.biojava3.core.sequence.template.Compound
 
getLongName() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
getLongName() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getLostCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getLostCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getLostCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getLostCount() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getLs_d_res_high() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_d_res_low() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_number_parameters() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_number_reflns_all() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_number_reflns_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_number_reflns_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_number_restraints() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_percent_reflns_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_percent_reflns_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_R_factor_all() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_R_factor_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_R_factor_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_R_factor_R_free_error() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_R_factor_R_free_error_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_R_factor_R_work() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_redundancy_reflns_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_wR_factor_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getLs_wR_factor_R_work() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getM() - Method in class org.biojava.bio.structure.align.model.AFP
 
getMainPanel() - Method in class org.forester.archaeopteryx.TreePanel
 
getMandatoryArgs() - Method in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
getMappingCount() - Method in class org.forester.go.PfamToGoParser
 
getMappingSequence() - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
 
getMass() - Method in class org.biojava3.aaproperties.xml.Element
 
getMass() - Method in class org.biojava3.aaproperties.xml.Isotope
 
getMatches(File, double) - Static method in class org.biojava3.genome.homology.BlastHomologyHits
 
getMatchingAtomRes(Chain, List<Chain>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
getMatMatrix() - Method in class org.biojava.bio.structure.align.ce.CECalculator
Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
getMatMatrix() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.
getMatrices() - Method in class org.biojava3.alignment.aaindex.AAIndexFileParser
 
getMatrix() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
getMatrix() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
getMatrix(int, int, int, int) - Method in class org.biojava.bio.structure.jama.Matrix
Get a submatrix.
getMatrix(int[], int[]) - Method in class org.biojava.bio.structure.jama.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class org.biojava.bio.structure.jama.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class org.biojava.bio.structure.jama.Matrix
Get a submatrix.
getMatrix(String) - Method in interface org.biojava3.alignment.aaindex.AAIndexProvider
 
getMatrix(String) - Method in class org.biojava3.alignment.aaindex.DefaultAAIndexProvider
 
getMatrix() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getMatrix() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getMatrix() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns entire matrix.
getMatrix() - Method in class org.biojava3.phylo.ScoreMatrix
 
getMatrix() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
 
getMatrixAsString() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getMatrixAsString() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getMatrixAsString() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns this matrix as a formatted String with Compound labels along the axes.
getMatrixFromAAINDEX(String) - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns any matrix from the AAINDEX database file
getMatrixPanel() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
getMax() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getMax() - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
getMax(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Scans through a list of locations to find the Location with the highest end
getMax(List<Location>) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Scans through a list of locations to find the Location with the highest end
getMax() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getMax() - Method in class org.forester.phylogeny.data.Date
 
getMax() - Method in class org.forester.util.BasicDescriptiveStatistics
 
getMax() - Method in interface org.forester.util.DescriptiveStatistics
 
getMaxAtoms() - Method in class org.biojava.bio.structure.io.FileParsingParameters
the maximum numbers of atoms to load in a protein structure (prevents memory overflows)
getMaxGap() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getMaxGapFrag() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getMaxGapSize() - Method in class org.biojava.bio.structure.align.ce.CeParameters
the Max gap size parameter G .
getMaxGapSize() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
CE specific parameter: set the Max gap size parameter G (during AFP extension).
getMaximalDifference() - Method in interface org.forester.surfacing.DomainSimilarity
For pairwise similarities, this should return the "difference"; for example the difference in counts for copy number based features (the same as getMaximalDifferenceInCounts(), or the number of actually different domain combinations.
getMaximalDifference() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getMaximalDifferenceInCounts() - Method in interface org.forester.surfacing.DomainSimilarity
For pairwise similarities, this should return the difference in counts, while for comparisons of more than two domains, this should return the maximal difference in counts
getMaximalDifferenceInCounts() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getMaximalSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
 
getMaximalSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getMaximumConfidenceValue(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
Returns the largest confidence value found on phy.
getMaximumCovalentValence() - Method in enum org.biojava.bio.structure.Element
Returns the maximum valence for this Element.
getMaximumValence() - Method in enum org.biojava.bio.structure.Element
Returns the maximum valence for this Element.
getMaxIter() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getMaxIterations() - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
getMaxNrIterationsForOptimization() - Method in class org.biojava.bio.structure.align.ce.CeParameters
Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
getMaxNrSuggestions() - Method in interface org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider
Get the maximun nr of suggestions
getMaxNrSuggestions() - Method in class org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
getMaxNrSuggestions() - Method in class org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
getMaxOptRMSD() - Method in class org.biojava.bio.structure.align.ce.CeParameters
Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
getMaxOptRMSD() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
(jCE specific): maximum RMSD that shall be calculated for the alignment.
getMaxPenalty() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getMaxrefine() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getMaxScore() - Method in class org.biojava3.alignment.FractionalIdentityScorer
 
getMaxScore() - Method in class org.biojava3.alignment.FractionalSimilarityScorer
 
getMaxScore() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getMaxScore() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getMaxScore() - Method in interface org.biojava3.alignment.template.Scorer
Returns maximum possible score.
getMaxSingleCompoundStringLength() - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getMaxSingleCompoundStringLength() - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
getMaxSingleCompoundStringLength() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
getMaxSingleCompoundStringLength() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
getMaxSingleCompoundStringLength() - Method in interface org.biojava3.core.sequence.template.CompoundSet
Returns the maximum size of a compound String this set holds
getMaxTra() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
get the maximum number of Twists that are allowed...
getMaxTra() - Method in class org.biojava.bio.structure.align.model.AFPChain
get the maximum nr of Twists that are allowed...
getMaxValue() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getMaxValue() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getMaxValue() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns the maximum value in this matrix.
getMean() - Method in class org.forester.sdi.DistanceCalculator
Returns the mean distance.
getMeanBasedOutlierSpecies(double) - Method in class org.forester.surfacing.DomainLengths
 
getMeanSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
 
getMeanSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getMenuName() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getMenuName() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
A name/description which can appear on a menu.
getMessage() - Method in class org.biojava.bio.structure.align.gui.SystemInfo
 
getMethod() - Method in class org.biojava.bio.structure.align.xml.PdbPairsMessage
 
getMethod() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getMethod() - Method in class org.biojava.bio.structure.PDBHeader
 
getMethod_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
getMin() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getMin() - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
getMin(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Scans through a list of locations to find the Location with the lowest start
getMin(List<Location>) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Scans through a list of locations to find the Location with the lowest start
getMin() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getMin() - Method in class org.forester.phylogeny.data.Date
 
getMin() - Method in class org.forester.util.BasicDescriptiveStatistics
 
getMin() - Method in interface org.forester.util.DescriptiveStatistics
 
getMinimalDiffInSubTreeHeights() - Method in class org.forester.sdi.SDIR
Returns the (absolue value of the) minimal difference in tree heights of the two subtrees at the root (of the (re)rooted gene tree) - as determined by method "infer" - if minimize_height is set to true.
getMinimalDuplications() - Method in class org.forester.sdi.SDIR
Returns the minimal number of duplications - as determined by method "infer".
getMinimalMappingCost() - Method in class org.forester.sdi.SDIR
Returns the minimal mapping cost L - as determined by method "infer" - if minimize_mapping_cost is set to true.
getMinimalSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
 
getMinimalSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getMinimalTreeHeight() - Method in class org.forester.sdi.SDIR
Returns the minimal tree height - as determined by method "infer" - if minimize_height is set to true.
getMinimumValence() - Method in enum org.biojava.bio.structure.Element
Returns the minimum valence for this Element.
getMinLen() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getMinScore() - Method in class org.biojava3.alignment.FractionalIdentityScorer
 
getMinScore() - Method in class org.biojava3.alignment.FractionalSimilarityScorer
 
getMinScore() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getMinScore() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getMinScore() - Method in interface org.biojava3.alignment.template.Scorer
Returns minimum possible score.
getMinValue() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getMinValue() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getMinValue() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns the minimum value in this matrix.
getMisCut() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getMisLen() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getMisScore() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getMod_type() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
getModDate() - Method in class org.biojava.bio.structure.PDBHeader
 
getModel(int) - Method in interface org.biojava.bio.structure.Structure
retrieve all Chains belonging to a model .
getModel(int) - Method in class org.biojava.bio.structure.StructureImpl
retrieve all Chains belonging to a model .
getModel(int) - Method in class org.biojava3.ronn.ModelLoader
 
getModelNumber() - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
getModification() - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
getModification() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
getMolecularSequence() - Method in class org.forester.phylogeny.data.Sequence
 
getMolecularWeight(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the molecular weight of sequence.
getMolecularWeight(ProteinSequence, File) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the molecular weight of sequence.
getMolecularWeight(ProteinSequence, File, File) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the molecular weight of sequence.
getMolecularWeight(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the molecular weight of sequence.
getMolecularWeight(String, File, File) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the molecular weight of sequence.
getMolecularWeight(String, File) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the molecular weight of sequence.
getMolecularWeight(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getMolecularWeight(ProteinSequence, File) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getMolecularWeight(ProteinSequence, File, File) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getMolecularWeight(Character) - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
getMolecularWeight() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getMolecularWeight() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
getMolecularWeight() - Method in interface org.biojava3.core.sequence.template.Compound
 
getMolecularWeight() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
getMolecularWeight() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the molecular weight of sequence.
getMolecularWeightBasedOnXML(String, AminoAcidCompositionTable) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method that returns the molecular weight of sequence.
getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getMolId() - Method in class org.biojava.bio.structure.Compound
Returns the mol id value.
getMolName() - Method in class org.biojava.bio.structure.Compound
 
getMon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
getMon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getMon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getMon_nstd_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getMon_nstd_parent_comp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getMostPromiscuosDomain() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getMostPromiscuosDomain() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
getMultipleSequenceAlignment(List<S>, Object...) - Static method in class org.biojava3.alignment.Alignments
Factory method which computes a multiple sequence alignment for the given List of Sequences.
getMutation() - Method in class org.biojava.bio.structure.Compound
 
getN() - Method in interface org.biojava.bio.structure.AminoAcid
get N atom.
getN() - Method in class org.biojava.bio.structure.AminoAcidImpl
get N atom.
getN() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
getN() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getN() - Method in class org.forester.sdi.DistanceCalculator
Returns the sum of all Nodes used to calculate the mean.
getN() - Method in interface org.forester.surfacing.DomainSimilarity
This should return the number of pairwise distances used to calculate this similarity score
getN() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getN() - Method in class org.forester.util.BasicDescriptiveStatistics
 
getN() - Method in interface org.forester.util.DescriptiveStatistics
 
getName() - Method in class org.biojava.bio.structure.align.client.StructureName
 
getName() - Method in interface org.biojava.bio.structure.Atom
get trimmed version of atom name, e.g.
getName() - Method in class org.biojava.bio.structure.AtomImpl
Gets this object's name.
getName() - Method in interface org.biojava.bio.structure.Chain
Deprecated.
replaced by Chain.getChainID()
getName() - Method in class org.biojava.bio.structure.ChainImpl
 
getName() - Method in class org.biojava.bio.structure.io.mmcif.model.AuditAuthor
 
getName() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getName() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
getName() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
getName() - Method in interface org.biojava.bio.structure.Structure
get biological name of Structure.
getName() - Method in class org.biojava.bio.structure.StructureImpl
get biological name of Structure.
getName() - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
getName() - Method in class org.biojava3.aaproperties.xml.Element
 
getName() - Method in class org.biojava3.aaproperties.xml.Isotope
 
getName() - Method in class org.biojava3.aaproperties.xml.Name2Count
 
getName() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getName() - Method in class org.biojava3.alignment.GuideTree.Node
 
getName() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getName() - Method in interface org.biojava3.alignment.template.GuideTreeNode
Returns the name of this node.
getName() - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns the name (short description) of this matrix.
getName() - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
 
getName() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getName() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getName() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
The name of the webservice.
getName() - Method in class org.forester.development.AminoAcidSequence
 
getName() - Method in class org.forester.go.BasicGoTerm
 
getName() - Method in interface org.forester.go.GoTerm
 
getName() - Method in class org.forester.phylogeny.data.ProteinDomain
 
getName() - Method in class org.forester.phylogeny.data.Sequence
 
getName() - Method in class org.forester.phylogeny.Phylogeny
Returns the name of this Phylogeny.
getName() - Method in class org.forester.surfacing.BasicProtein
 
getName() - Method in interface org.forester.surfacing.Protein
 
getName(int) - Method in class org.forester.util.CommandLineArguments
 
getName1() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getName1() - Method in class org.biojava.bio.structure.align.gui.SelectPDBPanel
 
getName1() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getName2() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getName2() - Method in class org.biojava.bio.structure.align.gui.SelectPDBPanel
 
getName2() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getNames() - Method in class org.forester.util.CommandLineArguments
 
getnAtom() - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getnAtom() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getNaturalPos() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getNChar() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
 
getNclose() - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
getNcuts() - Method in class org.biojava.bio.structure.domain.pdp.CutSites
 
getNdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getNdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getNdom() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getNetCharge(ProteinSequence, boolean, double) - Method in interface org.biojava3.aaproperties.IPeptideProperties
Returns the net charge of sequence at pH 7.
getNetCharge(ProteinSequence, boolean) - Method in interface org.biojava3.aaproperties.IPeptideProperties
 
getNetCharge(ProteinSequence) - Method in interface org.biojava3.aaproperties.IPeptideProperties
 
getNetCharge(String, boolean, double) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method to return the net charge of sequence at pH 7.
getNetCharge(String, boolean) - Static method in class org.biojava3.aaproperties.PeptideProperties
 
getNetCharge(String) - Static method in class org.biojava3.aaproperties.PeptideProperties
 
getNetCharge(ProteinSequence) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getNetCharge(ProteinSequence, boolean) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getNetCharge(ProteinSequence, boolean, double) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
getNetGainsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getNeutronsNum() - Method in class org.biojava3.aaproperties.xml.Isotope
 
getNewDocument() - Static method in class org.biojava3.core.util.XMLHelper
 
getNewickString(boolean, boolean) - Method in class org.biojava3.phylo.TreeConstructor
 
getNextExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
getNextSubproblem(int[]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
Returns the coordinates for the next subproblem.
getNode() - Method in class org.forester.phylogeny.iterators.PostOrderStackObject
DOCUMENT ME!
getNode(int) - Method in class org.forester.phylogeny.Phylogeny
Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
getNode(String) - Method in class org.forester.phylogeny.Phylogeny
Returns a PhylogenyNode of this Phylogeny which has a matching name.
getNodeCount() - Static method in class org.forester.phylogeny.PhylogenyNode
Returns the total number of all Nodes created so far.
getNodeData() - Method in class org.forester.phylogeny.PhylogenyNode
 
getNodeDistance(PhylogenyNode, PhylogenyNode) - Method in class org.biojava3.phylo.CheckTreeAccuracy
 
getNodeDistance(PhylogenyNode, PhylogenyNode) - Method in class org.forester.application.CheckTreeAccuracy
 
getNodeField() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getNodeField() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
The node data field in which to place node names from simple unannotated formats (such as Newick).
getNodeId() - Method in class org.forester.phylogeny.PhylogenyNode
Returns the ID (int) of this PhylogenyNode.
getNodeId() - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
getNodeIdentifier() - Method in class org.forester.phylogeny.data.NodeData
 
getNodeName() - Method in class org.forester.phylogeny.PhylogenyNode
Returns the name of this node.
getNodeName() - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
getNodes(String) - Method in class org.forester.phylogeny.Phylogeny
Returns a List with references to all Nodes of this Phylogeny which have a matching name.
getNodesViaSequenceName(String) - Method in class org.forester.phylogeny.Phylogeny
 
getNodesViaTaxonomyCode(String) - Method in class org.forester.phylogeny.Phylogeny
 
getNodesWithMatchingSpecies(String) - Method in class org.forester.phylogeny.Phylogeny
Returns a Vector with references to all Nodes of this Phylogeny which have a matching species name.
getNodeViaSequenceName(String) - Method in class org.forester.phylogeny.Phylogeny
 
getNodeViaTaxonomyCode(String) - Method in class org.forester.phylogeny.Phylogeny
 
getNormAlignScore() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.BranchCountingBasedScoringMethod
 
getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.BranchLengthBasedScoringMethod
 
getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.LogBranchLengthBasedScoringMethod
 
getNormalizationFactor(Phylogeny) - Method in interface org.forester.pccx.ScoringMethodForExternalNode
This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.
getNotesList() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getNotObserved() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getNParents() - Method in class org.forester.go.etc.OntologizerResult
 
getNrAlignments() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
getNrAtoms(Structure) - Static method in class org.biojava.bio.structure.StructureTools
Count how many number of Atoms are contained within a Structure object.
getNrCPUs() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
getNreported() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getNrEQR() - Method in class org.biojava.bio.structure.align.model.AFPChain
Get the number of structurally equivalent residues
getNrGroups(Structure) - Static method in class org.biojava.bio.structure.StructureTools
Count how many groups are contained within a structure object.
getNseg() - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
getNTax() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
 
getNuc4_2() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Nuc 4.2 matrix by Lowe
getNuc4_4() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns Nuc 4.4 matrix by Lowe
getNullValue() - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
 
getNum() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
getNum() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
getNumber() - Method in class org.forester.surfacing.BasicDomain
 
getNumber() - Method in interface org.forester.surfacing.Domain
 
getNumber() - Method in class org.forester.surfacing.SimpleDomain
 
getNumberOfBranches() - Method in class org.forester.phylogeny.Phylogeny
 
getNumberOfCharacters() - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getNumberOfCharacters() - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getNumberOfChildElements() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getNumberOfColumns() - Method in class org.forester.util.BasicTable
 
getNumberOfCombinableDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getNumberOfCombinableDomains() - Method in interface org.forester.surfacing.CombinableDomains
 
getNumberOfConfidences() - Method in class org.forester.phylogeny.data.BranchData
 
getNumberOfDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
 
getNumberOfDifferentDomains() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
 
getNumberOfDomains() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getNumberOfDomains() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
getNumberOfDuplications() - Method in class org.forester.phylogeny.data.Event
 
getNumberOfExternalNodes() - Method in class org.forester.phylogeny.Phylogeny
Returns the sum of external Nodes of this Phylogeny (int).
getNumberOfExternalNodes() - Method in class org.forester.phylogeny.PhylogenyNode
Returns the total number of external Nodes originating from this PhylogenyNode (int).
getNumberOfGeneLosses() - Method in class org.forester.phylogeny.data.Event
 
getNumberOfGoIds() - Method in class org.forester.surfacing.BasicDomain
 
getNumberOfGoIds() - Method in interface org.forester.surfacing.Domain
 
getNumberOfGoIds() - Method in class org.forester.surfacing.DomainId
 
getNumberOfGoIds() - Method in class org.forester.surfacing.SimpleDomain
 
getNumberOfIdentifiers() - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getNumberOfIdentifiers() - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getNumberOfInvalidChar(String, Set<Character>, boolean) - Static method in class org.biojava3.aaproperties.Utils
Return the number of invalid characters in sequence.
getNumberOfNames() - Method in class org.forester.util.CommandLineArguments
 
getNumberOfNodesLackingName(Phylogeny, StringBuilder) - Static method in class org.forester.surfacing.SurfacingUtil
 
getNumberOfParents() - Method in class org.forester.phylogeny.PhylogenyNode
 
getNumberOfProteinDomains() - Method in class org.forester.surfacing.BasicProtein
 
getNumberOfProteinDomains() - Method in interface org.forester.surfacing.Protein
 
getNumberOfProteinsExhibitingCombination(DomainId) - Method in class org.forester.surfacing.BasicCombinableDomains
 
getNumberOfProteinsExhibitingCombination(DomainId) - Method in interface org.forester.surfacing.CombinableDomains
 
getNumberOfRows() - Method in class org.forester.util.BasicTable
 
getNumberOfSameDomains() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
 
getNumberOfSequences() - Method in class org.forester.development.BasicMsa
 
getNumberOfSequences() - Method in interface org.forester.development.Msa
 
getNumberOfSequences() - Method in class org.forester.development.SimpleMutableMsa
 
getNumberOfSpeciations() - Method in class org.forester.phylogeny.data.Event
 
getNumericRepresentation() - Method in enum org.biojava3.core.sequence.Strand
 
getNumGaps() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getNumGaps() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns number of gaps in the sequence.
getNumIdenticals() - Method in class org.biojava3.alignment.SimpleSequencePair
 
getNumIdenticals() - Method in interface org.biojava3.alignment.template.SequencePair
Returns the number of indices for which both the query and target sequences have an identical Compound.
getNumRes() - Method in class org.biojava.bio.structure.Compound
 
getNumSimilars() - Method in class org.biojava3.alignment.SimpleSequencePair
 
getNumSimilars() - Method in interface org.biojava3.alignment.template.SequencePair
Returns the number of indices for which both the query and target sequences have a similar Compound.
getO() - Method in interface org.biojava.bio.structure.AminoAcid
get O atom.
getO() - Method in class org.biojava.bio.structure.AminoAcidImpl
get O atom.
getO() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
getOccupancy() - Method in interface org.biojava.bio.structure.Atom
get occupancy.
getOccupancy() - Method in class org.biojava.bio.structure.AtomImpl
 
getOccupancy() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getOccupancy_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getOccupancy_max() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOccupancy_min() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOccurrenceType() - Method in interface org.biojava3.protmod.ProteinModification
 
getOccurrenceType() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getOne() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getOne() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
getOne() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getOne_letter_code() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
getOneLetterCode(ChemComp) - Static method in class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
 
getOnelineFasta() - Method in class org.biojava3.data.sequence.FastaSequence
 
getOpenPDBMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getOpenPenalty() - Method in class org.biojava3.alignment.SimpleGapPenalty
 
getOpenPenalty() - Method in interface org.biojava3.alignment.template.GapPenalty
Returns penalty given when a deletion or insertion gap first opens
getOptAln() - Method in class org.biojava.bio.structure.align.model.AFPChain
Tracks the Atom positions in the optimal alignment.
getOptAlnAsList(AFPChain) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Retrieves the optimum alignment from an AFPChain and returns it as a java collection.
getOptions() - Method in class org.forester.archaeopteryx.ArchaeopteryxE
 
getOptionValue(String) - Method in class org.forester.util.CommandLineArguments
 
getOptionValueAsCleanString(String) - Method in class org.forester.util.CommandLineArguments
Removes quotes
getOptionValueAsDouble(String) - Method in class org.forester.util.CommandLineArguments
 
getOptionValueAsInt(String) - Method in class org.forester.util.CommandLineArguments
 
getOptionValueAsLong(String) - Method in class org.forester.util.CommandLineArguments
 
getOptLen() - Method in class org.biojava.bio.structure.align.model.AFPChain
The length of each block
getOptLength() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getOptRmsd() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getOrder(int) - Static method in class org.forester.sdi.RIO
Returns the order in which ortholog (o), "super ortholog" (s) and distance (d) are returned and sorted (priority of sort always goes from left to right), given sort.
getOrderHelp() - Static method in class org.forester.sdi.RIO
 
getOrgan() - Method in class org.biojava.bio.structure.Compound
 
getOrganelle() - Method in class org.biojava.bio.structure.Compound
 
getOrganismCommon() - Method in class org.biojava.bio.structure.Compound
 
getOrganismName() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
Get the organism name assigned to this sequence
getOrganismScientific() - Method in class org.biojava.bio.structure.Compound
 
getOrganismTaxId() - Method in class org.biojava.bio.structure.Compound
 
getOriginal() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
getOriginalHeader() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getOriginalModificationId() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
Deprecated.
use getModification().getId()
getOriginalSequence() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getOriginalSequence() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the original Sequence before alignment.
getOriginalSequences() - Method in class org.biojava3.alignment.SimpleProfile
 
getOriginalSequences() - Method in interface org.biojava3.alignment.template.Profile
Returns a List containing the original Sequences used for alignment.
getOriginalSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getOriginalSize() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
 
getORmsdThr() - Method in class org.biojava.bio.structure.align.ce.CeParameters
Get the Original RMSD threshold from which the alignment optimization is started
getOrthologousNodes(Phylogeny, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyMethods
Returns all orthologs of the external PhylogenyNode n of this Phylogeny.
getOrthologs() - Method in class org.forester.sdi.RIOn
 
getOutFile() - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
getOutFile() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getOutFileLocation() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
getOutputFormat() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
 
getOutputOption(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
This method forwards to NCBIQBlastOutputProperties.getOutputOption(BlastOutputParameterEnum).
getOutputOption(BlastOutputParameterEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Gets the value of specified parameter or null if it is not set
getOutputOption(String) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
Method that returns the value associated with the key given in parameter.
getOutputOptions() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Gets output parameters, which are currently set
getOutputOptions() - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
Method to get all keys to the information stored in this object.
getOverall_FOM_free_R_set() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOverall_FOM_work_R_set() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOverall_SU_B() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOverall_SU_ML() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOverall_SU_R_Cruickshank_DPI() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOverall_SU_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getOverlapCount() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getOverlapCount() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the maximum number of elements contributed to a column of an alignment by this Sequence.
getOxidationState() - Method in enum org.biojava.bio.structure.Element
Returns a typical oxidation state for this Element.
getP() - Method in class org.forester.go.etc.OntologizerResult
 
getP1() - Method in class org.biojava.bio.structure.align.model.AFP
 
getP2() - Method in class org.biojava.bio.structure.align.model.AFP
 
getPAdjusted() - Method in class org.forester.go.etc.OntologizerResult
 
getPair() - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
getPair() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getPair() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getPair() - Method in interface org.biojava3.alignment.template.PairwiseSequenceAligner
Returns sequence alignment pair.
getPair() - Method in interface org.biojava3.alignment.template.ProfileProfileAligner
Returns alignment profile pair.
getPairInProfileScorer() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getPairInProfileScorer() - Method in interface org.biojava3.alignment.template.RescoreRefiner
Returns class type of pairwise scoring subroutine.
getPairs() - Method in class org.biojava.bio.structure.align.xml.PdbPairsMessage
 
getPairwiseAligner(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava3.alignment.Alignments
Factory method which constructs a pairwise sequence aligner.
getPairwiseAlignment(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava3.alignment.Alignments
Factory method which computes a sequence alignment for the given Sequence pair.
getPairwiseScore(String, String) - Method in class org.biojava3.phylo.ScoreMatrix
 
getPairwiseScore(char, char) - Method in class org.biojava3.phylo.ScoreMatrix
 
getPAM250() - Static method in class org.biojava3.alignment.SubstitutionMatrixHelper
Returns PAM 250 matrix by Dayhoff
getPAM250(String, String) - Static method in class org.biojava3.phylo.ResidueProperties
 
getPAM250(char, char) - Static method in class org.biojava3.phylo.ResidueProperties
 
getPanelPos(int, int) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
get the position of the sequence position on the Panel
getPanelPos(int) - Method in class org.biojava.bio.structure.gui.util.CoordManager
 
getPara(int, int) - Method in class org.biojava.bio.structure.align.fatcat.calc.SigEva
 
getParalogousNodes(PhylogenyNode, String[]) - Method in class org.forester.phylogeny.Phylogeny
Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
getParalogs() - Method in class org.forester.sdi.RIOn
 
getParameter() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getParameter() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
 
getParameters() - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
getParameters() - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
getParameters() - Method in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
getParameters() - Method in class org.biojava.bio.structure.align.ce.CeMain
 
getParameters() - Method in class org.biojava.bio.structure.align.ce.CeSideChainMain
 
getParameters() - Method in class org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor
 
getParameters() - Method in class org.biojava.bio.structure.align.ce.CeUserArgumentProcessor
 
getParameters() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
getParameters() - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
getParameters() - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
getParameters() - Method in class org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor
 
getParameters() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
getParameters() - Method in class org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
getParameters() - Method in interface org.biojava.bio.structure.align.StructureAlignment
Return the paramers for this algorithm.
getParams() - Method in class org.biojava.bio.structure.align.FarmJob
 
getParams() - Method in class org.biojava.bio.structure.align.StructurePairAligner
get the parameters.
getParent() - Method in interface org.biojava.bio.structure.Atom
Deprecated.
replaced by Atom.getGroup()
getParent() - Method in class org.biojava.bio.structure.AtomImpl
 
getParent() - Method in interface org.biojava.bio.structure.Chain
Returns the parent Structure of this chain.
getParent() - Method in class org.biojava.bio.structure.ChainImpl
Returns the parent Structure of this chain.
getParent() - Method in class org.biojava.bio.structure.DBRef
Get the structure object that this DBRef relates to.
getParent() - Method in interface org.biojava.bio.structure.Group
Deprecated.
replaced by Group.getChain()
getParent() - Method in class org.biojava.bio.structure.HetatomImpl
Returns the parent Chain of the Group
getParent(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
Get the parent of a component.
getParent() - Method in class org.biojava3.alignment.GuideTree.Node
 
getParent() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getParent() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.
getParentChromosomeSequence() - Method in class org.biojava3.core.sequence.GeneSequence
The parent ChromosomeSequence which contains the actual DNA sequence data
getParentFeature() - Method in class org.biojava3.core.sequence.features.AbstractFeature
Get the parent Feature
getParentFeature() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Get the parent feature
getParentSequence() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getParentSunid() - Method in class org.biojava.bio.structure.scop.ScopNode
 
getPartner() - Method in class org.biojava.bio.structure.secstruc.HBond
 
getPath() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getPath() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
getPath() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getPath() - Method in class org.biojava.bio.structure.align.util.AtomCache
Get the path that is used to cache PDB files.
getPath() - Method in class org.biojava.bio.structure.io.LocalCacheStructureProvider
Returns the path value.
getPath() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
getPath() - Method in class org.biojava.bio.structure.io.PDBFileReader
Returns the path value.
getPath() - Method in interface org.biojava.bio.structure.io.StructureIOFile
get the directory path to the files
getPathSize() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getPathSize() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getPathToParent() - Method in class org.forester.phylogeny.PhylogenyNode
 
getPaulingElectronegativity() - Method in enum org.biojava.bio.structure.Element
Returns the Pauling electronegativity for this Element.
getPdb1() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getPdb1() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getPdb2() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getPdb2() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
getPdb_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getPdb_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getPdb_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getPdb_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getPdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getPdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getPdb_strand_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getPdb_strand_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getPdbAln() - Method in class org.biojava.bio.structure.align.model.AFPChain
used temporarily during XML serialization to track the PDB positions of the alignmnet
getPdbccId() - Method in interface org.biojava3.protmod.ProteinModification
 
getPdbccId() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getPdbccIds() - Method in class org.biojava3.protmod.Component
 
getPdbccName() - Method in interface org.biojava3.protmod.ProteinModification
 
getPdbccName() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Creates formatted String for a single character of PDB output
getPDBCode() - Method in interface org.biojava.bio.structure.Group
Deprecated.
replaced by Group.getResidueNumber()
getPDBCode() - Method in class org.biojava.bio.structure.HetatomImpl
Deprecated.
replaced by #getSeqNum
getPDBCode() - Method in interface org.biojava.bio.structure.server.StructureEvent
 
getPDBCode() - Method in class org.biojava.bio.structure.server.StructureEventImpl
 
getPDBCode() - Method in interface org.biojava.bio.structure.Structure
get PDB code of structure.
getPDBCode() - Method in class org.biojava.bio.structure.StructureImpl
get PDB code of structure .
getPDBCode1() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getPDBCode2() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Creates formatted String for displaying conservation in PDB output
getPDBDirField() - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
getPdbFilePath() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getPdbFilePath() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
getPdbFilePath() - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
getPDBHeader(String) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
getPDBHeader(String) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
getPDBHeader(String) - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
get the PDB header for a single protein structure
getPDBHeader() - Method in interface org.biojava.bio.structure.Structure
return the header information for this PDB file
getPDBHeader() - Method in class org.biojava.bio.structure.StructureImpl
 
getPdbId() - Method in class org.biojava.bio.structure.align.client.StructureName
PDB IDs are always returned as upper case
getPdbId() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getPdbId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getPdbInfo(Atom) - Static method in class org.biojava.bio.structure.align.gui.jmol.JmolTools
get jmol style info: jmol style: [MET]508:A.CA/1 #3918 insertion code: [ASP]1^A:A.CA/1 #2
getPdbInfo(Atom, boolean) - Static method in class org.biojava.bio.structure.align.gui.jmol.JmolTools
 
getPDBInfoFile() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
getPDBInstallation() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
getPDBInstallation() - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
getPDBLegend() - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Creates formatted String for displaying conservation legend in PDB output
getPDBline() - Method in interface org.biojava.bio.structure.Atom
Deprecated.
@deprecated replaced by PDBRecord.toPDB()
getPDBline() - Method in class org.biojava.bio.structure.AtomImpl
Deprecated. 
getPDBName() - Method in interface org.biojava.bio.structure.Group
Get the PDB 3 character name for this group.
getPDBName() - Method in class org.biojava.bio.structure.HetatomImpl
Returns the PDBName.
getPDBName() - Method in class org.biojava3.protmod.structure.StructureGroup
 
getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava3.protmod.ModificationLinkage
 
getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava3.protmod.ModificationLinkage
 
getPdbPairs(String, int, String) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getPDBResidueNumber(Group) - Static method in class org.biojava.bio.structure.StructureTools
Deprecated.
replaced by Group.getResidueNumber()
getPDBResidueNumber() - Method in class org.biojava3.protmod.structure.StructureGroup
 
getPdbResName() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getPDBresnum(int, AFPChain, Atom[]) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
 
getPdbResNum() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getPDBresnum1() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
getPDBresnum2() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
getPDBserial() - Method in interface org.biojava.bio.structure.Atom
get PDB atom number.
getPDBserial() - Method in class org.biojava.bio.structure.AtomImpl
get PDB atom number.
getPdbSplit() - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
getPDBUploadPanel() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
getPdbx_align_begin() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getPdbx_ambiguous_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_auth_seq_align_beg() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_auth_seq_align_end() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_blank_PDB_chainid_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
getPdbx_CASP_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
getPdbx_data_cutoff_high_absF() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_data_cutoff_high_rms_absF() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_data_cutoff_low_absF() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_db_accession() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getPdbx_db_accession() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_db_align_beg_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_db_align_end_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_description() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getPdbx_descriptor() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
getPdbx_ec() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getPdbx_formal_charge() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getPdbx_formal_charge() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_fragment() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getPdbx_ideal_coordinates_details() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_ideal_coordinates_missing_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_initial_date() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_isotropic_thermal_model() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_keywords() - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
getPdbx_ls_cross_valid_method() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_ls_sigma_F() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_ls_sigma_I() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_method_to_determine_struct() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_model_coordinates_db_code() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_model_coordinates_details() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_model_coordinates_missing_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_model_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
getPdbx_model_type_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
getPdbx_modified() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
getPdbx_modified_date() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_mutation() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getPdbx_number_of_molecules() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getPdbx_ordinal() - Method in class org.biojava.bio.structure.io.mmcif.model.AuditAuthor
 
getPdbx_overall_ESU_R() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_overall_ESU_R_Free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_overall_phase_error() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_PDB_id_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_PDB_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getPdbx_PDB_model_num() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getPdbx_processing_site() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_R_Free_selection_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_refine_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_release_status() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_replaced_by() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_replaces() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_seq_align_beg_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_seq_align_end_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_seq_one_letter_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
getPdbx_solvent_ion_probe_radii() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_solvent_shrinkage_radii() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_solvent_vdw_probe_radii() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_starting_model() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_stereochem_target_val_spec_case() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_stereochemistry_target_values() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getPdbx_strand_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getPdbx_subcomponent_list() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_synonyms() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPdbx_type() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPDPDomainNamesForPDB(String) - Method in interface org.biojava.bio.structure.domain.PDPProvider
 
getPDPDomainNamesForPDB(String) - Method in class org.biojava.bio.structure.domain.RemotePDPProvider
 
getPdpprovider() - Method in class org.biojava.bio.structure.align.util.AtomCache
 
getPenultimateGoTerm(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
 
getPercId() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
getPerDomainEvalue() - Method in class org.forester.surfacing.BasicDomain
 
getPerDomainEvalue() - Method in interface org.forester.surfacing.Domain
 
getPerDomainEvalue() - Method in class org.forester.surfacing.SimpleDomain
 
getPerDomainScore() - Method in class org.forester.surfacing.BasicDomain
 
getPerDomainScore() - Method in interface org.forester.surfacing.Domain
 
getPerDomainScore() - Method in class org.forester.surfacing.SimpleDomain
 
getPerGenomeDomainPromiscuityStatistics() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getPerGenomeDomainPromiscuityStatistics() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
This should return a statistic for per domain promiscuity in a genome.
getPeriod() - Method in enum org.biojava.bio.structure.Element
Returns the period in the periodic table of this Element.
getPermutationSize() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getPerSequenceEvalue() - Method in class org.forester.surfacing.BasicDomain
 
getPerSequenceEvalue() - Method in interface org.forester.surfacing.Domain
 
getPerSequenceEvalue() - Method in class org.forester.surfacing.SimpleDomain
 
getPerSequenceScore() - Method in class org.forester.surfacing.BasicDomain
 
getPerSequenceScore() - Method in interface org.forester.surfacing.Domain
 
getPerSequenceScore() - Method in class org.forester.surfacing.SimpleDomain
 
getPhase() - Method in class org.biojava3.core.sequence.CDSSequence
 
getPhase() - Method in class org.forester.phylogeny.iterators.PostOrderStackObject
DOCUMENT ME!
getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
phi angle.
getPivot() - Method in class org.biojava.bio.structure.jama.LUDecomposition
Return pivot permutation vector
getPmid() - Method in class org.biojava.bio.structure.JournalArticle
Get the value of PMID field.
getPMin() - Method in class org.forester.go.etc.OntologizerResult
 
getPolymerType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getPopFamily() - Method in class org.forester.go.etc.OntologizerResult
 
getPopTerm() - Method in class org.forester.go.etc.OntologizerResult
 
getPopTotal() - Method in class org.forester.go.etc.OntologizerResult
 
getPos(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
getPos1() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getPos1() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
getPos2() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getPos2() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
getPosition() - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
getPosition() - Method in class org.biojava3.core.sequence.location.SimplePoint
 
getPosition() - Method in interface org.biojava3.core.sequence.location.template.Point
Returns the position held by this object
getPositionInQueue(String, String, String, String) - Method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getPositionInQueue(String, String, String, String, int) - Method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getPreciseDistance(Atom, Atom) - Static method in class org.biojava.bio.structure.secstruc.SecStruc
calculate distance between two atoms.
getPreferredHeight() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
Y coordinate size
getPreferredWidth() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
X coordinate size
getPresentCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getPresentCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getPresentCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getPresentCount() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getPreviousExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode
Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
getPrintMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getProbability() - Method in class org.biojava.bio.structure.align.model.AFPChain
The probability (FATCAT) or Z-score (CE) of the alignment.
getProcessingInstructions() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getProcessingInstructions() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
This is used to indicate any kind of special processing.
getProfile() - Method in class org.biojava3.alignment.FractionalIdentityInProfileScorer
 
getProfile() - Method in class org.biojava3.alignment.FractionalSimilarityInProfileScorer
 
getProfile() - Method in class org.biojava3.alignment.GuideTree.Node
 
getProfile() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getProfile() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getProfile() - Method in interface org.biojava3.alignment.template.Aligner
Returns the alignment Profile produced by this alignment algorithm.
getProfile() - Method in interface org.biojava3.alignment.template.GuideTreeNode
Returns the profile stored at this node.
getProfile() - Method in interface org.biojava3.alignment.template.PairInProfileScorer
Returns the Profile from which the aligned pair originated.
getProfileFuture() - Method in class org.biojava3.alignment.GuideTree.Node
 
getProfileFuture() - Method in interface org.biojava3.alignment.template.GuideTreeNode
Returns the profile future stored at this node, but does not force the calculation, yet.
getProfileProfileAligner() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getProfileProfileAligner() - Method in interface org.biojava3.alignment.template.PartitionRefiner
Returns class type of profile-profile alignment subroutine.
getProfileProfileAligner() - Method in interface org.biojava3.alignment.template.RescoreRefiner
Returns class type of profile-profile alignment subroutine.
getProgram() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
getProgram_version() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
getProgressiveAlignment(GuideTree<S, C>, Alignments.ProfileProfileAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava3.alignment.Alignments
Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
getProperties() - Method in interface org.biojava.bio.structure.Group
return properties.
getProperties() - Method in class org.biojava.bio.structure.HetatomImpl
return properties.
getProperties() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
Get the properties
getProperties() - Method in class org.forester.phylogeny.data.Annotation
 
getProperties() - Method in class org.forester.phylogeny.data.NodeData
 
getProperties() - Method in class org.forester.phylogeny.data.PropertiesMap
 
getPropertiesArray() - Method in class org.forester.phylogeny.data.PropertiesMap
 
getProperty(String) - Method in interface org.biojava.bio.structure.Group
get a single property .
getProperty(String) - Method in class org.biojava.bio.structure.HetatomImpl
get a single property .
getProperty(String) - Method in class org.forester.phylogeny.data.PropertiesMap
 
getPropertyRefs() - Method in class org.forester.phylogeny.data.PropertiesMap
Returns all property refs of this PhylogenyNode as String array.
getPropertyRefs(Phylogeny) - Static method in class org.forester.util.ForesterUtil
Returns all custom data tag names of this Phylogeny as Hashtable.
getProteinCDSSequences() - Method in class org.biojava3.core.sequence.TranscriptSequence
Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.
getProteinDomain(int) - Method in class org.forester.surfacing.BasicProtein
 
getProteinDomain(int) - Method in interface org.forester.surfacing.Protein
 
getProteinDomainCount(DomainId) - Method in class org.forester.surfacing.BasicProtein
 
getProteinDomainCount(DomainId) - Method in interface org.forester.surfacing.Protein
 
getProteinDomains() - Method in class org.forester.surfacing.BasicProtein
 
getProteinDomains(DomainId) - Method in class org.forester.surfacing.BasicProtein
 
getProteinDomains() - Method in interface org.forester.surfacing.Protein
 
getProteinDomains(DomainId) - Method in interface org.forester.surfacing.Protein
 
getProteinId() - Method in class org.forester.surfacing.BasicProtein
 
getProteinId() - Method in interface org.forester.surfacing.Protein
 
getProteinsEncountered() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getProteinsEncountered() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getProteinSequence() - Method in class org.biojava3.core.sequence.RNASequence
Get the ProteinSequence from the RNA sequence
getProteinSequence(TranscriptionEngine) - Method in class org.biojava3.core.sequence.RNASequence
Get the ProteinSequene from the RNA sequence with user defined transcription engine
getProteinSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence
Get the protein sequence
getProteinSequence(TranscriptionEngine) - Method in class org.biojava3.core.sequence.TranscriptSequence
Get the protein sequence with user defined TranscriptEngine
getProteinSequenceCreator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.bio.structure.io.StructureSequenceMatcher
Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.
getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
getProteinSequences() - Method in class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
 
getProteinsIgnoredDueToFilter() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getProteinsIgnoredDueToFilter() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getProteinsStored() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getProteinsStored() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getProvider() - Method in class org.forester.phylogeny.data.Identifier
 
getProxySequenceReader() - Method in interface org.biojava3.core.sequence.location.template.AccesionedLocation
Return the proxy reader used to get sequence for this location.
getProxySequenceReader() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
psi angle.
getPsimodId() - Method in interface org.biojava3.protmod.ProteinModification
 
getPsimodId() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getPsimodName() - Method in interface org.biojava3.protmod.ProteinModification
 
getPsimodName() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getPublicationDate() - Method in class org.biojava.bio.structure.JournalArticle
 
getPublisher() - Method in class org.biojava.bio.structure.JournalArticle
 
getPvalue() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getPx() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getQ() - Method in class org.biojava.bio.structure.jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getQualifiedName() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getQualities() - Method in class org.biojava3.core.sequence.features.QualityFeature
 
getQualities(int, int) - Method in class org.biojava3.core.sequence.features.QualityFeature
 
getQuality() - Method in class org.biojava3.sequencing.io.fastq.Fastq
Return the quality scores for this FASTQ formatted sequence.
getQualityAt(int) - Method in class org.biojava3.core.sequence.features.QualityFeature
 
getQuantities() - Method in class org.biojava3.core.sequence.features.QuantityFeature
 
getQuery() - Method in class org.biojava3.alignment.FractionalIdentityScorer
 
getQuery() - Method in class org.biojava3.alignment.FractionalSimilarityScorer
 
getQuery() - Method in class org.biojava3.alignment.SimpleProfilePair
 
getQuery() - Method in class org.biojava3.alignment.SimpleSequencePair
 
getQuery() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getQuery() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getQuery() - Method in interface org.biojava3.alignment.template.PairwiseSequenceScorer
Returns the first sequence of the pair.
getQuery() - Method in interface org.biojava3.alignment.template.ProfilePair
Returns the first Profile of the pair.
getQuery() - Method in interface org.biojava3.alignment.template.ProfileProfileScorer
Returns the first profile of the pair.
getQuery() - Method in interface org.biojava3.alignment.template.SequencePair
Returns the first AlignedSequence of the pair.
getQueryIndex() - Method in class org.biojava3.alignment.routines.AlignerHelper.Cut
 
getR() - Method in class org.biojava.bio.structure.jama.QRDecomposition
Return the upper triangular factor
getRandomSleepTime() - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getRandomUsername() - Static method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
getRanges() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getRank() - Method in class org.forester.phylogeny.data.Taxonomy
 
getRealEigenvalues() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRealEnd() - Method in class org.biojava3.core.sequence.edits.Edit.Delete
 
getRealStart() - Method in class org.biojava3.core.sequence.edits.Edit.Delete
 
getRecordAdditionalAttachments() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
getRecordType() - Method in interface org.biojava.bio.structure.AminoAcid
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
getRecordType() - Method in class org.biojava.bio.structure.AminoAcidImpl
 
getRecordUnidentifiableCompounds() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
getReducedStructure(Structure, String) - Static method in class org.biojava.bio.structure.StructureTools
Reduce a structure to provide a smaller representation .
getReducedStructure(Structure, int) - Static method in class org.biojava.bio.structure.StructureTools
Reduce a structure to provide a smaller representation.
getRef() - Method in class org.biojava.bio.structure.JournalArticle
Get the value of REF field.
getRef() - Method in class org.forester.phylogeny.data.Annotation
 
getRef() - Method in class org.forester.phylogeny.data.Property
 
getRef_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getRefChainId() - Method in class org.biojava.bio.structure.Compound
Returns the ref chain id value.
getReference() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getReference() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
To get a type of reference for the webservice (an URL or citation, for example).
getReference() - Method in class org.forester.phylogeny.data.NodeData
 
getRefn() - Method in class org.biojava.bio.structure.JournalArticle
Get the value of REFN field.
getRegistryInfo() - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
getRelevantSubLocations() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
Returns the normalised list of sub locations i.e.
getRelevantSubLocations() - Method in interface org.biojava3.core.sequence.location.template.Location
An extension to Location.getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
getRelevantSubSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava3.core.sequence.location.template.Location
Will return a SequenceReader object which offers a view of all resolved locations i.e.
getRemoteBlastInfo() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
A simple method to check the availability of the QBlast service.
getRenderingFactorWidth() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getRenderingSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getRenderingSize() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
 
getReplaced(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
if ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.
getReplaced(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
getReplacement(String, boolean, boolean) - Static method in class org.biojava.bio.structure.PDBStatus
Gets the PDB which superseded oldPdbId.
getReplacer(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
if ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.
getReplacer(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
getReplaces() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
getReplaces(String, boolean) - Static method in class org.biojava.bio.structure.PDBStatus
Get the ID of the protein which was made obsolete by newPdbId.
getRepresentativeDomains() - Method in interface org.biojava.bio.structure.domain.DomainProvider
 
getRepresentativeDomains() - Method in class org.biojava.bio.structure.domain.RemoteDomainProvider
 
getRepresentatives(String, int) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getResidId() - Method in interface org.biojava3.protmod.ProteinModification
 
getResidId() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getResidName() - Method in interface org.biojava3.protmod.ProteinModification
 
getResidName() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getResidue(byte) - Static method in class org.forester.development.AminoAcid
 
getResidueAt(int) - Method in class org.forester.development.AminoAcidSequence
 
getResidueAt(int, int) - Method in class org.forester.development.BasicMsa
 
getResidueAt(int, int) - Method in interface org.forester.development.Msa
 
getResidueAt(int) - Method in interface org.forester.development.Sequence
 
getResidueAt(int, int) - Method in class org.forester.development.SimpleMutableMsa
 
getResidueName() - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
getResidueNumber() - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
getResidueNumber() - Method in interface org.biojava.bio.structure.Group
returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueNumber() - Method in class org.biojava.bio.structure.HetatomImpl
returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
getResidueNumber() - Method in class org.biojava3.protmod.structure.StructureGroup
 
getResidues() - Method in class org.biojava.bio.structure.io.FastaStructureParser
For each residue in the fasta file, return the ResidueNumber in the corresponding structure.
getResidues() - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
getResidueType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getResidueTypeFromString(String) - Static method in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
 
getResNames() - Method in class org.biojava.bio.structure.Compound
 
getResnum1() - Method in class org.biojava.bio.structure.SSBond
get residue number for first CYS.
getResnum2() - Method in class org.biojava.bio.structure.SSBond
get residue number for second CYS.
getResolution() - Method in class org.biojava.bio.structure.PDBHeader
 
getResolver() - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
getResourceManager(String) - Static method in class org.biojava.bio.structure.align.util.ResourceManager
 
getResScore() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getReturnFormat() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getReturnFormat() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
The expected format of the response.
getReverse() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
getReverse() - Method in class org.biojava3.core.sequence.DNASequence
Returns a Sequence which runs in the current reverse order
getReverse() - Method in enum org.biojava3.core.sequence.Strand
 
getReverseComplement() - Method in class org.biojava3.core.sequence.DNASequence
Delegates to AbstractSequence.getInverse() for the reverse complement
getReverseComplement() - Method in class org.biojava3.core.sequence.RNASequence
Get reverse complement view of the sequence
getReverseFrames() - Static method in enum org.biojava3.core.sequence.transcription.Frame
Returns all frames which are in the reverse orientation
getRms() - Method in class org.biojava.bio.structure.align.helper.JointFragments
 
getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
get the RMS of the JointFragments pair frag
getRms() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getRMS(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.SVDSuperimposer
Calculate the RMS (root mean square) deviation of two sets of atoms.
getRmsd() - Method in class org.biojava.bio.structure.align.model.AFP
 
getRmsd() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
getRmsdCut() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
The cutoff to be used during AFP detection
getRmsdThr() - Method in class org.biojava.bio.structure.align.ce.CeParameters
RMSD Threshold
getRmsdThrJoin() - Method in class org.biojava.bio.structure.align.ce.CeParameters
RMSD threshold for joining of AFPs
getRnaAminoAcidTranslator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getRnaCompounds() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getRNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.RNACompoundSet
 
getRNASequence() - Method in class org.biojava3.core.sequence.DNASequence
Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
getRNASequence(TranscriptionEngine) - Method in class org.biojava3.core.sequence.DNASequence
Allow a user to pass in a rules engine to do the DNA to RNA translation
getRNASequence(Frame) - Method in class org.biojava3.core.sequence.DNASequence
Allows the user to pass in the Frame shift.
getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava3.core.sequence.DNASequence
 
getRnaSequenceCreator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getRnaToDna() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
getRoot() - Method in class org.biojava3.alignment.GuideTree
Returns the root GuideTree.Node which corresponds to the full multiple sequence alignment.
getRoot() - Method in interface org.biojava3.alignment.template.HierarchicalClusterer
Returns the root node of the tree resulting from this clustering algorithm.
getRoot() - Method in class org.forester.phylogeny.Phylogeny
Returns the root PhylogenyNode of this Phylogeny.
getRot() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getRotation() - Method in class org.biojava.bio.structure.SVDSuperimposer
Get the Rotation matrix that is required to superimpose the two atom sets.
getRotationMatrix() - Method in class org.biojava.bio.structure.align.ce.CECalculator
Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
Gets the rotation matrix from the last call to calc_rmsd.
getRotationMatrix() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
getRow() - Method in class org.biojava.bio.structure.align.helper.IndexPair
 
getRowDimension() - Method in class org.biojava.bio.structure.jama.Matrix
Get row dimension.
getRowIdentifiers() - Method in class org.forester.util.GeneralTable
 
getRowPackedCopy() - Method in class org.biojava.bio.structure.jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getRows() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getRows() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getRows() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getS() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getSaturation() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
Deprecated.
getSaturation() - Method in class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
 
getSaveAlignmentMenuItem(AFPChain) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getSaveOutputDir() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getScale() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
getScale() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
getScale() - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
getScale() - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
getScale() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
getScalevalue() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
Deprecated.
getScalevalue() - Method in class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
 
getScientificName() - Method in class org.forester.phylogeny.data.Taxonomy
 
getSCOP() - Method in class org.biojava.bio.structure.gui.util.ScopInstallationInstance
 
getSCOP() - Static method in class org.biojava.bio.structure.scop.ScopFactory
 
getScopDescription() - Method in class org.biojava.bio.structure.scop.server.ScopDescriptions
 
getScopDescriptionBySunid(int) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getScopDescriptionBySunid(int) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getScopDescriptionBySunid(int) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Return the SCOP description for a node in the hierarchy by its "sunid" id.
getScopDescriptionBySunid(int) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getScopDescriptionFromXML(String) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopDescriptionsXML(List<ScopDescription>) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopDescriptionXML(ScopDescription) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopDomain() - Method in class org.biojava.bio.structure.scop.server.ScopDomains
 
getScopDomainFromXML(String) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopDomainsBySunid(Integer) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getScopDomainsBySunid(Integer) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getScopDomainsBySunid(Integer) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Get a SCOP domain by its sunid
getScopDomainsBySunid(Integer) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getScopDomainsXML(List<ScopDomain>) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopDomainXML(ScopDomain) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopDownloadURL() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getScopId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getScopInstallation() - Method in class org.biojava.bio.structure.align.util.AtomCache
 
getScopNode(int) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getScopNode(int) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getScopNode(int) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Access a particular ScopNode.
getScopNode(int) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getScopNode() - Method in class org.biojava.bio.structure.scop.server.ScopNodes
 
getScopNodeFromXML(String) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopNodesXML(List<ScopNode>) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopNodeXML(ScopNode) - Static method in class org.biojava.bio.structure.scop.server.XMLUtil
 
getScopSelectPanel() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
getScopVersion() - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getScopVersion() - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getScopVersion() - Method in interface org.biojava.bio.structure.scop.ScopDatabase
Returns the SCOP version
getScopVersion() - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getScore() - Method in class org.biojava.bio.structure.align.model.AFP
 
getScore() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
getScore() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
the alignment score
getScore() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
getScore() - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
getScore() - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
getScore() - Method in class org.biojava3.alignment.FractionalIdentityScorer
 
getScore() - Method in class org.biojava3.alignment.FractionalSimilarityScorer
 
getScore() - Method in class org.biojava3.alignment.StandardRescoreRefiner
 
getScore() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getScore() - Method in interface org.biojava3.alignment.template.Scorer
Returns score resulting from algorithm.
getScore() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
getScore() - Method in class org.forester.development.SimpleMutableMsa
 
getScore() - Method in interface org.forester.pccx.Coverage
 
getScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
getScoreMatrix() - Method in class org.biojava3.alignment.GuideTree
Returns the similarity matrix used to construct this guide tree.
getScoreMatrix() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getScoreMatrix() - Method in interface org.biojava3.alignment.template.MatrixAligner
Returns the entire score matrix built during alignment.
getScoreMatrix(String) - Static method in class org.biojava3.phylo.ResidueProperties
get a ScoreMatrix based on its string name
getScoreMatrixAsString() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getScoreMatrixAsString() - Method in interface org.biojava3.alignment.template.MatrixAligner
Returns a depiction of the score matrix as a String.
getScoreMatrixDimensions() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getScoreMatrixDimensions() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getScoreMatrixDimensions() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getScores(File) - Method in class org.biojava3.ronn.ORonnModel
 
getScoringMethod() - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions
 
getScoringStrategy() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getSD() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
 
getSearchParameter() - Method in class org.forester.surfacing.SimpleDomain
 
getSecondNode() - Method in interface org.forester.phylogeny.Edge
 
getSecondNode() - Method in class org.forester.phylogeny.PhylogenyBranch
 
getSecretion() - Method in class org.biojava.bio.structure.Compound
 
getSecStruc() - Method in interface org.biojava.bio.structure.AminoAcid
get secondary structure data .
getSecStruc() - Method in class org.biojava.bio.structure.AminoAcidImpl
get secondary structure data .
getSeedFragmentLength() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getSeedRmsdCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getSegId() - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
getSegmentAtPos(int) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
getSegments() - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
getSegments() - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
getSelectedAlignmentPos() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
getSelectedAlignmentPos() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
getSelection() - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
getSelection() - Method in interface org.biojava3.structure.gui.Selection
 
getSelection() - Method in class org.biojava3.structure.gui.SelectionImpl
 
getSelection() - Method in interface org.biojava3.structure.gui.StructureViewer
 
getSelectPDBPanel() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
getSeparatorSequence() - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
 
getSeq_align_beg() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getSeq_align_end() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
getSeq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
getSeq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
getSeqBegin() - Method in class org.biojava.bio.structure.DBRef
Initial sequence number of the PDB sequence segment.
getSeqEnd() - Method in class org.biojava.bio.structure.DBRef
Ending sequence number of the PDB sequence segment.
getSeqeunceFromString(String) - Method in class org.biojava3.core.util.SequenceTools
 
getSeqNum() - Method in class org.biojava.bio.structure.ResidueNumber
 
getSeqPos(int, Point) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
Convert from a X position in the JPanel to alignment position
getSeqPos(int) - Method in class org.biojava.bio.structure.gui.util.CoordManager
start counting at 0...
getSeqResGroup(int) - Method in interface org.biojava.bio.structure.Chain
return the Group at position X.
getSeqResGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
return the Group at position X.
getSeqResGroups(String) - Method in interface org.biojava.bio.structure.Chain
Return a List of all groups of a special type (e.g.
getSeqResGroups() - Method in interface org.biojava.bio.structure.Chain
Return all groups of this chain.
getSeqResGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
Return a List of all groups of a special type (e.g.
getSeqResGroups() - Method in class org.biojava.bio.structure.ChainImpl
Return all groups of this chain.
getSeqResLength() - Method in interface org.biojava.bio.structure.Chain
Returns the number of groups in the SEQRES records of the chain.
getSeqResLength() - Method in class org.biojava.bio.structure.ChainImpl
 
getSeqResName() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getSeqResSequence() - Method in interface org.biojava.bio.structure.Chain
Get the sequence for all amino acids as it is specified in the SEQRES residues.
getSeqResSequence() - Method in class org.biojava.bio.structure.ChainImpl
Get the sequence for all amino acids as it is specified in the SEQRES residues.
getSequence() - Method in interface org.biojava.bio.structure.Chain
Deprecated.
use getAtomSequence instead
getSequence() - Method in class org.biojava.bio.structure.ChainImpl
Deprecated.
use getAtomSequence instead
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
 
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
 
getSequence(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
Assumes all compounds were uppercase
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.DNASequenceCreator
 
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava3.core.sequence.io.DNASequenceCreator
 
getSequence(List<NucleotideCompound>) - Method in class org.biojava3.core.sequence.io.DNASequenceCreator
 
getSequence(DataInput, int) - Method in class org.biojava3.core.sequence.io.FastaSequenceParser
 
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator
Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator
Should be able to extend the same concept to a remote URL call or database connection.
getSequence(List<NucleotideCompound>) - Method in class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator
Not sure of use case and currently not supported
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator
Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator
Should be able to extend the same concept to a remote URL call or database connection.
getSequence(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator
Not sure of use case and currently not supported
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.ProteinSequenceCreator
 
getSequence(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.ProteinSequenceCreator
 
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava3.core.sequence.io.ProteinSequenceCreator
 
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.RNASequenceCreator
 
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava3.core.sequence.io.RNASequenceCreator
 
getSequence(List<NucleotideCompound>) - Method in class org.biojava3.core.sequence.io.RNASequenceCreator
 
getSequence(String, long) - Method in interface org.biojava3.core.sequence.io.template.SequenceCreatorInterface
 
getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava3.core.sequence.io.template.SequenceCreatorInterface
 
getSequence(List<C>) - Method in interface org.biojava3.core.sequence.io.template.SequenceCreatorInterface
 
getSequence(DataInput, int) - Method in interface org.biojava3.core.sequence.io.template.SequenceParserInterface
 
getSequence() - Method in class org.biojava3.core.sequence.location.SequenceLocation
 
getSequence() - Method in class org.biojava3.data.sequence.FastaSequence
Gets the value of sequence
getSequence() - Method in class org.biojava3.sequencing.io.fastq.Fastq
Return the sequence for this FASTQ formatted sequence.
getSequence(int) - Method in class org.forester.development.BasicMsa
 
getSequence(int) - Method in interface org.forester.development.Msa
 
getSequence(int) - Method in class org.forester.development.SimpleMutableMsa
 
getSequence() - Method in class org.forester.phylogeny.data.NodeData
 
getSequence5PrimeTo3Prime() - Method in class org.biojava3.core.sequence.GeneSequence
Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand
getSequenceAsString() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns the sequence as a String
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.storage.SequenceAsStringHelper
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Delegates to SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.template.AbstractSequence
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
getSequenceAsString() - Method in interface org.biojava3.core.sequence.template.Sequence
Returns the String representation of the Sequence
getSequenceAsString() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.views.ReversedSequenceView
 
getSequenceAsString() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
getSequenceAsString() - Method in class org.forester.development.AminoAcidSequence
 
getSequenceAsString() - Method in interface org.forester.development.Sequence
 
getSequenceCollection() - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
 
getSequenceIndexAt(int) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getSequenceIndexAt(int) - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the index in the original Sequence corresponding to the given index within an alignment.
getSequences() - Method in class org.biojava.bio.structure.io.FastaStructureParser
Gets the protein sequences read from the Fasta file.
getSequences() - Method in class org.biojava3.alignment.GuideTree
Returns the Sequences which make up the leaves of this tree.
getSequenceScore() - Method in class org.biojava3.core.sequence.template.AbstractSequence
Provide place holder for a metric that indicate a score associated with the sequence
getSequenceUsage() - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
 
getSeqWeight() - Method in class org.biojava.bio.structure.align.ce.CeParameters
Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
getSerNum() - Method in class org.biojava.bio.structure.SSBond
set serial number of this SSBOND in PDB file
getServer() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
getServer() - Method in class org.biojava.bio.structure.domain.RemotePDPProvider
 
getServer() - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getSharedBinaryCombinationsBasedDistances() - Method in class org.forester.surfacing.PairwiseGenomeComparator
 
getSharedBinaryDomainCombinations() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
getSharedDomains() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
getSharedDomainsBasedDistances() - Method in class org.forester.surfacing.PairwiseGenomeComparator
 
getShift() - Method in class org.biojava.bio.structure.align.ce.CECalculator
Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
Gets the shift from the last call to calc_rmsd.
getShift() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
returns the shift vector that has to be applied on structure to to shift on structure one
getShorName() - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
getShortDescription() - Method in class org.biojava3.core.sequence.features.AbstractFeature
 
getShortDescription() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Get the short description that can be used to describe the feature
getShortName() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getShortName() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
getShortName() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
getShortName() - Method in interface org.biojava3.core.sequence.template.Compound
 
getShortName() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
getShortName() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getShowDBresult() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
getShowPDBMenuItem() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
getSiftsMapping(String) - Static method in class org.biojava.bio.structure.io.sifts.SiftsMappingProvider
 
getSimCount() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getSimilarity() - Method in class org.biojava.bio.structure.align.model.AFPChain
Returns the similarity score for the alignment.
getSimilarity() - Method in class org.biojava3.alignment.template.AbstractScorer
 
getSimilarity(double) - Method in class org.biojava3.alignment.template.AbstractScorer
 
getSimilarity() - Method in interface org.biojava3.alignment.template.Scorer
Returns score as a similarity between 0.0 and 1.0.
getSimilarity(double) - Method in interface org.biojava3.alignment.template.Scorer
Returns score as a similarity between 0.0 and scale.
getSimilarity1() - Method in class org.biojava.bio.structure.align.model.AFPChain
Deprecated.
use getCoverage1() instead
getSimilarity2() - Method in class org.biojava.bio.structure.align.model.AFPChain
Deprecated.
use getCoverage2() instead
getSimilarityScore() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
 
getSimilarityScore() - Method in class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity
 
getSimilarityScore() - Method in interface org.forester.surfacing.PairwiseDomainSimilarity
 
getSingularValues() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSiteID() - Method in class org.biojava.bio.structure.Site
 
getSites() - Method in interface org.biojava.bio.structure.Structure
 
getSites() - Method in class org.biojava.bio.structure.StructureImpl
 
getSize() - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
getSize() - Method in class org.biojava3.alignment.SimpleProfile
 
getSize() - Method in interface org.biojava3.alignment.template.Profile
Returns the number of rows in this profile.
getSize() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Get the number of sequences in the MSA
getSize() - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns the number of rows in this profile.
getSize() - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
getSize() - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
getSize() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getSize() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
getSmallFont() - Method in class org.forester.archaeopteryx.TreeFontSet
 
getSolvent_model_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getSolvent_model_param_bsol() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getSolvent_model_param_ksol() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
getSource() - Method in class org.biojava3.core.sequence.features.AbstractFeature
The feature source
getSource() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
The source of the feature.
getSource() - Method in class org.biojava3.core.sequence.template.AbstractSequence
Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source
getSource() - Method in class org.forester.phylogeny.data.Accession
 
getSource() - Method in class org.forester.phylogeny.data.Annotation
 
getSpaceGroup() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getSparse() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getSpeciationOrDuplicationEventsSum() - Method in class org.forester.sdi.GSDI
 
getSpeciationsSum() - Method in class org.forester.sdi.GSDI
 
getSpecies(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method for display purposes.
getSpecies() - Method in class org.forester.surfacing.BasicCombinableDomains
 
getSpecies() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
getSpecies() - Method in class org.forester.surfacing.BasicProtein
 
getSpecies() - Method in interface org.forester.surfacing.CombinableDomains
Returns the species of this combinable domains.
getSpecies() - Method in class org.forester.surfacing.DomainLengthsTable
 
getSpecies() - Method in interface org.forester.surfacing.DomainSimilarity
 
getSpecies() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
getSpecies() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getSpecies() - Method in interface org.forester.surfacing.Protein
 
getSpeciesCustomOrder() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getSpeciesData() - Method in interface org.forester.surfacing.DomainSimilarity
This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData
getSpeciesData() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getSpeciesId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getSpeciesId() - Method in class org.forester.surfacing.BasicSpecies
 
getSpeciesId() - Method in interface org.forester.surfacing.Species
 
getSpeciesList() - Method in class org.forester.surfacing.DomainLengths
 
getSpeciesTree() - Method in class org.forester.sdi.SDI
Returns the species tree.
getSqFrom() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getSqTo() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
getSrc_method() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getSSBonds() - Method in interface org.biojava.bio.structure.Structure
get the list of SSBonds as they have been defined in the PDB files
getSSBonds() - Method in class org.biojava.bio.structure.StructureImpl
get the list of SSBonds as they have been defined in the PDB files
getStandardDeviation() - Method in class org.forester.sdi.DistanceCalculator
Returns the standard deviation.
getStandardDeviationOfSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
 
getStandardDeviationOfSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
getStart() - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
getStart() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getStart() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns the Point within an alignment of the first element of the original Sequence.
getStart() - Method in interface org.biojava3.alignment.template.ProfileView
Returns the column index of the viewed Profile corresponding to the first element in this view
getStart() - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
getStart() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getStart() - Method in interface org.biojava3.core.sequence.location.template.Location
Start of the location
getStartCodonSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence
 
getStartPage() - Method in class org.biojava.bio.structure.JournalArticle
 
getStartTimestamp() - Method in class org.biojava3.ws.alignment.qblast.BlastJob
 
getState(char) - Static method in class org.forester.development.AminoAcid
 
getState(int, int) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getState(String, int) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getState(String, String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
getState(int, int) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getState(String, int) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getState(String, String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
getStateAt(int) - Method in class org.forester.development.AminoAcidSequence
 
getStatus() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
getStatus(String) - Static method in class org.biojava.bio.structure.PDBStatus
Get the status of the PDB in question.
getStatus(String[]) - Static method in class org.biojava.bio.structure.PDBStatus
Get the status of the a collection of PDBs in question in a single query.
getStatusListener() - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
getStepSize() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
how many pairs should be requested for alignment from server?
getStopCodonSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence
 
getStoreEmptySeqRes() - Method in class org.biojava.bio.structure.io.FileParsingParameters
a flag to detrermine if SEQRES should be stored, even if alignSeqREs is disabled.
getStrain() - Method in class org.biojava.bio.structure.Compound
 
getStrand() - Method in class org.biojava3.core.sequence.CDSSequence
 
getStrand() - Method in class org.biojava3.core.sequence.GeneSequence
A gene should have Strand
getStrand() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getStrand() - Method in interface org.biojava3.core.sequence.location.template.Location
Strand which the location is located on
getStrand() - Method in class org.biojava3.core.sequence.TranscriptSequence
 
getString(String) - Method in class org.biojava.bio.structure.align.util.ResourceManager
 
getStringForCompound(AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
getStringForCompound(AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
getStringForCompound(AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
getStringForCompound(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
getStringForCompound(C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
getStringRepresentation() - Method in enum org.biojava3.core.sequence.Strand
 
getStructure() - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
getStructure(String) - Method in class org.biojava.bio.structure.align.util.AtomCache
Request a Structure based on a name.
getStructure() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
This method will return the parsed protein structure, once the parsing has been finished
getStructure(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
Opens filename, parses it and returns a Structure object .
getStructure(File) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
Opens filename, parses it and returns a Structure object.
getStructure(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
opens filename, parses it and returns aStructure object .
getStructure(File) - Method in class org.biojava.bio.structure.io.PDBFileReader
opens filename, parses it and returns a Structure object
getStructure(URL) - Method in class org.biojava.bio.structure.io.PDBFileReader
 
getStructure(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
open filename and returns a Structure object.
getStructure(File) - Method in interface org.biojava.bio.structure.io.StructureIOFile
read file from File and returns a Structure object.
getStructure(String) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
getStructure(String) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
getStructure(String) - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
request a structure by its PDB identifier
getStructure() - Method in interface org.biojava.bio.structure.server.StructureEvent
 
getStructure() - Method in class org.biojava.bio.structure.server.StructureEventImpl
 
getStructure1() - Method in class org.biojava.bio.structure.align.gui.SelectPDBPanel
 
getStructure1() - Method in class org.biojava.bio.structure.gui.util.PDBDirPanel
 
getStructure1() - Method in class org.biojava.bio.structure.gui.util.PDBServerPanel
 
getStructure1() - Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
getStructure1() - Method in class org.biojava.bio.structure.gui.util.ScopSelectPanel
 
getStructure1() - Method in interface org.biojava.bio.structure.gui.util.StructurePairSelector
 
getStructure2() - Method in class org.biojava.bio.structure.align.gui.SelectPDBPanel
 
getStructure2() - Method in class org.biojava.bio.structure.gui.util.PDBDirPanel
 
getStructure2() - Method in class org.biojava.bio.structure.gui.util.PDBServerPanel
 
getStructure2() - Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
getStructure2() - Method in class org.biojava.bio.structure.gui.util.ScopSelectPanel
 
getStructure2() - Method in interface org.biojava.bio.structure.gui.util.StructurePairSelector
 
getStructureAlignment() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
getStructureAlignment() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
getStructureAtom(Atom, boolean) - Static method in class org.biojava3.protmod.structure.StructureUtil
 
getStructureAtomLinkage(Atom, boolean, Atom, boolean) - Static method in class org.biojava3.protmod.structure.StructureUtil
 
getStructureById(String) - Method in class org.biojava.bio.structure.io.LocalCacheStructureProvider
 
getStructureById(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
Get a structure by PDB code.
getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
load a structure from local file system and return a PDBStructure object
getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBSRSReader
load a structure from from SRS installation using wgetz returns null if no structure found
getStructureById(String) - Method in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
 
getStructureById(String) - Method in interface org.biojava.bio.structure.io.StructureIO
Get a structure by providing a PDB code.
getStructureById(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
Get a Structure based on its PDB id.
getStructureById(String) - Method in interface org.biojava.bio.structure.io.StructureProvider
get the structure for a PDB ID
getStructureForDomain(ScopDomain) - Method in class org.biojava.bio.structure.align.util.AtomCache
Returns the representation of a ScopDomain as a BioJava Structure object
getStructureGroup(Group, boolean) - Static method in class org.biojava3.protmod.structure.StructureUtil
 
getStructureListeners() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
Deprecated.
 
getStructurePairAligner() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
getStructures() - Method in class org.biojava.bio.structure.io.FastaStructureParser
Gets the protein structures mapped from the Fasta file.
getStudyFamily() - Method in class org.forester.go.etc.OntologizerResult
 
getStudyTerm() - Method in class org.forester.go.etc.OntologizerResult
 
getStudyTotal() - Method in class org.forester.go.etc.OntologizerResult
 
getSubLocations() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
getSubLocations() - Method in interface org.biojava3.core.sequence.location.template.Location
Gives access to the sub locations for this location.
getSubProfile(Location) - Method in class org.biojava3.alignment.SimpleProfile
 
getSubProfile(Location) - Method in interface org.biojava3.alignment.template.Profile
Returns a ProfileView windowed to contain only the given Location.
getSubRanges(Structure, String) - Static method in class org.biojava.bio.structure.StructureTools
In addition to the functionality provided by getReducedStructure also provides a way to specify sub-regions of a structure with the following specification: ranges can be surrounded by ( and ).
getSubSequence(Integer, Integer) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
getSubSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
If circular this will return the sequence represented by the sub locations joined.
getSubSequence(Sequence<C>) - Method in interface org.biojava3.core.sequence.location.template.Location
Will return a SequenceReader object which represents the outer bounds of this Location
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
getSubSequence(int, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Returns a sub sequence view
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Creates a SequenceProxyView for the given coordinates
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getSubSequence(Integer, Integer) - Method in interface org.biojava3.core.sequence.template.Sequence
Returns a portion of the sequence from the different positions.
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getSubstitutionMatrix() - Method in class org.biojava.bio.structure.align.ce.CeParameters
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
getSubstitutionMatrix() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Returns the substitution matrix.
getSubstitutionScore(int, int) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getSubstitutionScore(int, int) - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getSubstitutionScore(int, int) - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getSubstitutionScoreVector(int) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getSubstitutionScoreVector(int, int[]) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
getSuggestion(String) - Method in interface org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider
get a list of suggestions for a userInput
getSuggestion(String) - Method in class org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
getSuggestion(String) - Method in class org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
getSum() - Method in class org.forester.util.BasicDescriptiveStatistics
 
getSum() - Method in interface org.forester.util.DescriptiveStatistics
 
getSummaryAsString() - Method in class org.forester.util.BasicDescriptiveStatistics
 
getSummaryAsString() - Method in interface org.forester.util.DescriptiveStatistics
 
getSummaryPos() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
 
getSumOfFailures() - Method in class org.forester.surfacing.MappingResults
 
getSumOfGainsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getSumOfLossesOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getSumOfPresentOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getSumOfSuccesses() - Method in class org.forester.surfacing.MappingResults
 
getSunID() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
getSunid() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getSunid() - Method in class org.biojava.bio.structure.scop.ScopNode
 
getSuperfamilyId() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
getSuperGoIds() - Method in class org.forester.go.BasicGoTerm
 
getSuperGoIds() - Method in interface org.forester.go.GoTerm
 
getSuperOrthologousNodes(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Returns all Nodes which are connected to external PhylogenyNode n of this Phylogeny by a path containing only speciation events.
getSuperOrthologs() - Method in class org.forester.sdi.RIOn
 
getSurname() - Method in class org.biojava.bio.structure.Author
 
getSwissprotId() - Method in interface org.biojava.bio.structure.Chain
Get the Swissprot id of this chain.
getSwissprotId() - Method in class org.biojava.bio.structure.ChainImpl
get the Swissprot id of this chains .
getSymbol() - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
getSymbol() - Method in class org.forester.phylogeny.data.Sequence
 
getSymbolSet() - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Helper for AlignmentTools.getSymmetryOrder(Map, Map, int, float) with a true identity function (X->X).
getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Tries to detect symmetry in an alignment.
getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Guesses the order of symmetry in an alignment
getSynonyms() - Method in class org.biojava.bio.structure.Compound
 
getSynonyms() - Method in class org.forester.phylogeny.data.Taxonomy
 
getSynthetic() - Method in class org.biojava.bio.structure.Compound
 
getSystematicName() - Method in interface org.biojava3.protmod.ProteinModification
 
getSystematicName() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
getT() - Method in class org.biojava.bio.structure.align.model.AFP
 
getTable(String) - Method in class org.biojava3.core.sequence.io.IUPACParser
Returns a table by its name
getTable(Integer) - Method in class org.biojava3.core.sequence.io.IUPACParser
Returns a table by its identifier i.e.
getTable() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
 
getTables() - Method in class org.biojava3.core.sequence.io.IUPACParser
Returns a list of all available IUPAC tables
getTabPane() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
getTarget() - Method in class org.biojava3.alignment.FractionalIdentityScorer
 
getTarget() - Method in class org.biojava3.alignment.FractionalSimilarityScorer
 
getTarget() - Method in class org.biojava3.alignment.SimpleProfilePair
 
getTarget() - Method in class org.biojava3.alignment.SimpleSequencePair
 
getTarget() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
getTarget() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
getTarget() - Method in interface org.biojava3.alignment.template.PairwiseSequenceScorer
Returns the second sequence of the pair.
getTarget() - Method in interface org.biojava3.alignment.template.ProfilePair
Returns the second Profile of the pair.
getTarget() - Method in interface org.biojava3.alignment.template.ProfileProfileScorer
Returns the second profile of the pair.
getTarget() - Method in interface org.biojava3.alignment.template.SequencePair
Returns the second AlignedSequence of the pair.
getTargetIndex(int) - Method in class org.biojava3.alignment.routines.AlignerHelper.Cut
 
getTargetSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
Returns the Sequence which is our edit.
getTaxonomy() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
getTaxonomy() - Method in class org.forester.phylogeny.data.NodeData
 
getTaxonomyCode() - Method in class org.forester.phylogeny.data.Taxonomy
 
getTaxonomyExtraction() - Method in class org.forester.io.parsers.nhx.NHXParser
 
getTaxonomyIdentifier(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method for display purposes.
getTechnique() - Method in class org.biojava.bio.structure.PDBHeader
 
getTempFactor() - Method in interface org.biojava.bio.structure.Atom
get set temp factor.
getTempFactor() - Method in class org.biojava.bio.structure.AtomImpl
 
getText() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
 
getText() - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
getThreadPool() - Static method in class org.biojava3.core.util.ConcurrencyTools
Returns current shared thread pool.
getThreads() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
getThree() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getThree() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
getThree() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getThree_letter_code() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getThreePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
Should return the 3-prime end of the given Sequence according to the edit.
getThreePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Delete
 
getThreePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Insert
 
getThreePrime(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Substitute
 
getTime() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
getTime() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
getTime() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
getTime() - Method in class org.forester.sdi.RIO
Returns the time (in ms) needed to run "inferOrthologs".
getTimeout() - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
getTimeStamp() - Method in class org.biojava.bio.structure.io.PDBFileParser
Returns a time stamp.
getTimeSumSDI() - Method in class org.forester.sdi.SDIR
Returns the sum of times (in ms) needed to run method infer of class SDI.
getTissue() - Method in class org.biojava.bio.structure.Compound
 
getTitle() - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
getTitle() - Method in class org.biojava.bio.structure.Compound
 
getTitle() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
getTitle() - Method in class org.biojava.bio.structure.JournalArticle
Get the value of title
getTitle() - Method in class org.biojava.bio.structure.PDBHeader
 
getTMScore() - Method in class org.biojava.bio.structure.align.model.AFPChain
Returns the tmScore of the alignment.
getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPChainScorer
 
getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.bio.structure.SVDSuperimposer
Calculate the TM-Score for the superposition.
getTo() - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
getTo() - Method in class org.forester.phylogeny.data.ProteinDomain
 
getTo() - Method in class org.forester.surfacing.BasicDomain
 
getTo() - Method in interface org.forester.surfacing.Domain
 
getTo() - Method in class org.forester.surfacing.SimpleDomain
 
getToCompoundSet() - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
getTool() - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Get the tool identifier for QBlast.
getTorsionPenalty() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getTotalCount() - Method in class org.forester.surfacing.BasicDomain
 
getTotalCount() - Method in interface org.forester.surfacing.Domain
 
getTotalCount() - Method in class org.forester.surfacing.SimpleDomain
 
getTotalGains() - Method in class org.forester.phylogenyinference.DolloParsimony
 
getTotalGains() - Method in class org.forester.phylogenyinference.FitchParsimony
 
getTotalGains() - Method in class org.forester.phylogenyinference.SankoffParsimony
 
getTotalGains() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getTotalLength() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
getTotalLength() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
getTotalLenIni() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getTotalLenOpt() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getTotalLosses() - Method in class org.forester.phylogenyinference.DolloParsimony
 
getTotalLosses() - Method in class org.forester.phylogenyinference.FitchParsimony
 
getTotalLosses() - Method in class org.forester.phylogenyinference.SankoffParsimony
 
getTotalLosses() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getTotalRmsdIni() - Method in class org.biojava.bio.structure.align.model.AFPChain
this is the init-RMSD, not the final RMSD after refinement.
getTotalRmsdOpt() - Method in class org.biojava.bio.structure.align.model.AFPChain
The RMSD of the final alignment.
getTotalUnchanged() - Method in class org.forester.phylogenyinference.DolloParsimony
 
getTotalUnchanged() - Method in class org.forester.phylogenyinference.FitchParsimony
 
getTotalUnchanged() - Method in class org.forester.phylogenyinference.SankoffParsimony
 
getTotalUnchanged() - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getTraceFlag() - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
getTrans() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getTranscript(String) - Method in class org.biojava3.core.sequence.GeneSequence
Get the transcript sequence by accession
getTranscripts() - Method in class org.biojava3.core.sequence.GeneSequence
Get the collection of transcription sequences assigned to this gene
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getTransition(ProteinSequence) - Method in interface org.biojava3.aaproperties.profeat.IProfeatProperties
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getTransition(ProteinSequence) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getTransition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getTransition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getTransition(String) - Static method in class org.biojava3.aaproperties.profeat.ProfeatProperties
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getTransition(ProteinSequence) - Method in class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.util.AFPAlignmentDisplay
 
getTranslation() - Method in class org.biojava.bio.structure.SVDSuperimposer
Get the shift vector.
getTree(ScopDomain) - Method in class org.biojava.bio.structure.scop.CachedRemoteScopInstallation
 
getTree(ScopDomain) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
getTree(ScopDomain) - Method in interface org.biojava.bio.structure.scop.ScopDatabase
get the SCOP sub-tree for a particular domain.
getTree(ScopDomain) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
getTreeFontSet() - Method in class org.forester.archaeopteryx.MainPanel
 
getTreshold(int) - Static method in enum org.biojava3.ronn.RonnConstraint.Threshold
 
getTriplet() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getTwi() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getTwistedGroups() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
getTwo() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
getTwo() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
getTwo() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
getType() - Method in class org.biojava.bio.structure.AminoAcidImpl
 
getType() - Method in class org.biojava.bio.structure.Bond
 
getType() - Method in interface org.biojava.bio.structure.Group
get Type of group, e.g.
getType() - Method in class org.biojava.bio.structure.HetatomImpl
Returns the type value.
getType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
getType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
getType() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
getType() - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
getType() - Method in class org.biojava.bio.structure.NucleotideImpl
 
getType() - Method in class org.biojava3.alignment.SimpleGapPenalty
 
getType() - Method in interface org.biojava3.alignment.template.GapPenalty
Returns GapPenalty.Type stored.
getType() - Method in class org.biojava3.core.sequence.features.AbstractFeature
The feature type
getType() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
The type of the feature.
getType() - Method in class org.forester.go.BasicGoRelationship
 
getType() - Method in class org.forester.go.BasicGoSubset
 
getType() - Method in class org.forester.go.BasicGoXRef
 
getType() - Method in class org.forester.go.etc.OntologizerResult
 
getType() - Method in class org.forester.go.GoNameSpace
 
getType() - Method in interface org.forester.go.GoRelationship
 
getType() - Method in interface org.forester.go.GoSubset
 
getType() - Method in interface org.forester.go.GoXRef
 
getType() - Method in class org.forester.phylogeny.data.Annotation
 
getType() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
getType() - Method in class org.forester.phylogeny.data.Confidence
 
getType() - Method in class org.forester.phylogeny.data.Sequence
 
getType() - Method in class org.forester.phylogeny.data.Uri
 
getType() - Method in class org.forester.phylogeny.Phylogeny
 
getType_symbol() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
getU() - Method in class org.biojava.bio.structure.jama.LUDecomposition
Return upper triangular factor
getU() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Return the left singular vectors
getUltimateGoTerm(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
 
getUltraParalogousNodes(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
Returns all Nodes which are connected to external PhylogenyNode n of this Phylogeny by a path containing, and leading to, only duplication events.
getUltraParalogs() - Method in class org.forester.sdi.RIOn
 
getUnderlyingCompound() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
getUnidentifiableAtomLinkages() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
getUnidentifiableModifiedResidues() - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
getUniProtAccessionId() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getUniprotbaseURL() - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
The current unirpot URL to deal with caching issues.
getUniprotDirectoryCache() - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
Local directory cache of XML that can be downloaded
getUniProtPos() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getUniProtResName() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
getUnit() - Method in class org.forester.phylogeny.data.Date
 
getUnit() - Method in class org.forester.phylogeny.data.Property
 
getUnitsGainedOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getUnitsLostOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getUnitsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
 
getUnitv() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getUpperedBase() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
getUri() - Method in class org.forester.phylogeny.data.Annotation
 
getUri() - Method in class org.forester.phylogeny.data.Sequence
 
getUri() - Method in class org.forester.phylogeny.data.Taxonomy
 
getUrl() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
getUrl() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
Use QUERY_PLACEHOLDER to indicate position of query variable.
getUrlString() - Method in class org.forester.archaeopteryx.ArchaeopteryxA
 
getUsed() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
getUsedAtomNames() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
getUserCollection() - Method in class org.biojava3.core.sequence.template.AbstractSequence
Provided for convience if the developer needs to associate data with a sequence
getUserConfigHelp() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getUserConfigHelp() - Method in interface org.biojava.bio.structure.align.ce.ConfigStrucAligParams
The help text for each of these parameters.
getUserConfigHelp() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
getUserConfigHelp() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigHelp() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigParameterNames() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getUserConfigParameterNames() - Method in interface org.biojava.bio.structure.align.ce.ConfigStrucAligParams
The labels to be displayed to the user for each parameter
getUserConfigParameterNames() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
getUserConfigParameterNames() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigParameterNames() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigParameters() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getUserConfigParameters() - Method in interface org.biojava.bio.structure.align.ce.ConfigStrucAligParams
get the list of parameters that the user can change through the user interface.
getUserConfigParameters() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
getUserConfigParameters() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigParameters() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
getUserConfigTypes() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
getUserConfigTypes() - Method in interface org.biojava.bio.structure.align.ce.ConfigStrucAligParams
Get the data types of the parameters
getUserConfigTypes() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
getUserConfigTypes() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
getUserConfigTypes() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
getUsername() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
getUserObject() - Method in class org.biojava3.core.sequence.features.AbstractFeature
 
getUserObject() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
 
getV() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Return the right singular vectors
getValenceElectronCount() - Method in enum org.biojava.bio.structure.Element
Returns the number of valence electrons for this Element.
getValue() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
 
getValue() - Method in class org.biojava.bio.structure.align.helper.GapArray
 
getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
getValue(C, C) - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
getValue(C, C) - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Returns value in matrix for conversion from first Compound to the second.
getValue() - Method in class org.biojava3.core.util.CRC64Checksum
 
getValue() - Method in interface org.forester.go.Mapping
 
getValue() - Method in class org.forester.go.PfamToGoMapping
 
getValue() - Method in class org.forester.phylogeny.data.Accession
 
getValue() - Method in class org.forester.phylogeny.data.BranchColor
 
getValue() - Method in class org.forester.phylogeny.data.BranchWidth
 
getValue() - Method in class org.forester.phylogeny.data.Confidence
 
getValue() - Method in class org.forester.phylogeny.data.Date
 
getValue() - Method in class org.forester.phylogeny.data.Identifier
 
getValue() - Method in class org.forester.phylogeny.data.Property
 
getValue() - Method in class org.forester.phylogeny.data.Reference
 
getValue() - Method in class org.forester.phylogeny.data.Uri
 
getValue(int, int) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
getValue(int, int) - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
getValue(int) - Method in class org.forester.util.BasicDescriptiveStatistics
 
getValue(int, int) - Method in class org.forester.util.BasicTable
 
getValue(int) - Method in interface org.forester.util.DescriptiveStatistics
 
getValue(IDENTIFIER_TYPE, IDENTIFIER_TYPE) - Method in class org.forester.util.GeneralTable
 
getValueAsBoolean() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getValueAsDouble() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getValueAsInt() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getValueAsString() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
getValueAsString(int, int) - Method in class org.forester.util.BasicTable
 
getValueAsString(IDENTIFIER_TYPE, IDENTIFIER_TYPE) - Method in class org.forester.util.GeneralTable
 
getValues() - Method in enum org.biojava3.ronn.RonnConstraint.Threshold
 
getVariance() - Method in class org.forester.sdi.DistanceCalculator
Returns the variance.
getVariant() - Method in class org.biojava.bio.structure.Compound
 
getVariant() - Method in class org.biojava3.sequencing.io.fastq.Fastq
Return the FASTQ sequence format variant for this FASTQ formatted sequence.
getVariant() - Method in class org.biojava3.sequencing.io.fastq.IlluminaFastqReader
Return the FASTQ sequence format variant for this reader.
getVariant() - Method in class org.biojava3.sequencing.io.fastq.SangerFastqReader
Return the FASTQ sequence format variant for this reader.
getVariant() - Method in class org.biojava3.sequencing.io.fastq.SolexaFastqReader
Return the FASTQ sequence format variant for this reader.
getVDWRadius() - Method in enum org.biojava.bio.structure.Element
Returns the van der Waals radius of this Element.
getVersion() - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
getVersion() - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
getVersion() - Method in class org.biojava.bio.structure.align.ce.CeCPMain
 
getVersion() - Method in class org.biojava.bio.structure.align.ce.CeMain
 
getVersion() - Method in class org.biojava.bio.structure.align.ce.CeSideChainMain
 
getVersion() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
getVersion() - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
getVersion() - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
getVersion() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
getVersion() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
getVersion() - Method in interface org.biojava.bio.structure.align.StructureAlignment
Get the Version information for this Algorithm.
getViewedProfile() - Method in interface org.biojava3.alignment.template.ProfileView
Returns the entire Profile being viewed
getViewedSequence() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
getViewedSequence() - Method in interface org.biojava3.core.sequence.template.SequenceView
 
getViewer() - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
getVolume() - Method in class org.biojava.bio.structure.JournalArticle
 
getWarningCount() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
getWarningCount() - Method in class org.forester.io.parsers.tol.TolParser
 
getWarningMessages() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
getWarningMessages() - Method in class org.forester.io.parsers.tol.TolParser
 
getWebStartConfig() - Static method in class org.biojava.bio.structure.align.webstart.WebStartMain
 
getWindowSize() - Method in class org.biojava3.core.sequence.views.WindowedSequence
Access the current window size
getWinSize() - Method in class org.biojava.bio.structure.align.ce.CeParameters
The window size to look at
getX() - Method in interface org.biojava.bio.structure.Atom
Get coordinate X.
getX() - Method in class org.biojava.bio.structure.AtomImpl
Get the X coordinate.
getXcoord() - Method in class org.forester.phylogeny.PhylogenyNode
Used for drawing of Trees.
getXRef() - Method in class org.forester.go.BasicGoXRef
 
getXRef() - Method in interface org.forester.go.GoXRef
 
getXSecondary() - Method in class org.forester.phylogeny.PhylogenyNode
 
getXYZEuler(Matrix) - Static method in class org.biojava.bio.structure.Calc
Convert a rotation Matrix to Euler angles.
getY() - Method in interface org.biojava.bio.structure.Atom
Get coordinate Y.
getY() - Method in class org.biojava.bio.structure.AtomImpl
Get the Y coordinate.
getYcoord() - Method in class org.forester.phylogeny.PhylogenyNode
Used for drawing of Trees.
getYSecondary() - Method in class org.forester.phylogeny.PhylogenyNode
 
getZ() - Method in interface org.biojava.bio.structure.Atom
Get coordinate Z.
getZ() - Method in class org.biojava.bio.structure.AtomImpl
Get the Z coordinate.
getZ() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
getZYZEuler(Matrix) - Static method in class org.biojava.bio.structure.Calc
Gget euler angles for a matrix given in ZYZ convention.
GFF3FromUniprotBlastHits - Class in org.biojava3.genome.homology
 
GFF3FromUniprotBlastHits() - Constructor for class org.biojava3.genome.homology.GFF3FromUniprotBlastHits
 
GFF3Reader - Class in org.biojava3.genome.parsers.gff
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GFF3Reader() - Constructor for class org.biojava3.genome.parsers.gff.GFF3Reader
 
GFF3Writer - Class in org.biojava3.genome.parsers.gff
 
GFF3Writer() - Constructor for class org.biojava3.genome.parsers.gff.GFF3Writer
 
Gln - Static variable in class org.biojava3.phylo.ResidueProperties
 
GLOBAL_ALIGN1 - Static variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
GLOBAL_ALIGN2 - Static variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
Glu - Static variable in class org.biojava3.phylo.ResidueProperties
 
Gly - Static variable in class org.biojava3.phylo.ResidueProperties
 
GO_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
goac - Class in org.forester.application
 
goac() - Constructor for class org.forester.application.goac
 
GOC_STR - Static variable in interface org.forester.go.GoXRef
 
GoId - Class in org.forester.go
 
GoId(String) - Constructor for class org.forester.go.GoId
 
gold - Static variable in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
GoNameSpace - Class in org.forester.go
 
GoNameSpace(GoNameSpace.GoNamespaceType) - Constructor for class org.forester.go.GoNameSpace
 
GoNameSpace(String) - Constructor for class org.forester.go.GoNameSpace
 
GoNameSpace.GoNamespaceType - Enum in org.forester.go
 
GOOGLE_SCHOLAR_LIMITS - Static variable in class org.forester.surfacing.SurfacingConstants
 
GOOGLE_SCHOLAR_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
GOOGLE_WEB_SEARCH_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
GoRelationship - Interface in org.forester.go
 
GoRelationship.Type - Enum in org.forester.go
 
GOSLIM_CANDIDA_STR - Static variable in interface org.forester.go.GoSubset
 
GOSLIM_GENERIC_STR - Static variable in interface org.forester.go.GoSubset
 
GOSLIM_GOA_STR - Static variable in interface org.forester.go.GoSubset
 
GOSLIM_PIR_STR - Static variable in interface org.forester.go.GoSubset
 
GOSLIM_PLANT_STR - Static variable in interface org.forester.go.GoSubset
 
GOSLIM_POMBE_STR - Static variable in interface org.forester.go.GoSubset
 
GOSLIM_YEAST_STR - Static variable in interface org.forester.go.GoSubset
 
GoSubset - Interface in org.forester.go
 
GoSubset.Type - Enum in org.forester.go
 
GOSUBSET_PROK_STR - Static variable in interface org.forester.go.GoSubset
 
GoTerm - Interface in org.forester.go
 
Gotoh - Class in org.biojava.bio.structure.align.pairwise
a class to perform Gotoh algorithm
Gotoh(Alignable) - Constructor for class org.biojava.bio.structure.align.pairwise.Gotoh
 
GoUtils - Class in org.forester.go
 
GoXRef - Interface in org.forester.go
 
GoXRef.Type - Enum in org.forester.go
 
GradientMapper - Class in org.biojava.bio.structure.gui.util.color
Maps a set of real values onto a gradient.
GradientMapper() - Constructor for class org.biojava.bio.structure.gui.util.color.GradientMapper
 
GradientMapper(Color, Color) - Constructor for class org.biojava.bio.structure.gui.util.color.GradientMapper
 
GradientMapper(Color, Color, ColorSpace) - Constructor for class org.biojava.bio.structure.gui.util.color.GradientMapper
 
GradientPanel - Class in org.biojava.bio.structure.gui.util.color
 
GradientPanel(ContinuousColorMapper, double, double) - Constructor for class org.biojava.bio.structure.gui.util.color.GradientPanel
 
gradients - Variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
Group - Interface in org.biojava.bio.structure
This is the data structure for a single Group of atoms.
group() - Method in class org.biojava3.genome.parsers.gff.Feature
Get the first item (everything before first semicolon, if it has one) in the attribute field, which is assumed to be a group identifer.
group() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get the group id of the feature.
group1 - Static variable in class org.biojava3.aaproperties.profeat.convertor.Convertor
Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
The seven different attributes are

Hydrophobicity (Polar, Neutral, Hydrophobicity)
Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)
Charge (Positive, Neutral, Negative)
Secondary structure (Helix, Strand, Coil)
Solvent accessibility (Buried, Exposed, Intermediate)

group2 - Static variable in class org.biojava3.aaproperties.profeat.convertor.Convertor
 
group3 - Static variable in class org.biojava3.aaproperties.profeat.convertor.Convertor
 
GroupIterator - Class in org.biojava.bio.structure
An iterator over all groups of a structure.
GroupIterator(Structure) - Constructor for class org.biojava.bio.structure.GroupIterator
Constructs a GroupIterator object.
GroupType - Class in org.biojava.bio.structure
contains only the static declaration of which types of Groups are available
GroupType() - Constructor for class org.biojava.bio.structure.GroupType
 
groupValues() - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a collection of all unique group ids in the list, as defined by the group() method of the features.
GSDI - Class in org.forester.sdi
 
GSDI(Phylogeny, Phylogeny, boolean) - Constructor for class org.forester.sdi.GSDI
Constructor which sets the gene tree and the species tree to be compared.
GuanUberbacher<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment.routines
Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
GuanUberbacher() - Constructor for class org.biojava3.alignment.routines.GuanUberbacher
Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.routines.GuanUberbacher
Prepares for a pairwise global sequence alignment.
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava3.alignment.routines.GuanUberbacher
Prepares for a pairwise global sequence alignment.
guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Takes a potentially non-sequential alignment and guesses a sequential version of it.
GUIAlignmentProgressListener - Class in org.biojava.bio.structure.align.gui
a GUI that allows to watch progress as multiple alignments are being processed.
GUIAlignmentProgressListener() - Constructor for class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
GuideTree<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements a data structure for a guide tree used during progressive multiple sequence alignment.
GuideTree(List<S>, List<PairwiseSequenceScorer<S, C>>) - Constructor for class org.biojava3.alignment.GuideTree
Creates a guide tree for use during progressive multiple sequence alignment.
GuideTree.Node - Class in org.biojava3.alignment
Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GuideTreeNode<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GUIFarmJobRunnable - Class in org.biojava.bio.structure.align.gui
 
GUIFarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.bio.structure.align.gui.GUIFarmJobRunnable
 
GuiWrapper - Class in org.biojava.bio.structure.align.ce
A class to wrap some of the strucutre.gui classes using Reflection
GuiWrapper() - Constructor for class org.biojava.bio.structure.align.ce.GuiWrapper
 
GZIP_MAGIC - Static variable in class org.biojava3.core.util.InputStreamProvider
The magic number found at the start of a GZIP stream.

H

H - Static variable in class org.biojava3.aaproperties.Constraints
 
handleEvent(ValidationEvent) - Method in class org.biojava3.aaproperties.xml.MyValidationEventHandler
 
handlePopupMenu(int, int) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
has3D() - Method in interface org.biojava.bio.structure.Group
returns true or false, depending if this group has 3D coordinates or not.
has3D() - Method in class org.biojava.bio.structure.HetatomImpl
returns true or false, depending if this group has 3D coordinates or not.
hasAltLoc() - Method in interface org.biojava.bio.structure.Group
Test if this group has alternate locations.
hasAltLoc() - Method in class org.biojava.bio.structure.HetatomImpl
 
hasAminoAtoms() - Method in interface org.biojava.bio.structure.Group
calculate if a groups has all atoms required for an amino acid.
hasAminoAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
calculate if a groups has all atoms required for an amino acid this allows to include chemically modified amino acids that are labeled hetatoms into some computations ...
hasAtom(String) - Method in interface org.biojava.bio.structure.Group
Teturns flag whether a particular atom is existing within this group .
hasAtom(String) - Method in class org.biojava.bio.structure.HetatomImpl
test is an Atom with name is existing.
hasAttribute(String) - Method in class org.biojava3.genome.parsers.gff.Feature
 
hasAttribute(String, String) - Method in class org.biojava3.genome.parsers.gff.Feature
 
hasAttribute(String) - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Check if the feature has a value defined for the specified key.
hasAttribute(String, String) - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Check if the feature attributes include the specified key/value pair.
hasAttribute(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Check if any feature in list has the specified attribute key.
hasAttribute(String, String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Check if any feature in list has the specified attribute key/value pair.
hasChain(String) - Method in interface org.biojava.bio.structure.Structure
check if a chain with the id chainId is contained in this structure.
hasChain(String) - Method in class org.biojava.bio.structure.StructureImpl
 
hasChainID() - Method in class org.biojava.bio.structure.align.client.StructureName
 
hasCompound(AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
hasCompound(AminoAcidCompound) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
hasCompound(AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
hasCompound(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
hasCompound(C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
hasGap(int) - Method in class org.biojava3.alignment.SimpleProfile
 
hasGap(int) - Method in interface org.biojava3.alignment.template.Profile
Returns true if any AlignedSequence has a gap at the given index.
hasGaps(int) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Check size of gaps between successive features in list.
hash(int, boolean) - Static method in class org.biojava3.core.util.Hashcoder
 
hash(int, char) - Static method in class org.biojava3.core.util.Hashcoder
 
hash(int, int) - Static method in class org.biojava3.core.util.Hashcoder
Used for ints, bytes and shorts
hash(int, long) - Static method in class org.biojava3.core.util.Hashcoder
long support done by shifting by 32 (using unsigned shift)
hash(int, float) - Static method in class org.biojava3.core.util.Hashcoder
float support done via Float.floatToIntBits(float) which allows the encoding of a float as an int.
hash(int, double) - Static method in class org.biojava3.core.util.Hashcoder
double support which is done using the same techinque as float hashing except we convert to a long not to an int.
hash(int, Object) - Static method in class org.biojava3.core.util.Hashcoder
o is a possibly-null object field, and possibly an array.
hashCode() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
hashCode() - Method in class org.biojava.bio.structure.align.client.StructureName
 
hashCode() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
hashCode() - Method in class org.biojava.bio.structure.Author
 
hashCode() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
hashCode() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
hashCode() - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
hashCode() - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
hashCode() - Method in class org.biojava.bio.structure.ResidueNumber
 
hashCode() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
hashCode() - Method in class org.biojava.bio.structure.Site
 
hashCode() - Method in class org.biojava3.core.sequence.AccessionID
 
hashCode() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
 
hashCode() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
hashCode() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
hashCode() - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
hashCode() - Method in class org.biojava3.core.sequence.location.SimplePoint
 
hashCode() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
hashCode() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
hashCode() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
hashCode() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
 
hashCode() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
 
hashCode() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
hashCode() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
hashCode() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
hashCode() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
hashCode() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
hashCode() - Method in class org.biojava3.data.sequence.FastaSequence
 
hashCode() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
hashCode() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
hashCode() - Method in class org.biojava3.protmod.structure.StructureAtom
 
hashCode() - Method in class org.biojava3.protmod.structure.StructureAtomLinkage
 
hashCode() - Method in class org.biojava3.protmod.structure.StructureGroup
 
hashCode() - Method in class org.biojava3.ronn.Jronn.Range
 
hashCode() - Method in class org.biojava3.ronn.ModelLoader.Model
 
hashCode() - Method in class org.forester.go.BasicGoTerm
Hashcode is based on hashcode of GO id.
hashCode() - Method in class org.forester.go.GoId
 
hashCode() - Method in class org.forester.phylogeny.data.Accession
 
hashCode() - Method in class org.forester.phylogeny.data.Identifier
 
hashCode() - Method in class org.forester.phylogeny.data.Sequence
 
hashCode() - Method in class org.forester.phylogeny.data.Taxonomy
 
hashCode() - Method in class org.forester.phylogeny.PhylogenyBranch
 
hashCode() - Method in class org.forester.phylogeny.PhylogenyNode
 
hashCode() - Method in class org.forester.phylogenyinference.DiscreteState
 
hashCode() - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
hashCode() - Method in class org.forester.surfacing.BasicDomain
 
hashCode() - Method in class org.forester.surfacing.BasicSpecies
 
hashCode() - Method in class org.forester.surfacing.DomainId
 
hashCode() - Method in class org.forester.surfacing.ProteinId
 
Hashcoder - Class in org.biojava3.core.util
Contains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders.
Hashcoder() - Constructor for class org.biojava3.core.util.Hashcoder
 
hashIDs() - Method in class org.forester.phylogeny.Phylogeny
Hashes the ID number of each PhylogenyNode of this Phylogeny to its corresponding PhylogenyNode, in order to make method getNode( id ) run in constant time.
hasJournalArticle() - Method in interface org.biojava.bio.structure.Structure
return whether or not the entry has an associated journal article or publication.
hasJournalArticle() - Method in class org.biojava.bio.structure.StructureImpl
Return whether or not the entry has an associated journal article or publication.
hasNext() - Method in class org.biojava.bio.structure.AtomIterator
Is there a next atom ?
hasNext() - Method in class org.biojava.bio.structure.GroupIterator
is there a group after the current one in the structure?
hasNext() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
hasNext() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
hasNext() - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
return if the iteration over all structures will return another structure
hasNext() - Method in class org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator
 
hasNext(int, int) - Method in class org.biojava3.genome.parsers.gff.LocIterator
Check if next window of specified size is available.
hasNext() - Method in class org.biojava3.genome.parsers.gff.LocIterator
Check if next window of default size is available.
hasNext() - Method in class org.forester.io.parsers.nhx.NHXParser
 
hasNext() - Method in class org.forester.phylogeny.iterators.ChildNodeIteratorForward
Returns true is this iterator has at least one more element, false otherwise.
hasNext() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator
 
hasNext() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator
Returns true is this iterator has at least one more element, false otherwise.
hasNext() - Method in interface org.forester.phylogeny.iterators.PhylogenyNodeIterator
 
hasNext() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator
DOCUMENT ME!
hasNext() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator
 
hasNextStructure() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
hasNextStructure() - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
hasParent() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
hasPrecalculatedResult(String, String, String, String) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
hasPrecalculatedResult(String, String, String, String, int) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
HasResultXMLConverter - Class in org.biojava.bio.structure.align.xml
 
HasResultXMLConverter() - Constructor for class org.biojava.bio.structure.align.xml.HasResultXMLConverter
 
HBond - Class in org.biojava.bio.structure.secstruc
 
HBond() - Constructor for class org.biojava.bio.structure.secstruc.HBond
 
HBONDHIGHENERGY - Static variable in class org.biojava.bio.structure.secstruc.SecStruc
higher limit for H-bond energy
HBONDLOWENERGY - Static variable in class org.biojava.bio.structure.secstruc.SecStruc
Minimal H-bond energy in cal / mol
HeaderParseException - Error in org.biojava3.core.exceptions
Currently not used
HeaderParseException(String) - Constructor for error org.biojava3.core.exceptions.HeaderParseException
 
HELIX - Static variable in class org.biojava.bio.structure.io.PDBFileParser
Helix secondary structure assignment.
helix - Static variable in class org.biojava3.phylo.ResidueProperties
 
helixmax - Static variable in class org.biojava3.phylo.ResidueProperties
 
helixmin - Static variable in class org.biojava3.phylo.ResidueProperties
 
HelpDialog - Class in org.biojava.bio.structure.align.gui
 
HelpDialog() - Constructor for class org.biojava.bio.structure.align.gui.HelpDialog
 
HETATM - Static variable in class org.biojava.bio.structure.GroupType
the type for hetero groups
HetatomImpl - Class in org.biojava.bio.structure
Generic Implementation of a Group interface.
HetatomImpl() - Constructor for class org.biojava.bio.structure.HetatomImpl
 
hexPropertyNames - Static variable in class org.biojava.bio.structure.align.gui.SystemInfo
 
hideSuggest() - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
Force the suggestions to be hidden (Useful for buttons, e.g.
hieFileName - Static variable in class org.biojava.bio.structure.scop.BerkeleyScopInstallation
 
hieFileName - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
HierarchicalClusterer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a clustering algorithm that converts a distance matrix into a tree.
His - Static variable in class org.biojava3.phylo.ResidueProperties
 
HMMER_SERVICE - Static variable in class org.biojava3.ws.hmmer.RemoteHmmerScan
 
HmmerDomain - Class in org.biojava3.ws.hmmer
Provides the details of a domain hit
HmmerDomain() - Constructor for class org.biojava3.ws.hmmer.HmmerDomain
 
HmmerResult - Class in org.biojava3.ws.hmmer
The results of a Hmmer search for a single sequence
HmmerResult() - Constructor for class org.biojava3.ws.hmmer.HmmerResult
 
HmmerScan - Interface in org.biojava3.ws.hmmer
Interface for performing Hmmscans on sequences.
HmmPfamOutputParser - Class in org.forester.io.parsers
 
HmmPfamOutputParser(File, String, String) - Constructor for class org.forester.io.parsers.HmmPfamOutputParser
 
HmmPfamOutputParser(File, String, String, Set<DomainId>, HmmPfamOutputParser.FilterType) - Constructor for class org.forester.io.parsers.HmmPfamOutputParser
 
HmmPfamOutputParser.FilterType - Enum in org.forester.io.parsers
 
HmmPfamOutputParser.ReturnType - Enum in org.forester.io.parsers
 
HmmscanPerDomainTableParser - Class in org.forester.io.parsers
 
HmmscanPerDomainTableParser(File, String, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF) - Constructor for class org.forester.io.parsers.HmmscanPerDomainTableParser
 
HmmscanPerDomainTableParser(File, String, Set<DomainId>, HmmscanPerDomainTableParser.FilterType, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF) - Constructor for class org.forester.io.parsers.HmmscanPerDomainTableParser
 
HmmscanPerDomainTableParser.FilterType - Enum in org.forester.io.parsers
 
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF - Enum in org.forester.io.parsers
 
HmmscanPerDomainTableParser.ReturnType - Enum in org.forester.io.parsers
 
HSVColorSpace - Class in org.biojava.bio.structure.gui.util.color
 
HSVColorSpace() - Constructor for class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
HTTPConnectionTools - Class in org.biojava.bio.structure.align.util
a class that takes care about opening HttpURLConnections and sets the proper timeouts
HTTPConnectionTools() - Constructor for class org.biojava.bio.structure.align.util.HTTPConnectionTools
 
hyd - Static variable in class org.biojava3.phylo.ResidueProperties
 
hyd2 - Static variable in class org.biojava3.phylo.ResidueProperties
 
hydmax - Static variable in class org.biojava3.phylo.ResidueProperties
 
hydmin - Static variable in class org.biojava3.phylo.ResidueProperties
 
hydrophobic - Static variable in class org.biojava3.phylo.ResidueProperties
 
hypot(double, double) - Static method in class org.biojava.bio.structure.jama.Maths
sqrt(a^2 + b^2) without under/overflow.

I

I - Static variable in class org.biojava3.aaproperties.Constraints
 
ID_REF - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
IDENTIFIER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Identifier - Class in org.forester.phylogeny.data
 
Identifier() - Constructor for class org.forester.phylogeny.data.Identifier
 
Identifier(String) - Constructor for class org.forester.phylogeny.data.Identifier
 
Identifier(String, String) - Constructor for class org.forester.phylogeny.data.Identifier
 
IDENTIFIER_DEFAULT - Static variable in class org.forester.phylogeny.data.ProteinDomain
 
IDENTIFIER_PROVIDER_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
IdentifierParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
identify(Structure) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
Identify all registered modifications in a structure.
identify(Structure, Set<ProteinModification>) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
Identify a set of modifications in a structure.
identify(Chain) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
Identify all registered modifications in a chain.
identify(List<Chain>) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
Identify all registered modifications in chains.
identify(Chain, Set<ProteinModification>) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
Identify a set of modifications in a a chains.
identify(List<Chain>, Set<ProteinModification>) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
Identify a set of modifications in a a list of chains.
identity(int, int) - Static method in class org.biojava.bio.structure.jama.Matrix
Generate identity matrix
IDX_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
IdxComparator - Class in org.biojava.bio.structure.align.helper
 
IdxComparator() - Constructor for class org.biojava.bio.structure.align.helper.IdxComparator
 
Ile - Static variable in class org.biojava3.phylo.ResidueProperties
 
IlluminaFastqReader - Class in org.biojava3.sequencing.io.fastq
Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqReader() - Constructor for class org.biojava3.sequencing.io.fastq.IlluminaFastqReader
 
IlluminaFastqWriter - Class in org.biojava3.sequencing.io.fastq
Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter() - Constructor for class org.biojava3.sequencing.io.fastq.IlluminaFastqWriter
 
IMG_STR - Static variable in interface org.forester.go.GoXRef
 
increaseCountingMap(Map<String, Integer>, String) - Static method in class org.forester.util.ForesterUtil
 
INDENT_PHYLOXML_DEAFULT - Static variable in class org.forester.io.writers.PhylogenyWriter
 
index - Variable in class org.biojava.bio.structure.align.helper.GapArray
 
INDEX - Static variable in class org.biojava3.ronn.RonnConstraint
 
indexOf(Sequence<C>, C) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Performs a linear search of the given Sequence for the given compound.
IndexPair - Class in org.biojava.bio.structure.align.helper
 
IndexPair() - Constructor for class org.biojava.bio.structure.align.helper.IndexPair
 
IndexPair(short, short) - Constructor for class org.biojava.bio.structure.align.helper.IndexPair
 
infer(File, File, File, File, String, boolean, boolean, boolean, boolean) - Static method in class org.forester.sdi.SDIdirectory
Runs method "infer" of class SDIunrooted on all gene trees in directory indir.
infer(Phylogeny, Phylogeny, boolean, boolean, boolean, boolean, int) - Method in class org.forester.sdi.SDIR
Infers gene duplications on a possibly unrooted gene Phylogeny gene_tree.
inferCommonPartOfScientificNameOfDescendants(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
inferOrthologs(File, Phylogeny, String) - Method in class org.forester.sdi.RIO
Infers the orthologs (as well the "super orthologs", the "subtree neighbors", and the "ultra paralogs") for each external node of the gene Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR, for example).
inferredOrthologsToArrayList(String, double) - Method in class org.forester.sdi.RIO
Returns an ArrayList containg the names of orthologs of the PhylogenyNode with seq name seq_name.
inferredOrthologsToString(String, int, double, double) - Method in class org.forester.sdi.RIO
Returns a String containg the names of orthologs of the PhylogenyNode with seq name query_name.
inferredOrthologTableToFile(File) - Method in class org.forester.sdi.RIO
Writes the orthologs for each external node of the gene trees to outfile in the form of a table.
inferredSuperOrthologTableToFile(File) - Method in class org.forester.sdi.RIO
Writes the "super orthologs" for each external nodes of the gene trees to outfile in the form of a table.
inferredUltraParalogsToString(String, boolean, double) - Method in class org.forester.sdi.RIO
Returns a String containg the names of orthologs of the PhylogenyNode with seq name query_name.
init() - Static method in class org.biojava3.protmod.ProteinModificationRegistry
Initialization the static variables and register common modifications.
init(InputStream) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
Initialization the static variables and register common modifications.
init() - Method in class org.forester.archaeopteryx.ArchaeopteryxA
 
init() - Method in class org.forester.archaeopteryx.ArchaeopteryxE
 
init() - Method in class org.forester.phylogeny.data.Confidence
 
init() - Method in class org.forester.phylogeny.data.Sequence
 
init() - Method in class org.forester.phylogeny.data.Taxonomy
 
init() - Method in class org.forester.phylogeny.Phylogeny
Deletes this Phylogeny.
initAlignmentGUIMenu(JFrame) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
initCache() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
initExtinctionCoefficient() - Static method in class org.biojava3.aaproperties.Constraints
Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html
initializeBreakFlag(boolean[][]) - Method in interface org.biojava.bio.structure.align.ce.MatrixListener
 
initializeData() - Method in class org.forester.phylogeny.PhylogenyNode
Deletes data of this PhylogenyNode.
initMenu(JFrame, StructureAlignmentJmol, AFPChain) - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
provide a JMenuBar that can be added to a JFrame
initMenu() - Static method in class org.biojava.bio.structure.gui.util.MenuCreator
provide a JMenuBar that can be added to a JFrame
initMet(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
initMolecularWeight() - Static method in class org.biojava3.aaproperties.Constraints
Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
InputStreamProvider - Class in org.biojava3.core.util
A class that provides an InputStream from a File.
InputStreamProvider() - Constructor for class org.biojava3.core.util.InputStreamProvider
 
inputStreamToDocument(InputStream) - Static method in class org.biojava3.core.util.XMLHelper
 
InsdcLocations - Class in org.biojava3.core.sequence.location
A collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appear in records.
InsdcLocations() - Constructor for class org.biojava3.core.sequence.location.InsdcLocations
 
InsdcLocations.BondLocation - Class in org.biojava3.core.sequence.location
Used to represent bond locations equivalent to bond(7,8) or bond(7).
InsdcLocations.BondLocation(Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.BondLocation
 
InsdcLocations.BondLocation(List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.BondLocation
 
InsdcLocations.GroupLocation - Class in org.biojava3.core.sequence.location
Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.
InsdcLocations.GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
 
InsdcLocations.GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
 
InsdcLocations.GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
 
InsdcLocations.GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
 
InsdcLocations.GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
 
InsdcLocations.GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
 
InsdcLocations.OneOfLocation - Class in org.biojava3.core.sequence.location
Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g.
InsdcLocations.OneOfLocation(Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OneOfLocation
 
InsdcLocations.OneOfLocation(List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OneOfLocation
 
InsdcLocations.OrderLocation - Class in org.biojava3.core.sequence.location
Used to describe a 5' to 3' ordering but no firm assurance it is correct
InsdcLocations.OrderLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
 
InsdcLocations.OrderLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
 
InsdcLocations.OrderLocation(int, int, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
 
InsdcLocations.OrderLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
 
InsdcLocations.OrderLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
 
InsdcLocations.OrderLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
 
InsdcParser - Class in org.biojava3.core.sequence.location
Parser for working with INSDC style locations.
InsdcParser() - Constructor for class org.biojava3.core.sequence.location.InsdcParser
 
InsdcParser(DataSource) - Constructor for class org.biojava3.core.sequence.location.InsdcParser
 
insertResidueAt(int, int) - Method in class org.forester.development.SimpleMutableMsa
 
interpolate(Color, Color, float) - Method in interface org.biojava.bio.structure.gui.util.color.ColorInterpolator
Interpolates to a color between a and b
interpolate(Color, Color, float) - Method in class org.biojava.bio.structure.gui.util.color.LinearColorInterpolator
Interpolates to a color between a and b
interrupt() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalc
stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
stops what is currently happening and does not continue
interrupt() - Method in interface org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable
 
interrupt() - Method in class org.biojava.bio.structure.gui.util.AlignmentCalc
stops what is currently happening and does not continue
intersection(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Return the intersection, or null if no overlap.
intervalNumberSpecies(Phylogeny, int) - Static method in class org.forester.development.DevelopmentTools
Sets the species name of the external Nodes of Phylogeny t to 1, 1+i, 2, 2+i, 3, 3+i, ....
IntronSequence - Class in org.biojava3.core.sequence
 
IntronSequence(GeneSequence, int, int) - Constructor for class org.biojava3.core.sequence.IntronSequence
Place holder for Intron sequence features
intValue() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
Attempts to provide an int version of this codon which multiplies each position by
inverse() - Method in class org.biojava.bio.structure.jama.Matrix
Matrix inverse or pseudoinverse
inverse(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
A method which attempts to do the right thing when is comes to a reverse/reverse complement
invert(Atom) - Static method in class org.biojava.bio.structure.Calc
 
IOUtils - Class in org.biojava3.core.sequence.io.util
 
IOUtils() - Constructor for class org.biojava3.core.sequence.io.util.IOUtils
 
IOUtils.ReaderProcessor - Interface in org.biojava3.core.sequence.io.util
Closure interface used when working with IOUtils#processReader(String).
IPeptideProperties - Interface in org.biojava3.aaproperties
An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:

Molecular weight
Absorbance
Extinction coefficient
Instability index
Apliphatic index
Average hydropathy value
Isoelectric point
Net charge at pH 7
Composition of specified amino acid
Composition of the 20 standard amino acid

IProfeatProperties - Interface in org.biojava3.aaproperties.profeat
 
IProfeatProperties.ATTRIBUTE - Enum in org.biojava3.aaproperties.profeat
Enumeration of the seven different attributes
IProfeatProperties.DISTRIBUTION - Enum in org.biojava3.aaproperties.profeat
Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
IProfeatProperties.GROUPING - Enum in org.biojava3.aaproperties.profeat
Enumeration of the three different groupings for each attributes
IProfeatProperties.TRANSITION - Enum in org.biojava3.aaproperties.profeat
Enumeration of the transition between groupA and groupB
IS_DUPLICATION - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
isAfter(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location is entirely after the other location (no overlap).
isAlignSeqRes() - Method in class org.biojava.bio.structure.io.FileParsingParameters
Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
isAllNonEmptyInternalLabelsArePositiveNumbers(Phylogeny) - Static method in class org.forester.util.ForesterUtil
 
isAmbiguosProtein(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
Check whether the sequence confirms to amboguous protein sequence
isAmbiguous() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
 
isAminoAcid() - Method in class org.biojava3.protmod.structure.StructureGroup
 
isAppearsAligned() - Method in class org.forester.development.BasicMsa
 
isAreOrthologous(PhylogenyNode, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyMethods
 
isAutoFetch() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isAutoFetch() - Method in class org.biojava.bio.structure.align.util.AtomCache
Does the cache automatically download files that are missing from the local installation from the PDB FTP site?
isAutoFetch() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
isAutoFetch() - Method in class org.biojava.bio.structure.io.PDBFileReader
 
isAutoFetch() - Method in interface org.biojava.bio.structure.io.StructureIOFile
Fetch files automatically from FTP server.
isAutoFetch() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is false
isBefore(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location is entirely before other location (no overlap).
isBetweenCompounds() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
isBetweenCompounds() - Method in interface org.biojava3.core.sequence.location.template.Location
Returns true if the position is meant to represent a point between two points such as 78^79.
isBiologicalAssembly() - Method in interface org.biojava.bio.structure.Structure
Gets flag that indicates if this structure is a biological assembly
isBiologicalAssembly() - Method in class org.biojava.bio.structure.StructureImpl
Gets flag that indicates if this structure is a biological assembly
isBiologicalProcess() - Method in class org.forester.go.GoNameSpace
 
isCacheEnabled() - Method in class org.biojava.bio.structure.domain.SerializableCache
 
isCellularComponent() - Method in class org.forester.go.GoNameSpace
 
isChalcogen() - Method in enum org.biojava.bio.structure.Element
Returns true if Element is a chalcogen (O, S, Se, Te, Po).
isCircular() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
isCircular() - Method in class org.biojava3.alignment.SimpleProfile
 
isCircular() - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns true if this Sequence wraps around from the last alignment column back to the first.
isCircular() - Method in interface org.biojava3.alignment.template.Profile
Returns true if any AlignedSequence is circular.
isCircular() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
isCircular() - Method in interface org.biojava3.core.sequence.location.template.Location
Indicates if this location is circular.
isCollapse() - Method in class org.forester.phylogeny.PhylogenyNode
Returns whether this PhylogenyNode should be drawn as collapsed.
isCombinable(DomainId) - Method in class org.forester.surfacing.BasicCombinableDomains
 
isCombinable(DomainId) - Method in interface org.forester.surfacing.CombinableDomains
 
isComplementable() - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
isComplementable() - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
isComplementable() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
isComplementable() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
isComplementable() - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
NucleotideCompounds can always complement
isComplementable() - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
isCompletelyBinary() - Method in class org.forester.phylogeny.Phylogeny
Returns whether this is a completely binary tree (i.e.
isCompleteQueryMatch() - Method in class org.forester.surfacing.SimpleDomain
 
isCompleteTargetMatch() - Method in class org.forester.surfacing.SimpleDomain
 
isComplex() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
isComplex() - Method in interface org.biojava3.core.sequence.location.template.Location
Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
isCompoundStringLengthEqual() - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
isCompoundStringLengthEqual() - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
isCompoundStringLengthEqual() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
isCompoundStringLengthEqual() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
isCompoundStringLengthEqual() - Method in interface org.biojava3.core.sequence.template.CompoundSet
Returns true if all String representations of Compounds are of the same length.
isConnected(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
test if two amino acids are connected, i.e.
isCrossLink() - Method in enum org.biojava3.protmod.ModificationCategory
 
isCrystallographic() - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
Returns true if structure was solved by a crystallographic method, i.e., the values returned by this class are meaningful.
isCTerminal() - Method in class org.biojava3.protmod.Component
 
isDebug() - Method in class org.biojava.bio.structure.align.StructurePairAligner
check if debug mode is set on
isDebug() - Method in class org.biojava.bio.structure.domain.SerializableCache
 
isDEBUG() - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
isDirected() - Method in class org.forester.phylogeny.PhylogenyBranch
 
isDirectionTowards(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch
 
isDisplayDomainNames() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
isDNA() - Method in class org.biojava3.phylo.ScoreMatrix
 
isDoAngleCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
isDoDensityCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
isDoDistanceCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
isDomainSplit() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
isDoRMSCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
isDownloadAll() - Method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
By default this provider will download only some of the ChemComp files.
isDuplication() - Method in class org.forester.phylogeny.data.Event
Returns true if this event contains one or more duplications events only
isDuplication() - Method in class org.forester.phylogeny.PhylogenyNode
Returns true if this PhylogenyNode represents a _duplication event, false otherwise.
isEmpty() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
isEmpty() - Method in class org.forester.datastructures.Queue
Returns whether or not this queue is empty.
isEmpty() - Method in class org.forester.development.BasicMsa
 
isEmpty() - Method in class org.forester.phylogeny.data.Sequence
 
isEmpty() - Method in class org.forester.phylogeny.data.Taxonomy
 
isEmpty() - Method in class org.forester.phylogeny.Phylogeny
Checks whether a Phylogeny object is deleted (or empty).
isEmpty() - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
isEmpty() - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
isEmpty() - Method in class org.forester.util.BasicTable
 
isEmpty(String) - Static method in class org.forester.util.ForesterUtil
 
isEngulfed(Domain, List<Boolean>) - Static method in class org.forester.surfacing.SurfacingUtil
Returns true is Domain domain falls in an uninterrupted stretch of covered positions.
isEqual(PhylogenyData) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
isEqual(PhylogenyData) - Method in class org.forester.development.AminoAcidSequence
 
isEqual(PhylogenyData) - Method in class org.forester.go.BasicGoTerm
 
isEqual(double, double) - Static method in class org.forester.go.TestGo
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Accession
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Annotation
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BinaryCharacters
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BranchColor
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BranchData
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BranchWidth
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Confidence
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Date
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Distribution
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.DomainArchitecture
Returns true if the names and the order of the domains match (domain and linker lengths are ignored).
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Event
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Identifier
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.NodeData
 
isEqual(PhylogenyData) - Method in interface org.forester.phylogeny.data.PhylogenyData
Compares this PhylogenyData to PhylogenyData data.
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Point
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.PropertiesMap
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Property
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.ProteinDomain
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Reference
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Sequence
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.SequenceRelation
 
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Taxonomy
If this and taxonomy 'data' has an identifier, comparison will be based on that.
isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Uri
 
isEqual(double, double) - Static method in class org.forester.phylogenyinference.TestPhylogenyReconstruction
 
isEqual(double, double) - Static method in class org.forester.surfacing.TestSurfacing
 
isEqual(double, double) - Static method in class org.forester.test.Test
 
isEqual(double, double) - Static method in class org.forester.util.ForesterUtil
 
isErrorXML(String) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
returns true if the alignment XML contains an error message
isEven(int) - Static method in class org.forester.util.ForesterUtil
 
isExternal() - Method in class org.forester.phylogeny.PhylogenyNode
Checks whether this PhylogenyNode is external (tip).
isFetchCurrent() - Method in class org.biojava.bio.structure.align.util.AtomCache
N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
isFetchCurrent() - Method in class org.biojava.bio.structure.io.PDBFileReader
N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
isFetchFileEvenIfObsolete() - Method in class org.biojava.bio.structure.align.util.AtomCache
forces the cache to fetch the file if its status is OBSOLETE.
isFetchFileEvenIfObsolete() - Method in class org.biojava.bio.structure.io.PDBFileReader
forces the reader to fetch the file if its status is OBSOLETE.
isFirstChildNode() - Method in class org.forester.phylogeny.PhylogenyNode
DOCUMENT ME!
isFirstExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode
DOCUMENT ME!
isFlexible() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isFullRank() - Method in class org.biojava.bio.structure.jama.QRDecomposition
Is the matrix full rank?
isFusion() - Method in class org.forester.phylogeny.data.Event
 
isGap(int) - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
isGap(int) - Method in interface org.biojava3.alignment.template.AlignedSequence
Returns true if this Sequence has a gap at a particular alignment column.
isGap(char) - Static method in class org.biojava3.phylo.Comparison
DOCUMENT ME!
isGap(byte) - Static method in class org.forester.development.AminoAcid
 
isGeneLoss() - Method in class org.forester.phylogeny.data.Event
Returns true if this event contains one or more gene loss events only
isGuiModuleInstalled() - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
isHalogen() - Method in enum org.biojava.bio.structure.Element
Returns true if Element is a halogen (F, Cl, Br, I, At).
isHasAssignedEvent() - Method in class org.forester.phylogeny.PhylogenyNode
Returns whether a _duplication or speciation event has been assigned for this PhylogenyNode.
isHasAtLeastNodeWithEvent(Phylogeny) - Static method in class org.forester.util.ForesterUtil
 
isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny) - Static method in class org.forester.util.ForesterUtil
Returns true if at least one branch has a length larger than zero.
isHasAtLeastOneBranchWithSupportValues(Phylogeny) - Static method in class org.forester.util.ForesterUtil
 
isHasAttribute(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
isHasBinaryCharacters() - Method in class org.forester.phylogeny.data.NodeData
 
isHasBranchColor() - Method in class org.forester.phylogeny.data.BranchData
 
isHasBranchWidth() - Method in class org.forester.phylogeny.data.BranchData
 
isHasConfidences() - Method in class org.forester.phylogeny.data.BranchData
 
isHasDate() - Method in class org.forester.phylogeny.data.NodeData
 
isHasDistribution() - Method in class org.forester.phylogeny.data.NodeData
 
isHasEvent() - Method in class org.forester.phylogeny.data.NodeData
 
isHasExternalDescendant(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
isHasLengthStatistic(Species) - Method in class org.forester.surfacing.DomainLengths
 
isHasNodeIdentifier() - Method in class org.forester.phylogeny.data.NodeData
 
isHasProperties() - Method in class org.forester.phylogeny.data.NodeData
 
isHasReference() - Method in class org.forester.phylogeny.data.NodeData
 
isHasSequence() - Method in class org.forester.phylogeny.data.NodeData
 
isHasTaxonomy() - Method in class org.forester.phylogeny.data.NodeData
 
isHasValue() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
isHeaderOnly() - Method in class org.biojava.bio.structure.io.FileParsingParameters
Parse only the PDB file header out of the files
isHeavyAtom() - Method in enum org.biojava.bio.structure.Element
Returns true is the Element is an not Hydrogen.
isHeteroAtom() - Method in enum org.biojava.bio.structure.Element
Returns true if Element is not Hydrogen and not Carbon.
isHexProperty(String) - Method in class org.biojava.bio.structure.align.gui.SystemInfo
 
isHigher(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
isHigher(Point) - Method in interface org.biojava3.core.sequence.location.template.Point
Returns true if the point is higher in value to the current point
isHydrogen() - Method in enum org.biojava.bio.structure.Element
Returns true if this Element is Hydrogen.
isIllumina() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_ILLUMINA.
isInitialized() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
isInternal() - Method in class org.forester.phylogeny.PhylogenyNode
Checks whether this PhylogenyNode is internal (tip).
isInterrupted() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
isIntersecting(String[], String[]) - Static method in class org.forester.util.ForesterUtil
This determines whether String[] a and String[] b have at least one String in common (intersect).
isJoinFast() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
isJoinPlo() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
isLargerOrEqualToZero(double) - Static method in class org.forester.util.ForesterUtil
 
isLastChildNode() - Method in class org.forester.phylogeny.PhylogenyNode
Returns true if this node is the last child node of its _parent.
isLastExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode
DOCUMENT ME!
isLeaf() - Method in class org.biojava3.alignment.GuideTree.Node
 
isLoadChemCompInfo() - Method in class org.biojava.bio.structure.io.FileParsingParameters
Should the chemical component information be automatically be downloade from the web? If set to false, a limited set of ChemComps is being used.
isLocal() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Returns whether alignment finds a region of similarity rather than aligning every compound.
isLower(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
isLower(Point) - Method in interface org.biojava3.core.sequence.location.template.Point
Returns true if the current point is at a lower position than the point given.
isMetal() - Method in enum org.biojava.bio.structure.Element
Returns true if ElementType is a metal.
isMetal() - Method in enum org.biojava.bio.structure.ElementType
Returns true if ElementType is a metal.
isMetalloid() - Method in enum org.biojava.bio.structure.Element
Returns true if ElementType is a metalloid.
isMetalloid() - Method in enum org.biojava.bio.structure.ElementType
Returns true if ElementType is a metalloid.
isMolecularFunction() - Method in class org.forester.go.GoNameSpace
 
isNegative() - Method in class org.biojava3.genome.parsers.gff.Location
Check if location is on negative strand.
isNmr() - Method in interface org.biojava.bio.structure.Structure
test if this structure is an nmr structure.
isNmr() - Method in class org.biojava.bio.structure.StructureImpl
is this structure an nmr structure ?
isNonAmbNucleotideSequence(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char
isNonMetal() - Method in enum org.biojava.bio.structure.Element
Returns true if ElementType is a non-metal.
isNonMetal() - Method in enum org.biojava.bio.structure.ElementType
Returns true if ElementType is a non-metal.
isNonsingular() - Method in class org.biojava.bio.structure.jama.LUDecomposition
Is the matrix nonsingular?
isNTerminal() - Method in class org.biojava3.protmod.Component
 
isNucleotide(String) - Static method in class org.biojava.bio.structure.StructureTools
 
isNucleotideSequence(String) - Static method in class org.biojava3.core.util.SequenceTools
 
isNucleotideSequence(FastaSequence) - Static method in class org.biojava3.data.sequence.SequenceUtil
 
isNull(BigDecimal) - Static method in class org.forester.util.ForesterUtil
 
isObsolete() - Method in class org.forester.go.BasicGoTerm
 
isObsolete() - Method in interface org.forester.go.GoTerm
 
isOptionHasAValue(String) - Method in class org.forester.util.CommandLineArguments
 
isOptionSet(String) - Method in class org.forester.util.CommandLineArguments
 
isOptionValueSet(String) - Method in class org.forester.util.CommandLineArguments
 
isOther() - Method in class org.forester.phylogeny.data.Event
 
Isotope - Class in org.biojava3.aaproperties.xml
 
Isotope() - Constructor for class org.biojava3.aaproperties.xml.Isotope
 
Isotope(String, int, double) - Constructor for class org.biojava3.aaproperties.xml.Isotope
 
isOutputPDB() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
When writing the results to a file, don;t write as XML but write aligned PDB file
isParseCAOnly() - Method in class org.biojava.bio.structure.io.FileParsingParameters
the flag if only the C-alpha atoms of the structure should be parsed.
isParseSecStruc() - Method in class org.biojava.bio.structure.io.FileParsingParameters
is secondary structure assignment being parsed from the file? default is null
isPdbDirectorySplit() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).
isPdbDirectorySplit() - Method in class org.biojava.bio.structure.io.PDBFileReader
Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).
isPdbDirectorySplit() - Method in interface org.biojava.bio.structure.io.StructureIOFile
The PDB files are organized hierarchically (as on the PDB - FTP server.
isPdbDirSplit() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isPdbDirSplit() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
isPDPDomain() - Method in class org.biojava.bio.structure.align.client.StructureName
 
isPrint - Static variable in class org.biojava.bio.structure.align.ce.CECalculator
 
isPrint - Static variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
isPrintCE() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
Display the output string in CE style
isPrintFatCat() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isPrintXML() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isProtein() - Method in class org.biojava3.phylo.ScoreMatrix
 
isProteinSequence(String) - Static method in class org.biojava3.data.sequence.SequenceUtil
 
isPublished() - Method in class org.biojava.bio.structure.JournalArticle
 
isQueryInteger() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
 
isQueryInteger() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
Is the query a number?
isReadableFile(File) - Static method in class org.forester.util.ForesterUtil
 
isReadableFile(String) - Static method in class org.forester.util.ForesterUtil
 
isReady() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
isReady() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
isReady() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
isReady(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Wrapper method for NCBIQBlastService.isReady(String, long), omitting unnecessary present property.
isReady(String, long) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Checks for completion of request.
isReady(String, long) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentService
Simple method to check if the specified request has been completed by the service used.
isReplaced(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
isReplaced(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
isReplacer(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
isReplacer(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
 
isRerootable() - Method in class org.forester.phylogeny.Phylogeny
 
isRoot() - Method in class org.forester.phylogeny.data.Event
 
isRoot() - Method in class org.forester.phylogeny.PhylogenyNode
Checks whether this PhylogenyNode is a root.
isRooted() - Method in class org.forester.phylogeny.Phylogeny
Returns true is this Phylogeny is rooted.
isRunBackground() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
Flag if a job that only runs one parallell job should be run in its own thread or in the main thread.
isSameStrand(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location is on same strand as other location.
isSanger() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SANGER.
isScopName() - Method in class org.biojava.bio.structure.align.client.StructureName
 
isSequentialAlignment() - Method in class org.biojava.bio.structure.align.model.AFPChain
Get whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.
isSequentialAlignment(AFPChain, boolean) - Static method in class org.biojava.bio.structure.align.util.AlignmentTools
Checks that the alignment given by afpChain is sequential.
isShortAlign() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
isShow3d() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isShowAFPRanges() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
isShowAFPRanges() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isShowMenu() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
isSignificantResult() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
isSolexa() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return true if this FASTQ sequence format variant is FastqVariant.FASTQ_SOLEXA.
isSPD() - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
isSpeciation() - Method in class org.forester.phylogeny.data.Event
Returns true if this event contains one or more speciation events only
isSpeciation() - Method in class org.forester.phylogeny.PhylogenyNode
 
isSpeciationOrDuplication() - Method in class org.forester.phylogeny.data.Event
 
isSplit() - Method in class org.biojava.bio.structure.align.util.AtomCache
Is the organization of files within the directory split, as on the PDB FTP servers, or are all files contained in one directory.
isSplit() - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
isStandard() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
isStandardChemComp(ChemComp) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
 
isStart() - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
isStart(AminoAcidCompound) - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
Returns true if the given compound was a start codon in this codon table.
isStart() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
isStart(AminoAcidCompound) - Method in interface org.biojava3.core.sequence.transcription.Table
Returns true if the given compound could have been a start amino acid; this does not assert if the codon that actually coded for the amino acid was a start codon.
isStop() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
isStoringScoreMatrix() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.
isStrictSCOP() - Method in class org.biojava.bio.structure.align.util.AtomCache
Reports whether strict scop naming will be enforced, or whether this AtomCache should try to guess some simple variants on scop domains.
isSuggestVisible() - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
isTerminate(byte) - Static method in class org.forester.development.AminoAcid
 
isTransfer() - Method in class org.forester.phylogeny.data.Event
 
isTree() - Method in class org.forester.phylogeny.Phylogeny
 
isTrivial() - Method in class org.forester.go.etc.OntologizerResult
 
isTryAllCPs() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
isUnassignable(byte) - Static method in class org.forester.development.AminoAcid
 
isUnassigned() - Method in class org.forester.go.GoNameSpace
 
isUnassigned() - Method in class org.forester.phylogeny.data.Event
 
isUncertain() - Method in class org.biojava3.core.sequence.location.SimplePoint
 
isUncertain() - Method in interface org.biojava3.core.sequence.location.template.Point
Returns a true if the exact point is unknown.
isUnknown() - Method in class org.biojava3.core.sequence.location.SimplePoint
 
isUnknown() - Method in interface org.biojava3.core.sequence.location.template.Point
Returns true if the current position is unknown but is beyond the position encoded for.
isUnknown(byte) - Static method in class org.forester.development.AminoAcid
 
isUpdateRemediatedFiles() - Method in class org.biojava.bio.structure.io.FileParsingParameters
A flag if local files should be replaced with the latest version of remediated PDB files.
isURLProperty(String) - Method in class org.biojava.bio.structure.align.gui.SystemInfo
 
isValid() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
isValid() - Method in class org.forester.io.parsers.tol.TolParser
 
isVerbose() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
Flag if the job should be run in verbose mode.
isWaitForAlignments() - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
isWritableFile(File) - Static method in class org.forester.util.ForesterUtil
 
iterateChildNodesForward() - Method in class org.forester.phylogeny.PhylogenyNode
 
iterator() - Method in interface org.biojava.bio.structure.Group
get an Atom Iterator.
iterator() - Method in class org.biojava.bio.structure.HetatomImpl
return an AtomIterator.
iterator() - Method in class org.biojava3.alignment.GuideTree
Returns a post-order Iterator that traverses the tree from leaves to root.
iterator() - Method in class org.biojava3.alignment.SimpleAlignedSequence
 
iterator() - Method in class org.biojava3.alignment.SimpleProfile
 
iterator() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
iterator() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
iterator() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
iterator() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
Iterates through all known sub-locations for this location but does not descend
iterator() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
iterator() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Provides basic iterable access to this class
iterator() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
iterator() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Returns an instance of SequenceMixin.SequenceIterator
iterator() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
iterator() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
iterator() - Method in class org.biojava3.core.sequence.views.WindowedSequence
Returns an iterator which will return the windows in a sequence in sequential order.
iterator() - Method in class org.biojava3.genome.parsers.gff.Location
Create a location iterator over this location with a window size of 1 and an increment of +1 (successive symbols from start to end).
iterator(int, int) - Method in class org.biojava3.genome.parsers.gff.Location
Create a location iterator over this location, using specified window size and increment.
iteratorExternalForward() - Method in class org.forester.phylogeny.Phylogeny
 
iteratorLevelOrder() - Method in class org.forester.phylogeny.Phylogeny
 
iteratorPostorder() - Method in class org.forester.phylogeny.Phylogeny
 
iteratorPreorder() - Method in class org.forester.phylogeny.Phylogeny
 
IUPAC_LOCATION - Static variable in class org.biojava3.core.sequence.io.IUPACParser
 
IUPACParser - Class in org.biojava3.core.sequence.io
Available translations 1 - UNIVERSAL 2 - VERTEBRATE_MITOCHONDRIAL 3 - YEAST_MITOCHONDRIAL 4 - MOLD_MITOCHONDRIAL 5 - INVERTEBRATE_MITOCHONDRIAL 6 - CILIATE_NUCLEAR 9 - ECHINODERM_MITOCHONDRIAL 10 - EUPLOTID_NUCLEAR 11 - BACTERIAL 12 - ALTERNATIVE_YEAST_NUCLEAR 13 - ASCIDIAN_MITOCHONDRIAL 14 - FLATWORM_MITOCHONDRIAL 15 - BLEPHARISMA_MACRONUCLEAR 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL 21 - TREMATODE_MITOCHONDRIAL 23 - SCENEDESMUS_MITOCHONDRIAL Taken from NCBI with slight modification and put into the classpath resource.
IUPACParser() - Constructor for class org.biojava3.core.sequence.io.IUPACParser
Default version and uses the classpath based IUPAC table
IUPACParser(InputStream) - Constructor for class org.biojava3.core.sequence.io.IUPACParser
Allows you to specify a different IUPAC table.
IUPACParser.IUPACTable - Class in org.biojava3.core.sequence.io
Holds the concept of a codon table from the IUPAC format
IUPACParser.IUPACTable(String, int, String, String, String, String, String) - Constructor for class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
 
IUPACParser.IUPACTable(String, Integer, String, String) - Constructor for class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
Constructor which uses the basic IUPAC codon table format.

J

JAutoSuggest - Class in org.biojava.bio.structure.align.gui.autosuggest
A JTextField that can make suggestions for auto-complete.
JAutoSuggest() - Constructor for class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
JAutoSuggest(int) - Constructor for class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
JAutoSuggest(Frame) - Constructor for class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
JAVA_VENDOR - Static variable in class org.forester.util.ForesterUtil
 
JAVA_VERSION - Static variable in class org.forester.util.ForesterUtil
 
JAXP_SCHEMA_LANGUAGE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
JAXP_SCHEMA_LANGUAGE - Static variable in class org.forester.io.parsers.tol.TolParser
 
JAXP_SCHEMA_SOURCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
JAXP_SCHEMA_SOURCE - Static variable in class org.forester.io.parsers.tol.TolParser
 
JFatCatClient - Class in org.biojava.bio.structure.align.client
 
JFatCatClient() - Constructor for class org.biojava.bio.structure.align.client.JFatCatClient
 
JMatrixPanel - Class in org.biojava.bio.structure.gui
a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment
JMatrixPanel() - Constructor for class org.biojava.bio.structure.gui.JMatrixPanel
 
JmolAlignedPositionListener - Class in org.biojava.bio.structure.gui.events
 
JmolAlignedPositionListener(BiojavaJmol, StructurePairAligner) - Constructor for class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
jmolColorByChain() - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
assign a custom color to the Jmol chains command.
jmolInClassPath() - Static method in class org.biojava.bio.structure.gui.BiojavaJmol
returns true if Jmol can be found in the classpath, otherwise false.
JmolPanel - Class in org.biojava.bio.structure.align.gui.jmol
 
JmolPanel() - Constructor for class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
JmolTools - Class in org.biojava.bio.structure.align.gui.jmol
 
JmolTools() - Constructor for class org.biojava.bio.structure.align.gui.jmol.JmolTools
 
JmolViewerImpl - Class in org.biojava3.structure.gui
 
JmolViewerImpl() - Constructor for class org.biojava3.structure.gui.JmolViewerImpl
 
JNLPProxy - Class in org.biojava.bio.structure.align.webstart
 
JobKillException - Exception in org.biojava.bio.structure.align.client
 
JobKillException(String) - Constructor for exception org.biojava.bio.structure.align.client.JobKillException
 
JoiningSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence.
JoiningSequenceReader(Sequence<C>...) - Constructor for class org.biojava3.core.sequence.storage.JoiningSequenceReader
Allows creation of the store from Vargs Sequence objects.
JoiningSequenceReader(List<Sequence<C>>) - Constructor for class org.biojava3.core.sequence.storage.JoiningSequenceReader
Allows creation of the store from List>.
JoiningSequenceReader(CompoundSet<C>, Sequence<C>...) - Constructor for class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
JoiningSequenceReader(CompoundSet<C>, List<Sequence<C>>) - Constructor for class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
JointFragments - Class in org.biojava.bio.structure.align.helper
A utility class that defines which set of atoms are considered to be on equivalent positions.
JointFragments() - Constructor for class org.biojava.bio.structure.align.helper.JointFragments
 
jointFragments(JointFragments[]) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
 
JournalArticle - Class in org.biojava.bio.structure
PDB-specific
JournalArticle() - Constructor for class org.biojava.bio.structure.JournalArticle
 
JPrintPanel - Class in org.biojava.bio.structure.align.gui
 
JPrintPanel() - Constructor for class org.biojava.bio.structure.align.gui.JPrintPanel
 
Jronn - Class in org.biojava3.ronn
This class gives public API to RONN functions.
Jronn() - Constructor for class org.biojava3.ronn.Jronn
 
Jronn.Range - Class in org.biojava3.ronn
Holder for the ranges, contain pointers to starting and ending position on the sequence which comprises a disordered region.
Jronn.Range(int, int) - Constructor for class org.biojava3.ronn.Jronn.Range
 

K

K - Static variable in class org.biojava3.aaproperties.Constraints
 
KEGG_STR - Static variable in interface org.forester.go.GoXRef
 
keyReleased(KeyEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
takes care of the cursor up/down keys.
keyReleased(KeyEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
takes care of the cursor up/down keys.
keySet() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 

L

L - Static variable in class org.biojava3.aaproperties.Constraints
 
label() - Method in enum org.biojava3.protmod.ModificationCategory
 
label() - Method in enum org.biojava3.protmod.ModificationOccurrenceType
 
lastIndexOf(Sequence<C>, C) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into SequenceMixin.indexOf(Sequence, Compound).
LENGTH - Static variable in class org.biojava3.core.sequence.features.AbstractFeature
Sort features by length.
length() - Method in class org.biojava3.genome.parsers.gff.Location
Get length of range.
Leu - Static variable in class org.biojava3.phylo.ResidueProperties
 
levelOrderReID(int) - Method in class org.forester.phylogeny.Phylogeny
Resets the ID numbers of the nodes of this Phylogeny in level order, starting with start_label (for the root).
LevelOrderTreeIterator - Class in org.forester.phylogeny.iterators
 
LevelOrderTreeIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.LevelOrderTreeIterator
Creates a new LevelOrderTreeIterator for iterating over all the nodes of Phylogeny phylogeny
LevelOrderTreeIterator(PhylogenyNode) - Constructor for class org.forester.phylogeny.iterators.LevelOrderTreeIterator
Creates a new LevelOrderTreeIterator for iterating over all the child nodes of PhylogenyNode node (including node itself).
lighter(Color, double) - Static method in class org.biojava.bio.structure.gui.util.color.ColorUtils
Make a color lighter.
LightweightProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.core.sequence.template
Defines a minimal data structure for reading and writing a sequence alignment.
LightweightProfile.StringFormat - Enum in org.biojava3.core.sequence.template
List of output formats.
LIMIT_SPECIES_NAMES_TO_FIVE_CHARS - Static variable in class org.forester.io.parsers.nhx.NHXParser
 
limitRangeForColor(int) - Static method in class org.forester.util.ForesterUtil
Helper for method "stringToColor".
LINE_HEIGHT - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
LINE_SEPARATOR - Static variable in class org.forester.util.ForesterUtil
 
LinearColorInterpolator - Class in org.biojava.bio.structure.gui.util.color
 
LinearColorInterpolator() - Constructor for class org.biojava.bio.structure.gui.util.color.LinearColorInterpolator
 
LinearColorInterpolator(ColorSpace) - Constructor for class org.biojava.bio.structure.gui.util.color.LinearColorInterpolator
 
LinearColorInterpolator.InterpolationDirection - Enum in org.biojava.bio.structure.gui.util.color
 
lineSplit - Static variable in class org.biojava.bio.structure.io.LocalCacheStructureProvider
 
lineSplit - Static variable in class org.biojava.bio.structure.io.MMCIFFileReader
 
lineSplit - Static variable in class org.biojava.bio.structure.io.PDBFileReader
 
linkChains2Compound(Structure) - Method in class org.biojava.bio.structure.io.PDBFileParser
After the parsing of a PDB file the Chain and Compound objects need to be linked to each other.
listToSortedCountsMap(List) - Static method in class org.forester.util.ForesterUtil
 
LIT_REF_DOI_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
load() - Method in class org.biojava.bio.structure.align.webstart.PersistentConfig
loads Config from PersistenceService returns null if no PErsistenceService has been created ...
LOAD_ALIGNMENT_XML - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
LOAD_CHEM_COMP_PROPERTY - Static variable in class org.biojava.bio.structure.io.PDBFileReader
 
LOAD_DB_RESULTS - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
loadFastaAddGeneFeaturesFromGeneIDGFF2(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm
loadFastaAddGeneFeaturesFromGeneMarkGTF(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
loadFastaAddGeneFeaturesFromGlimmerGFF3(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
loadFastaAddGeneFeaturesFromGmodGFF3(File, File, boolean) - Static method in class org.biojava3.genome.GeneFeatureHelper
Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File, File, boolean) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
loadXML(String) - Static method in class org.biojava3.core.util.XMLHelper
 
LOCAL_PHYLOXML_XSD_RESOURCE - Static variable in class org.forester.util.ForesterConstants
 
LocalCacheStructureProvider - Class in org.biojava.bio.structure.io
Provides structures based on locally cached PDB files.
LocalCacheStructureProvider() - Constructor for class org.biojava.bio.structure.io.LocalCacheStructureProvider
 
LocalProteinDomainParser - Class in org.biojava.bio.structure.domain
Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
location(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
location(List<Location>, String) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Builds a location from a List of locations; this can be circular or linear joins.
location(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
Location - Interface in org.biojava3.core.sequence.location.template
Sets of integers used to represent the location of features on sequence.
location(List<Location>, Integer, String) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Used for building a location from a series of sub-locations
location(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
location() - Method in class org.biojava3.genome.parsers.gff.Feature
Get location of feature.
location() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get the location of the feature.
Location - Class in org.biojava3.genome.parsers.gff
A location on a sequence.
Location(int, int) - Constructor for class org.biojava3.genome.parsers.gff.Location
Construct new location from coordinates.
Location(Location) - Constructor for class org.biojava3.genome.parsers.gff.Location
Clone other location.
Location.Tools - Class in org.biojava3.core.sequence.location.template
Helper methods for use with the Location classes.
Location.Tools() - Constructor for class org.biojava3.core.sequence.location.template.Location.Tools
 
LOCATION_LENGTH - Static variable in class org.biojava3.core.sequence.features.AbstractFeature
Sort features by start position and then longest length.
LocationHelper - Class in org.biojava3.core.sequence.location
Helper methods for use with the Location classes.
LocationHelper() - Constructor for class org.biojava3.core.sequence.location.LocationHelper
 
LocIterator - Class in org.biojava3.genome.parsers.gff
Move a sliding window over a Location.
LocIterator(Location, int, int) - Constructor for class org.biojava3.genome.parsers.gff.LocIterator
Construct an iterator that slides a window over a Location.
log(String) - Static method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
LogBranchLengthBasedScoringMethod - Class in org.forester.pccx
 
LogBranchLengthBasedScoringMethod() - Constructor for class org.forester.pccx.LogBranchLengthBasedScoringMethod
 
LogColorMapper - Class in org.biojava.bio.structure.gui.util.color
Performs a log10 transform on input before passing the values off to another colorMapper.
LogColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.bio.structure.gui.util.color.LogColorMapper
Creates a new LogColorMapper with base 10.
LogColorMapper(ContinuousColorMapper, int) - Constructor for class org.biojava.bio.structure.gui.util.color.LogColorMapper
If logspaceMapper maps values x1 to x2, this creates a mapper for values base^x1 to base^x2
logger - Static variable in class org.biojava.bio.structure.align.gui.AlignmentCalc
 
logger - Static variable in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
logger - Static variable in class org.biojava.bio.structure.align.gui.AlignmentGui
 
logger - Static variable in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
logger - Static variable in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
 
logger - Static variable in class org.biojava.bio.structure.align.webstart.BrowserOpener
 
logger - Static variable in class org.biojava.bio.structure.gui.util.AlignmentCalc
 
logger - Static variable in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
 
logger - Static variable in class org.biojava.bio.structure.gui.util.PDBDirPanel
 
logger - Static variable in class org.biojava.bio.structure.gui.util.PDBServerPanel
 
logger - Static variable in class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
logger - Static variable in class org.biojava.bio.structure.gui.util.ScopSelectPanel
 
logger - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
logger - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
logger - Static variable in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
logger - Static variable in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
logger - Static variable in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
 
logger - Static variable in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
logger - Static variable in class org.biojava.bio.structure.StructureTools
 
logPDBInfoFile(PrintWriter, PrintWriter, StructureIOFile, File[]) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
 
logStatus(String) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
logStatus(String) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
 
logStatus(String) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
LOOP_END - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
LOOP_START - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
lowercaseName() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
lu() - Method in class org.biojava.bio.structure.jama.Matrix
LU Decomposition
LUDecomposition - Class in org.biojava.bio.structure.jama
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.LUDecomposition
LU Decomposition provides a data structure to access L, U and piv.
Lys - Static variable in class org.biojava3.phylo.ResidueProperties
 

M

M - Static variable in class org.biojava3.aaproperties.Constraints
 
main(String[]) - Static method in class org.biojava.bio.structure.align.ce.CeCPMain
 
main(String[]) - Static method in class org.biojava.bio.structure.align.ce.CeMain
Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna
main(String[]) - Static method in class org.biojava.bio.structure.align.ce.CeSideChainMain
 
main(String[]) - Static method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
main(String[]) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
main(String[]) - Static method in class org.biojava.bio.structure.align.FarmJob
 
main(String[]) - Static method in class org.biojava.bio.structure.align.fatcat.FatCat
See demo/FatCatDemo.java for an example how to run.
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.DBResultTable
 
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.DotPlotPanel
 
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.jmol.AtomInfoParser
 
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.jmol.JmolTools
 
main(String[]) - Static method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
main(String[]) - Static method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
main(String[]) - Static method in class org.biojava.bio.structure.align.StructurePairAligner
example usage of this class
main(String[]) - Static method in class org.biojava.bio.structure.align.webstart.JNLPProxy
 
main(String[]) - Static method in class org.biojava.bio.structure.align.webstart.WebStartDBSearch
 
main(String[]) - Static method in class org.biojava.bio.structure.align.webstart.WebStartDBSearchResults
 
main(String[]) - Static method in class org.biojava.bio.structure.align.webstart.WebStartMain
If no arguments, shows AlignmentGui for pairwise alignments.
main(String[]) - Static method in class org.biojava.bio.structure.domain.RemoteDomainProvider
 
main(String[]) - Static method in class org.biojava.bio.structure.domain.RemotePDPProvider
 
main(String[]) - Static method in class org.biojava.bio.structure.gui.BiojavaJmol
 
main(String[]) - Static method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
main(String[]) - Static method in class org.biojava.bio.structure.gui.SequenceDisplay
 
main(String[]) - Static method in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
main(String[]) - Static method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
main(String[]) - Static method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
main(String[]) - Static method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
main(String[]) - Static method in class org.biojava.bio.structure.io.MMCIFFileReader
 
main(String[]) - Static method in class org.biojava.bio.structure.io.PDBFileReader
 
main(String[]) - Static method in class org.biojava.bio.structure.io.sifts.SiftsMappingProvider
 
main(String[]) - Static method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
main(String[]) - Static method in class org.biojava.bio.structure.secstruc.SecStruc
 
main(String[]) - Static method in class org.biojava3.aaproperties.CommandPrompt
The main method
main(String[]) - Static method in class org.biojava3.core.sequence.DNASequence
 
main(String[]) - Static method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
 
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaGeneWriter
 
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaReader
 
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
 
main(String[]) - Static method in class org.biojava3.core.sequence.io.FastaWriter
 
main(String[]) - Static method in class org.biojava3.core.sequence.io.GenericFastaHeaderParser
 
main(String[]) - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
main(String[]) - Static method in class org.biojava3.core.sequence.ProteinSequence
 
main(String[]) - Static method in class org.biojava3.core.util.UncompressInputStream
 
main(String[]) - Static method in class org.biojava3.genome.App
 
main(String[]) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
main(String[]) - Static method in class org.biojava3.genome.homology.GFF3FromUniprotBlastHits
 
main(String[]) - Static method in class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.Feature
Deprecated. 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.FeatureList
Deprecated. 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GeneMarkGTFReader
 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GFF3Reader
 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.GFF3Writer
 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.Location
Deprecated. 
main(String[]) - Static method in class org.biojava3.genome.parsers.gff.LocIterator
Deprecated. 
main(String[]) - Static method in class org.biojava3.genome.query.BlastXMLQuery
 
main(String[]) - Static method in class org.biojava3.genome.query.OutputHitsGFF
 
main(String[]) - Static method in class org.biojava3.genome.uniprot.UniprotToFasta
 
main(String[]) - Static method in class org.biojava3.genome.util.SplitFasta
 
main(String[]) - Static method in class org.biojava3.phylo.App
 
main(String[]) - Static method in class org.biojava3.phylo.ResidueProperties
 
main(String[]) - Static method in class org.biojava3.phylo.TreeConstructor
 
main(String[]) - Static method in class org.biojava3.ronn.ModelLoader
 
main(String[]) - Static method in class org.biojava3.ronn.ORonn
 
main(String[]) - Static method in class org.forester.application.confadd
 
main(String[]) - Static method in class org.forester.application.count_support
 
main(String[]) - Static method in class org.forester.application.decorator
 
main(String[]) - Static method in class org.forester.application.get_distances
 
main(String[]) - Static method in class org.forester.application.goac
 
main(String[]) - Static method in class org.forester.application.meta_ontologizer
 
main(String[]) - Static method in class org.forester.application.nhx_too
 
main(String[]) - Static method in class org.forester.application.nj
 
main(String[]) - Static method in class org.forester.application.obo_tool
 
main(String[]) - Static method in class org.forester.application.pccx
 
main(String[]) - Static method in class org.forester.application.perfume
 
main(String[]) - Static method in class org.forester.application.pfam2go_extractor
 
main(String[]) - Static method in class org.forester.application.pfam_go
 
main(String[]) - Static method in class org.forester.application.phyloxml_converter
 
main(String[]) - Static method in class org.forester.application.printAllSpecies
 
main(String[]) - Static method in class org.forester.application.printSameOrder
 
main(String[]) - Static method in class org.forester.application.rio
 
main(String[]) - Static method in class org.forester.application.sdi
 
main(String[]) - Static method in class org.forester.application.sdi_r
 
main(String[]) - Static method in class org.forester.application.shin
 
main(String[]) - Static method in class org.forester.application.strip
 
main(String[]) - Static method in class org.forester.application.support_statistics
 
main(String[]) - Static method in class org.forester.application.support_transfer
Transfers branch length values from one Phylogeny to another.
main(String[]) - Static method in class org.forester.application.surf_paup
 
main(String[]) - Static method in class org.forester.application.surfacing
 
main(String[]) - Static method in class org.forester.application.surfacing_old
 
main(String[]) - Static method in class org.forester.application.ta
 
main(String[]) - Static method in class org.forester.archaeopteryx.Archaeopteryx
 
main(String[]) - Static method in class org.forester.development.Test
 
main(String[]) - Static method in class org.forester.phylogenyinference.TestPhylogenyReconstruction
 
main(String[]) - Static method in class org.forester.sdi.DistanceCalculator
 
main(String[]) - Static method in class org.forester.sdi.ORcount
Main method for this class.
main(String[]) - Static method in class org.forester.sdi.SDIdirectory
Main method for this class.
main(String[]) - Static method in class org.forester.test.Test
 
MainFrame - Class in org.forester.archaeopteryx
 
MainFrameApplet - Class in org.forester.archaeopteryx
 
MainFrameApplication - Class in org.forester.archaeopteryx
 
MainPanel - Class in org.forester.archaeopteryx
 
mandatoryArgs - Static variable in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
mapper - Variable in class org.biojava.bio.structure.gui.util.color.ContinuousColorMapperTransform
 
Mapping - Interface in org.forester.go
 
MappingResults - Class in org.forester.surfacing
 
MappingResults() - Constructor for class org.forester.surfacing.MappingResults
 
mapToStringBuffer(Map, String) - Static method in class org.forester.util.ForesterUtil
 
MapToStringTransformer - Class in org.biojava3.ws.alignment.qblast
Transforms Map to String.
MapToStringTransformer() - Constructor for class org.biojava3.ws.alignment.qblast.MapToStringTransformer
Creates MapToStringTransformer with defaults:
MapToStringTransformer(String, String, String) - Constructor for class org.biojava3.ws.alignment.qblast.MapToStringTransformer
Creates MapToStringTransformer with given values
mark(int) - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Marks the present position in the stream.
markPathToRoot(PhylogenyNode, boolean) - Method in class org.biojava3.phylo.CheckTreeAccuracy
 
markPathToRoot(PhylogenyNode, boolean) - Method in class org.forester.application.CheckTreeAccuracy
 
markSupported() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Tells whether this stream supports the mark() operation, which it does.
markSupported() - Method in class org.biojava3.core.util.UncompressInputStream
This stream does not support mark/reset on the stream.
mat - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
mat - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
match(Set<PhylogenyNode>) - Method in class org.forester.tools.TreeSplitMatrix
 
matchSequenceToStructure(ProteinSequence, Structure) - Static method in class org.biojava.bio.structure.io.StructureSequenceMatcher
Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.
Maths - Class in org.biojava.bio.structure.jama
 
Maths() - Constructor for class org.biojava.bio.structure.jama.Maths
 
Matrix - Class in org.biojava.bio.structure.jama
Jama = Java Matrix class.
Matrix(int, int) - Constructor for class org.biojava.bio.structure.jama.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class org.biojava.bio.structure.jama.Matrix
Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class org.biojava.bio.structure.jama.Matrix
Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class org.biojava.bio.structure.jama.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class org.biojava.bio.structure.jama.Matrix
Construct a matrix from a one-dimensional packed array
matrix - Static variable in class org.biojava3.alignment.SimpleProfile
 
MATRIX - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
MatrixAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an Aligner which builds a score matrix during computation.
matrixFromEuler(double, double, double) - Static method in class org.biojava.bio.structure.Calc
This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank.
matrixInOptimizer(double[][]) - Method in interface org.biojava.bio.structure.align.ce.MatrixListener
 
MatrixListener - Interface in org.biojava.bio.structure.align.ce
 
max - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
MAX_ALLOWED_BL_VALUE - Static variable in class org.forester.pccx.LogBranchLengthBasedScoringMethod
 
MAX_ATOMS - Static variable in class org.biojava.bio.structure.io.FileParsingParameters
the maximum number of atoms we will add to a structure this protects from memory overflows in the few really big protein structures.
MAX_CUTS - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
MAX_RESOLVER - Static variable in class org.biojava3.core.sequence.location.FuzzyPoint
Always uses the max point to resolve a location
MAX_SCALE - Static variable in class org.biojava.bio.structure.gui.SequenceDisplay
the maximum value that the scale can get
MAX_SIMILARITY_SCORE - Static variable in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
MAXCONT - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
MAXDOM - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
maxGapSize - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
maximumQualityScore() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return the maximum quality score for this FASTQ sequence format variant.
MAXLEN - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
maxNrIterationsForOptimization - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
maxOptRMSD - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
MAXSIZE - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
MEAN_RESOLVER - Static variable in class org.biojava3.core.sequence.location.FuzzyPoint
Combines min and max and then gets the mean of it
median() - Method in class org.forester.util.BasicDescriptiveStatistics
 
median() - Method in interface org.forester.util.DescriptiveStatistics
 
MenuCreator - Class in org.biojava.bio.structure.align.gui
Create the menu for Fatcat/CE structure alignment stuff
MenuCreator() - Constructor for class org.biojava.bio.structure.align.gui.MenuCreator
 
MenuCreator - Class in org.biojava.bio.structure.gui.util
Create the menu for BiojavaJmol
MenuCreator() - Constructor for class org.biojava.bio.structure.gui.util.MenuCreator
 
Met - Static variable in class org.biojava3.phylo.ResidueProperties
 
META_CYC_STR - Static variable in interface org.forester.go.GoXRef
 
meta_ontologizer - Class in org.forester.application
 
meta_ontologizer() - Constructor for class org.forester.application.meta_ontologizer
 
MetaOntologizer - Class in org.forester.go.etc
 
MetaOntologizer() - Constructor for class org.forester.go.etc.MetaOntologizer
 
method1(List<File>, Phylogeny[], File) - Method in class org.forester.sdi.Shin
 
mid - Variable in class org.biojava.bio.structure.align.ce.CeCPMain.CPRange
midpoint of the alignment
midBlue - Static variable in class org.biojava3.phylo.ResidueProperties
 
midpointRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
midrange() - Method in class org.forester.util.BasicDescriptiveStatistics
 
midrange() - Method in interface org.forester.util.DescriptiveStatistics
 
min - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
MIN_ALLOWED_BL_VALUE - Static variable in class org.forester.pccx.BranchLengthBasedScoringMethod
 
MIN_ALLOWED_BL_VALUE - Static variable in class org.forester.pccx.LogBranchLengthBasedScoringMethod
 
MIN_DOMAIN_LENGTH - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
MIN_RESOLVER - Static variable in class org.biojava3.core.sequence.location.FuzzyPoint
Always uses the min point to resolve a location
MIN_SIMILARITY_SCORE - Static variable in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
MINDIST - Static variable in class org.biojava.bio.structure.secstruc.SecStruc
the minimal distance between two residues
MINIMUM_HEIGHT - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
minimumQualityScore() - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return the minimum quality score for this FASTQ sequence format variant.
minus(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
C = A - B
minus() - Method in class org.biojava3.genome.parsers.gff.Location
Return location that is in same position on negative strand.
minusEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
A = A - B
MMCIF_FORMAT - Static variable in class org.biojava.bio.structure.align.util.UserConfiguration
 
MMcifConsumer - Interface in org.biojava.bio.structure.io.mmcif
An interface for the events triggered by a MMcifParser.
MMCIFFileInstallation - Class in org.biojava.bio.structure.server
Deprecated. 
MMCIFFileInstallation(File) - Constructor for class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
MMCIFFileReader - Class in org.biojava.bio.structure.io
How to parse an mmCif file:
MMCIFFileReader() - Constructor for class org.biojava.bio.structure.io.MMCIFFileReader
 
MMcifParser - Interface in org.biojava.bio.structure.io.mmcif
Interface that needs to be implemented by an MMcifParser
ModelingUtils - Class in org.forester.pccx
 
ModelingUtils() - Constructor for class org.forester.pccx.ModelingUtils
 
ModelLoader - Class in org.biojava3.ronn
Class that loads data from the model files into ModelLoader.Model objects
ModelLoader() - Constructor for class org.biojava3.ronn.ModelLoader
 
ModelLoader.Model - Class in org.biojava3.ronn
Represent a RONN model
ModelLoader.Model(int, int) - Constructor for class org.biojava3.ronn.ModelLoader.Model
 
ModelLoader.Threshold - Class in org.biojava3.ronn
Represents a Threshold
ModelLoader.Threshold(int) - Constructor for class org.biojava3.ronn.ModelLoader.Threshold
 
ModificationCategory - Enum in org.biojava3.protmod
define modification categories.
ModificationCondition - Interface in org.biojava3.protmod
Conditions of a protein modification, e.g.
ModificationConditionImpl - Class in org.biojava3.protmod
 
ModificationConditionImpl(List<Component>, List<ModificationLinkage>) - Constructor for class org.biojava3.protmod.ModificationConditionImpl
 
ModificationLinkage - Class in org.biojava3.protmod
 
ModificationLinkage(List<Component>, int, int) - Constructor for class org.biojava3.protmod.ModificationLinkage
 
ModificationLinkage(List<Component>, int, String, int, String) - Constructor for class org.biojava3.protmod.ModificationLinkage
 
ModificationLinkage(List<Component>, int, List<String>, int, List<String>) - Constructor for class org.biojava3.protmod.ModificationLinkage
 
ModificationLinkage(List<Component>, int, List<String>, String, int, List<String>, String) - Constructor for class org.biojava3.protmod.ModificationLinkage
 
ModificationOccurrenceType - Enum in org.biojava3.protmod
 
ModifiedAminoAcidCompoundSet - Class in org.biojava3.aaproperties.xml
 
ModifiedAminoAcidCompoundSet(List<AminoAcidComposition>, Map<Character, Double>) - Constructor for class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
ModifiedCompound - Interface in org.biojava3.protmod.structure
Root interface for all modifications in structure.
ModifiedCompoundImpl - Class in org.biojava3.protmod.structure
 
ModifiedCompoundImpl() - Constructor for class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
ModifiedCompoundImpl(ProteinModification, StructureGroup) - Constructor for class org.biojava3.protmod.structure.ModifiedCompoundImpl
Create a ModifiedCompoundImpl that has only one involved component.
ModifiedCompoundImpl(ProteinModification, Collection<StructureAtomLinkage>) - Constructor for class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
ModifiedCompoundXMLConverter - Class in org.biojava3.protmod.io
 
ModifiedCompoundXMLConverter() - Constructor for class org.biojava3.protmod.io.ModifiedCompoundXMLConverter
 
modifiedStructure(StructureEvent) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
modifiedStructure(StructureEvent) - Method in interface org.biojava.bio.structure.server.StructureListener
 
modulateCircularIndex(int, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
modulateCircularIndex(int, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
MOLECULAR_FUNCTION_STR - Variable in class org.forester.go.GoNameSpace
 
mouseClicked(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseClicked(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
mouseClicked(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mouseClicked(MouseEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
mouseClicked(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseDragged(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseDragged(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mouseDragged(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
mouseEntered(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mouseEntered(MouseEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
mouseEntered(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseExited(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseExited(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
mouseExited(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mouseExited(MouseEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
mouseExited(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseMoved(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseMoved(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mouseMoved(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
mouseOverPosition(AlignedPosition) - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
 
mouseOverPosition(AlignedPosition) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
mousePressed(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mousePressed(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
mousePressed(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mousePressed(MouseEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
mousePressed(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
mouseReleased(MouseEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
mouseReleased(MouseEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
mouseReleased(MouseEvent) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.forester.archaeopteryx.TreePanel
 
moveBranchLengthsToBootstrap(Phylogeny) - Static method in class org.forester.application.support_transfer
Moves the values in the branch length field to the bootstrap field, for each PhylogenyNode of this Phylogeny.
mPanel - Variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
Msa - Interface in org.forester.development
 
MsaFactory - Interface in org.forester.development
 
multipleFrameTranslation(Sequence<NucleotideCompound>, Frame...) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
A way of translating DNA in a number of frames
MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.core.sequence
Implements a minimal data structure for reading and writing a sequence alignment.
MultipleSequenceAlignment() - Constructor for class org.biojava3.core.sequence.MultipleSequenceAlignment
 
MutableAlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
mutate(Structure, String, String, String) - Method in class org.biojava.bio.structure.Mutator
creates a new structure which is identical with the original one.
mutateResidue(AminoAcid, String) - Method in class org.biojava.bio.structure.Mutator
create a new residue which is of the new type.
Mutator - Class in org.biojava.bio.structure
A class that can change one amino acid to another.
Mutator() - Constructor for class org.biojava.bio.structure.Mutator
 
MyAlignmentLoadListener - Class in org.biojava.bio.structure.align.gui
 
MyAlignmentLoadListener(StructureAlignmentJmol) - Constructor for class org.biojava.bio.structure.align.gui.MyAlignmentLoadListener
 
MyDistMaxListener - Class in org.biojava.bio.structure.align.gui
 
MyExportListener - Class in org.biojava.bio.structure.align.gui
 
MyJmolStatusListener - Class in org.biojava.bio.structure.align.gui.jmol
 
MyJmolStatusListener() - Constructor for class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
MyOpenPdbFileListener - Class in org.biojava.bio.structure.align.gui
 
MyOpenPdbFileListener() - Constructor for class org.biojava.bio.structure.align.gui.MyOpenPdbFileListener
 
MySaveFileListener - Class in org.biojava.bio.structure.align.gui
 
MySaveFileListener(AFPChain) - Constructor for class org.biojava.bio.structure.align.gui.MySaveFileListener
 
MyTableRowSorter - Class in org.biojava.bio.structure.align.gui
 
MyTableRowSorter(TableModel) - Constructor for class org.biojava.bio.structure.align.gui.MyTableRowSorter
 
MyValidationEventHandler - Class in org.biojava3.aaproperties.xml
 
MyValidationEventHandler() - Constructor for class org.biojava3.aaproperties.xml.MyValidationEventHandler
 

N

n - Variable in class org.biojava.bio.structure.align.ce.CeCPMain.CPRange
last allowed n-term
N - Static variable in class org.biojava3.aaproperties.Constraints
 
name - Variable in class org.biojava.bio.structure.align.client.StructureName
 
NAME - Static variable in class org.forester.archaeopteryx.ArchaeopteryxA
 
Name2Count - Class in org.biojava3.aaproperties.xml
 
Name2Count() - Constructor for class org.biojava3.aaproperties.xml.Name2Count
 
Name2Count(String, int) - Constructor for class org.biojava3.aaproperties.xml.Name2Count
 
nAtomName - Static variable in class org.biojava.bio.structure.StructureTools
 
nBestTrace - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
nBestTrace - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
nBestTraces - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
nBestTraces - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
NCBIQBlastAlignmentProperties - Class in org.biojava3.ws.alignment.qblast
This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.
NCBIQBlastAlignmentProperties() - Constructor for class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
 
NCBIQBlastOutputProperties - Class in org.biojava3.ws.alignment.qblast
This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.
NCBIQBlastOutputProperties() - Constructor for class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:
NCBIQBlastService - Class in org.biojava3.ws.alignment.qblast
Provides a simple way of submitting BLAST request to the QBlast service at NCBI.
NCBIQBlastService() - Constructor for class org.biojava3.ws.alignment.qblast.NCBIQBlastService
 
NCHAR - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
NeedlemanWunsch<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
NeedlemanWunsch() - Constructor for class org.biojava3.alignment.NeedlemanWunsch
Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
NeedlemanWunsch(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.NeedlemanWunsch
Prepares for a pairwise global sequence alignment.
negative - Static variable in class org.biojava3.phylo.ResidueProperties
 
NEGATIVELY_REGULATES_STR - Static variable in interface org.forester.go.GoRelationship
 
NeighborJoining - Class in org.forester.phylogenyinference
 
newAtomSite(AtomSite) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newAtomSite(AtomSite) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
A new AtomSite record has been read.
newAtomSite(AtomSite) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newAuditAuthor(AuditAuthor) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newAuditAuthor(AuditAuthor) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
AuditAuthor contains the info from the PDB-AUTHOR records.
newAuditAuthor(AuditAuthor) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newChemComp(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newChemComp(ChemComp) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newChemComp(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newChemCompDescriptor(ChemCompDescriptor) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newDatabasePDBremark(DatabasePDBremark) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newDatabasePDBremark(DatabasePDBremark) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newDatabasePDBremark(DatabasePDBremark) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newDatabasePDBrev(DatabasePDBrev) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newDatabasePDBrev(DatabasePDBrev) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newDatabasePDBrev(DatabasePDBrev) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newEntity(Entity) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newEntity(Entity) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newEntity(Entity) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newEntityPolySeq(EntityPolySeq) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newEntityPolySeq(EntityPolySeq) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
The EntityPolySeq object provide the amino acid sequence objects for the Entities.
newExptl(Exptl) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newExptl(Exptl) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newExptl(Exptl) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newGenericData(String, List<String>, List<String>) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newGenericData(String, List<String>, List<String>) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
This method is called if no particular handler for the provided cif category has been implemented so far.
newGenericData(String, List<String>, List<String>) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newline - Static variable in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
newline - Static variable in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
newline - Static variable in class org.biojava.bio.structure.align.fatcat.FatCat
 
newline - Static variable in class org.biojava.bio.structure.align.model.AFPChain
 
newline - Static variable in class org.biojava.bio.structure.align.model.AfpChainWriter
 
newline - Static variable in class org.biojava.bio.structure.PDBHeader
 
NEWLINE - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
newline - Static variable in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.compound.DNACompoundSet
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.compound.RNACompoundSet
 
newNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
 
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newPdbxNonPolyScheme(PdbxNonPolyScheme) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newPdbxPolySeqScheme(PdbxPolySeqScheme) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newRefine(Refine) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newRefine(Refine) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newRefine(Refine) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newStructAsym(StructAsym) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newStructAsym(StructAsym) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newStructAsym(StructAsym) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newStructKeywords(StructKeywords) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newStructKeywords(StructKeywords) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newStructKeywords(StructKeywords) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newStructRef(StructRef) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newStructRef(StructRef) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newStructRef(StructRef) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
newStructRefSeq(StructRefSeq) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
newStructRefSeq(StructRefSeq) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
newStructRefSeq(StructRefSeq) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
create a DBRef record from the StrucRefSeq record:
newStructure(StructureEvent) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
newStructure(StructureEvent) - Method in interface org.biojava.bio.structure.server.StructureListener
 
next() - Method in class org.biojava.bio.structure.AtomIterator
Return next atom.
next() - Method in class org.biojava.bio.structure.GroupIterator
get next Group.
next() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
next() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
 
next() - Method in interface org.biojava.bio.structure.server.PDBInstallation
Deprecated.
iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
next() - Method in class org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator
 
next() - Method in class org.biojava3.genome.parsers.gff.LocIterator
Get next window of default size, then increment position by default amount.
next(int, int) - Method in class org.biojava3.genome.parsers.gff.LocIterator
Get next window of specified size, then increment position by specified amount.
next() - Method in class org.forester.phylogeny.iterators.ChildNodeIteratorForward
Returns the next PhylogenyNode.
next() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator
 
next() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator
Returns the next PhylogenyNode.
next() - Method in interface org.forester.phylogeny.iterators.PhylogenyNodeIterator
 
next() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator
Advances the Iterator by one.
next() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator
Advances the Iterator by one.
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
NEXUS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
NEXUS_EXTERNAL_DOMAIN_COMBINATIONS - Static variable in class org.forester.application.surfacing
 
NEXUS_EXTERNAL_DOMAIN_COMBINATIONS - Static variable in class org.forester.application.surfacing_old
 
NEXUS_EXTERNAL_DOMAINS - Static variable in class org.forester.application.surfacing
 
NEXUS_EXTERNAL_DOMAINS - Static variable in class org.forester.application.surfacing_old
 
NEXUS_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing
 
NEXUS_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing_old
 
NexusBinaryStatesMatrixParser - Class in org.forester.io.parsers.nexus
 
NexusBinaryStatesMatrixParser() - Constructor for class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
 
NexusCharactersParser - Class in org.forester.io.parsers.nexus
 
NexusCharactersParser() - Constructor for class org.forester.io.parsers.nexus.NexusCharactersParser
 
NexusConstants - Class in org.forester.io.parsers.nexus
 
NexusConstants() - Constructor for class org.forester.io.parsers.nexus.NexusConstants
 
NexusFormatException - Exception in org.forester.io.parsers.nexus
 
NexusFormatException() - Constructor for exception org.forester.io.parsers.nexus.NexusFormatException
 
NexusFormatException(String) - Constructor for exception org.forester.io.parsers.nexus.NexusFormatException
 
NexusPhylogeniesParser - Class in org.forester.io.parsers.nexus
 
NexusPhylogeniesParser() - Constructor for class org.forester.io.parsers.nexus.NexusPhylogeniesParser
 
NH_PARSING_IGNORE_QUOTES_DEFAULT - Static variable in class org.forester.archaeopteryx.Constants
 
NHX_SEPARATOR - Static variable in class org.forester.phylogeny.data.DomainArchitecture
 
nhx_too - Class in org.forester.application
 
nhx_too() - Constructor for class org.forester.application.nhx_too
 
NHXFormatException - Exception in org.forester.io.parsers.nhx
 
NHXFormatException() - Constructor for exception org.forester.io.parsers.nhx.NHXFormatException
 
NHXFormatException(String) - Constructor for exception org.forester.io.parsers.nhx.NHXFormatException
 
NHXParser - Class in org.forester.io.parsers.nhx
 
NHXParser() - Constructor for class org.forester.io.parsers.nhx.NHXParser
 
NHXParser.TAXONOMY_EXTRACTION - Enum in org.forester.io.parsers.nhx
 
NHXtags - Class in org.forester.io.parsers.nhx
 
NHXtags() - Constructor for class org.forester.io.parsers.nhx.NHXtags
 
nIter - Static variable in class org.biojava.bio.structure.align.ce.CECalculator
 
nIter - Static variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
nj - Class in org.forester.application
 
nj() - Constructor for class org.forester.application.nj
 
NJTreeProgressListener - Interface in org.biojava3.phylo
 
NL - Static variable in class org.forester.surfacing.SurfacingConstants
 
NODE_ID_ATTR - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
NODE_IDENTIFIER - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
NODE_ITALICIZENAME_ATTR - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
NODE_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
NodeData - Class in org.forester.phylogeny.data
 
NodeData() - Constructor for class org.forester.phylogeny.data.NodeData
 
NON_AA - Static variable in class org.biojava3.data.sequence.SequenceUtil
inversion of AA pattern
NON_NUCLEOTIDE - Static variable in class org.biojava3.data.sequence.SequenceUtil
Non nucleotide
NONE - Static variable in class org.forester.surfacing.SurfacingConstants
 
nonOverlappingKmers(Sequence<C>, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Produces kmers of the specified size e.g.
NONWORD - Static variable in class org.biojava3.data.sequence.SequenceUtil
Non word
norm1() - Method in class org.biojava.bio.structure.jama.Matrix
One norm
norm2() - Method in class org.biojava.bio.structure.jama.Matrix
Two norm
norm2() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Two norm
normalizeBootstrapValues(Phylogeny, double, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
normalizeMatrix(short) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
normalizeMatrix(short) - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
normalizeMatrix(short) - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.
normalizeString(String, int, boolean, char) - Static method in class org.forester.util.ForesterUtil
 
normF() - Method in class org.biojava.bio.structure.jama.Matrix
Frobenius norm
normInf() - Method in class org.biojava.bio.structure.jama.Matrix
Infinity norm
NOT_ALIGNED - Static variable in class org.biojava.bio.structure.gui.util.AlignedPosition
they can be shown in the same column (for a compact display) , but they are not structurally equivalent
notifyCalcFinished() - Method in class org.biojava.bio.structure.align.gui.AlignmentGui
 
notifyCalcFinished() - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
notifyCallback(EnumCallback, Object[]) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
notifyEnabled(org.jmol.constant.EnumCallback) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
notifyShutdown() - Method in class org.biojava.bio.structure.align.util.AtomCache
Send a signal to the cache that the system is shutting down.
nrModels() - Method in interface org.biojava.bio.structure.Structure
return number of models .
nrModels() - Method in class org.biojava.bio.structure.StructureImpl
return number of models.
NTAX - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
nTrace - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
nTrace - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
nTraces - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
nTraces - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
NUCLEOTIDE - Static variable in class org.biojava.bio.structure.GroupType
the type for nucelotide groups
NUCLEOTIDE - Static variable in class org.biojava3.data.sequence.SequenceUtil
Nucleotides a, t, g, c, u
nucleotide - Static variable in class org.biojava3.phylo.ResidueProperties
 
NUCLEOTIDE_LETTERS - Static variable in class org.biojava3.core.util.SequenceTools
 
NucleotideCompound - Class in org.biojava3.core.sequence.compound
 
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String) - Constructor for class org.biojava3.core.sequence.compound.NucleotideCompound
 
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String, NucleotideCompound[]) - Constructor for class org.biojava3.core.sequence.compound.NucleotideCompound
 
NucleotideImpl - Class in org.biojava.bio.structure
A nucleotide group is almost the same as a Hetatm group.
NucleotideImpl() - Constructor for class org.biojava.bio.structure.NucleotideImpl
 
nucleotideIndex - Static variable in class org.biojava3.phylo.ResidueProperties
 
nucleotideName - Static variable in class org.biojava3.phylo.ResidueProperties
 
NULL_BD - Static variable in class org.forester.util.ForesterUtil
 
NullOutputStream - Class in org.biojava3.ronn
The stream that void its input
NullOutputStream() - Constructor for class org.biojava3.ronn.NullOutputStream
 
numberSpeciesInDescOrder(Phylogeny) - Static method in class org.forester.development.DevelopmentTools
Sets the species namea of the external Nodes of Phylogeny t to descending integers, ending with 1.
numberSpeciesInOrder(Phylogeny) - Static method in class org.forester.development.DevelopmentTools
Sets the species namea of the external Nodes of Phylogeny t to ascending integers, starting with 1.
numericalEntity(char) - Method in class org.biojava3.core.util.PrettyXMLWriter
 

O

oAtomName - Static variable in class org.biojava.bio.structure.StructureTools
 
obo_tool - Class in org.forester.application
 
obo_tool() - Constructor for class org.forester.application.obo_tool
 
OBOparser - Class in org.forester.go
 
OBOparser(File, OBOparser.ReturnType) - Constructor for class org.forester.go.OBOparser
 
OBOparser.ReturnType - Enum in org.forester.go
 
obsoleteStructure(StructureEvent) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
obsoleteStructure(StructureEvent) - Method in interface org.biojava.bio.structure.server.StructureListener
 
obtainAllNodesAsSet(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
obtainAminoAcidCompositionTable(File) - Method in interface org.biojava3.aaproperties.IPeptideProperties
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Method in interface org.biojava3.aaproperties.IPeptideProperties
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File, File) - Static method in class org.biojava3.aaproperties.PeptideProperties
An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
obtainAminoAcidCompositionTable(File) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
obtainAminoAcidCompositionTable(File, File) - Method in class org.biojava3.aaproperties.PeptidePropertiesImpl
 
obtainReader(Object) - Static method in class org.forester.util.ForesterUtil
 
of(String) - Static method in class org.biojava3.protmod.Component
Get a Component that does not have to occur at terminals.
of(String, boolean, boolean) - Static method in class org.biojava3.protmod.Component
Get or create a Component.
of(Set<String>) - Static method in class org.biojava3.protmod.Component
Get a Component that does not have to occur at terminals.
of(Set<String>, boolean, boolean) - Static method in class org.biojava3.protmod.Component
Get or create a Component.
offset(int) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
offset(int) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
offset(int) - Method in interface org.biojava3.core.sequence.location.template.Point
Returns a new point offset by the given distance
omitOverlapping(String, Location, boolean) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that do not overlap the specified location on the specified sequence.
OntologizerResult - Class in org.forester.go.etc
 
OntologizerResult.TYPE - Enum in org.forester.go.etc
 
openFile(File) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
For a filename this code will check the extension of the file for a .gz extension.
openHttpURLConnection(URL, int) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
open HttpURLConnection.
openHttpURLConnection(URL) - Static method in class org.biojava.bio.structure.align.util.HTTPConnectionTools
open HttpURLConnection.
openStringInline(String) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
openTag(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
openTag(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
openTag(String, String) - Method in interface org.biojava3.core.util.XMLWriter
Open a new namespace-qualified XML tag.
openTag(String) - Method in interface org.biojava3.core.util.XMLWriter
Open a new unqualified XML tag.
opposite() - Method in class org.biojava3.genome.parsers.gff.Location
Return location that is in same position on opposite strand.
OptimalCECPMain - Class in org.biojava.bio.structure.align.ce
A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
OptimalCECPMain() - Constructor for class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
OptimalCECPParameters - Class in org.biojava.bio.structure.align.ce
Contains the parameters that can be sent to CE
OptimalCECPParameters() - Constructor for class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
optimizeAln(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
//optimize the alignment by dynamic programming
optimizeResult(int[], int, int[][]) - Method in class org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer
 
orange - Static variable in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
ORcount - Class in org.forester.sdi
 
ORcount(Phylogeny[]) - Constructor for class org.forester.sdi.ORcount
Default contructor which
orderAppearance(boolean) - Method in class org.forester.phylogeny.Phylogeny
Arranges the order of childern for each node of this Phylogeny in such a way that either the branch with more children is on top (right) or on bottom (left), dependent on the value of boolean order.
org.biojava.bio.structure - package org.biojava.bio.structure
Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align - package org.biojava.bio.structure.align
Classes for the alignment of structures.
org.biojava.bio.structure.align.ce - package org.biojava.bio.structure.align.ce
Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.bio.structure.align.client - package org.biojava.bio.structure.align.client
This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.bio.structure.align.events - package org.biojava.bio.structure.align.events
 
org.biojava.bio.structure.align.fatcat - package org.biojava.bio.structure.align.fatcat
Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.bio.structure.align.fatcat.calc - package org.biojava.bio.structure.align.fatcat.calc
 
org.biojava.bio.structure.align.gui - package org.biojava.bio.structure.align.gui
 
org.biojava.bio.structure.align.gui.aligpanel - package org.biojava.bio.structure.align.gui.aligpanel
 
org.biojava.bio.structure.align.gui.autosuggest - package org.biojava.bio.structure.align.gui.autosuggest
 
org.biojava.bio.structure.align.gui.jmol - package org.biojava.bio.structure.align.gui.jmol
Utility methods for better interaction with Jmol.
org.biojava.bio.structure.align.helper - package org.biojava.bio.structure.align.helper
Helper classes for structural alignment.
org.biojava.bio.structure.align.model - package org.biojava.bio.structure.align.model
 
org.biojava.bio.structure.align.pairwise - package org.biojava.bio.structure.align.pairwise
Classes for the pairwise alignment of structures.
org.biojava.bio.structure.align.seq - package org.biojava.bio.structure.align.seq
 
org.biojava.bio.structure.align.util - package org.biojava.bio.structure.align.util
 
org.biojava.bio.structure.align.webstart - package org.biojava.bio.structure.align.webstart
Classes related to Java Web Start
org.biojava.bio.structure.align.xml - package org.biojava.bio.structure.align.xml
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.bio.structure.domain - package org.biojava.bio.structure.domain
 
org.biojava.bio.structure.domain.pdp - package org.biojava.bio.structure.domain.pdp
 
org.biojava.bio.structure.gui - package org.biojava.bio.structure.gui
A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.bio.structure.gui.events - package org.biojava.bio.structure.gui.events
Some event classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util - package org.biojava.bio.structure.gui.util
Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util.color - package org.biojava.bio.structure.gui.util.color
 
org.biojava.bio.structure.io - package org.biojava.bio.structure.io
Input and Output of Structures
org.biojava.bio.structure.io.mmcif - package org.biojava.bio.structure.io.mmcif
Input and Output of mmcif files
org.biojava.bio.structure.io.mmcif.chem - package org.biojava.bio.structure.io.mmcif.chem
 
org.biojava.bio.structure.io.mmcif.model - package org.biojava.bio.structure.io.mmcif.model
Datamodel objects used for processing mmcif files.
org.biojava.bio.structure.io.sifts - package org.biojava.bio.structure.io.sifts
 
org.biojava.bio.structure.io.util - package org.biojava.bio.structure.io.util
 
org.biojava.bio.structure.jama - package org.biojava.bio.structure.jama
Matrix package for from JAMA
org.biojava.bio.structure.scop - package org.biojava.bio.structure.scop
Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.bio.structure.scop.server - package org.biojava.bio.structure.scop.server
 
org.biojava.bio.structure.secstruc - package org.biojava.bio.structure.secstruc
 
org.biojava.bio.structure.server - package org.biojava.bio.structure.server
classes for easier management of PDB installations As of BioJava 3.0.2 this package is deprecated.
org.biojava3.aaproperties - package org.biojava3.aaproperties
Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava3.aaproperties.profeat - package org.biojava3.aaproperties.profeat
Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava3.aaproperties.profeat.convertor - package org.biojava3.aaproperties.profeat.convertor
Set of classes that enable the conversion protein sequences into various attributes.
org.biojava3.aaproperties.xml - package org.biojava3.aaproperties.xml
Set of classes that handles the reading and writing of xml files.
org.biojava3.alignment - package org.biojava3.alignment
 
org.biojava3.alignment.aaindex - package org.biojava3.alignment.aaindex
 
org.biojava3.alignment.routines - package org.biojava3.alignment.routines
 
org.biojava3.alignment.template - package org.biojava3.alignment.template
 
org.biojava3.core.exceptions - package org.biojava3.core.exceptions
 
org.biojava3.core.sequence - package org.biojava3.core.sequence
 
org.biojava3.core.sequence.compound - package org.biojava3.core.sequence.compound
 
org.biojava3.core.sequence.edits - package org.biojava3.core.sequence.edits
 
org.biojava3.core.sequence.features - package org.biojava3.core.sequence.features
 
org.biojava3.core.sequence.io - package org.biojava3.core.sequence.io
 
org.biojava3.core.sequence.io.template - package org.biojava3.core.sequence.io.template
 
org.biojava3.core.sequence.io.util - package org.biojava3.core.sequence.io.util
 
org.biojava3.core.sequence.loader - package org.biojava3.core.sequence.loader
 
org.biojava3.core.sequence.location - package org.biojava3.core.sequence.location
 
org.biojava3.core.sequence.location.template - package org.biojava3.core.sequence.location.template
 
org.biojava3.core.sequence.storage - package org.biojava3.core.sequence.storage
 
org.biojava3.core.sequence.template - package org.biojava3.core.sequence.template
 
org.biojava3.core.sequence.transcription - package org.biojava3.core.sequence.transcription
 
org.biojava3.core.sequence.views - package org.biojava3.core.sequence.views
 
org.biojava3.core.util - package org.biojava3.core.util
 
org.biojava3.data.sequence - package org.biojava3.data.sequence
Set of classes that responsible for data handling.
org.biojava3.genome - package org.biojava3.genome
 
org.biojava3.genome.homology - package org.biojava3.genome.homology
 
org.biojava3.genome.parsers.geneid - package org.biojava3.genome.parsers.geneid
 
org.biojava3.genome.parsers.gff - package org.biojava3.genome.parsers.gff
 
org.biojava3.genome.query - package org.biojava3.genome.query
 
org.biojava3.genome.uniprot - package org.biojava3.genome.uniprot
 
org.biojava3.genome.util - package org.biojava3.genome.util
 
org.biojava3.phylo - package org.biojava3.phylo
 
org.biojava3.protmod - package org.biojava3.protmod
 
org.biojava3.protmod.io - package org.biojava3.protmod.io
 
org.biojava3.protmod.structure - package org.biojava3.protmod.structure
 
org.biojava3.ronn - package org.biojava3.ronn
BioJava provide a module biojava3-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava3.sequencing.io.fastq - package org.biojava3.sequencing.io.fastq
FASTQ and variants sequence format I/O.
org.biojava3.structure.gui - package org.biojava3.structure.gui
New MVC interface for structure-gui
org.biojava3.ws.alignment - package org.biojava3.ws.alignment
This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava3.ws.alignment.qblast - package org.biojava3.ws.alignment.qblast
 
org.biojava3.ws.hmmer - package org.biojava3.ws.hmmer
 
org.forester.application - package org.forester.application
 
org.forester.archaeopteryx - package org.forester.archaeopteryx
 
org.forester.archaeopteryx.phylogeny.data - package org.forester.archaeopteryx.phylogeny.data
 
org.forester.archaeopteryx.webservices - package org.forester.archaeopteryx.webservices
 
org.forester.datastructures - package org.forester.datastructures
 
org.forester.development - package org.forester.development
 
org.forester.go - package org.forester.go
 
org.forester.go.etc - package org.forester.go.etc
 
org.forester.io.parsers - package org.forester.io.parsers
 
org.forester.io.parsers.nexus - package org.forester.io.parsers.nexus
 
org.forester.io.parsers.nhx - package org.forester.io.parsers.nhx
 
org.forester.io.parsers.phyloxml - package org.forester.io.parsers.phyloxml
 
org.forester.io.parsers.phyloxml.phylogenydata - package org.forester.io.parsers.phyloxml.phylogenydata
 
org.forester.io.parsers.tol - package org.forester.io.parsers.tol
 
org.forester.io.writers - package org.forester.io.writers
 
org.forester.pccx - package org.forester.pccx
 
org.forester.phylogeny - package org.forester.phylogeny
 
org.forester.phylogeny.data - package org.forester.phylogeny.data
 
org.forester.phylogeny.factories - package org.forester.phylogeny.factories
 
org.forester.phylogeny.iterators - package org.forester.phylogeny.iterators
 
org.forester.phylogenyinference - package org.forester.phylogenyinference
 
org.forester.sdi - package org.forester.sdi
 
org.forester.surfacing - package org.forester.surfacing
 
org.forester.test - package org.forester.test
 
org.forester.tools - package org.forester.tools
 
org.forester.util - package org.forester.util
 
oRmsdThr - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
ORonn - Class in org.biojava3.ronn
Fully re-factored and enhanced version of RONN.
ORonnModel - Class in org.biojava3.ronn
Fully re-factored version of RONN model.
ORonnModel(String, ModelLoader.Model, float) - Constructor for class org.biojava3.ronn.ORonnModel
 
ORTHOLOGOUS - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
OS_ARCH - Static variable in class org.forester.util.ForesterUtil
 
OS_NAME - Static variable in class org.forester.util.ForesterUtil
 
OS_VERSION - Static variable in class org.forester.util.ForesterUtil
 
OTHERNAME - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
OTHERNAME_NAME - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
OTHERNAMES - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
outputFastaSequenceLengthGFF3(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file.
OutputHitsGFF - Class in org.biojava3.genome.query
 
OutputHitsGFF() - Constructor for class org.biojava3.genome.query.OutputHitsGFF
 
outputPhylipDistances(String) - Method in class org.biojava3.phylo.TreeConstructor
 
outputToStream(Document, OutputStream) - Static method in class org.biojava3.core.util.XMLHelper
 
outputToStream(Element, OutputStream) - Static method in class org.biojava3.core.util.XMLHelper
 
overlappingKmers(Sequence<C>, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Used to generate overlapping k-mers such i.e.
overlaps(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location and other location overlap.

P

P - Static variable in class org.biojava3.aaproperties.Constraints
 
pad(double, int, char, boolean) - Static method in class org.forester.util.ForesterUtil
 
pad(String, int, char, boolean) - Static method in class org.forester.util.ForesterUtil
 
pad(StringBuffer, int, char, boolean) - Static method in class org.forester.util.ForesterUtil
 
paint(Graphics) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
paint(Graphics) - Method in class org.forester.archaeopteryx.ArchaeopteryxA
Prints message when initialization is finished.
paintComponent(Graphics) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
paintComponent(Graphics) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
paintComponent(Graphics) - Method in class org.biojava.bio.structure.gui.util.color.GradientPanel
 
paintComponent(Graphics) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
paintComponent(Graphics) - Method in class org.forester.archaeopteryx.TreePanel
 
pair - Variable in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
pair - Variable in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
PairInProfileScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
PAIRS_ONLY - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
PairwiseDomainSimilarity - Interface in org.forester.surfacing
 
PairwiseDomainSimilarityCalculator - Interface in org.forester.surfacing
 
PairwiseGenomeComparator - Class in org.forester.surfacing
 
PairwiseGenomeComparator() - Constructor for class org.forester.surfacing.PairwiseGenomeComparator
 
PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an algorithm which computes a score for a pair of sequences.
ParameterGUI - Class in org.biojava.bio.structure.align.gui
 
ParameterGUI(StructureAlignment) - Constructor for class org.biojava.bio.structure.align.gui.ParameterGUI
 
params - Variable in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
params - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
params - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
params - Variable in class org.biojava.bio.structure.align.ce.CeMain
 
params - Variable in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
params - Variable in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
PARENT_BRANCH_WIDTH - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
parentGeneSequence - Variable in class org.biojava3.core.sequence.StartCodonSequence
 
parentGeneSequence - Variable in class org.biojava3.core.sequence.StopCodonSequence
 
parse(String) - Static method in class org.biojava.bio.structure.align.gui.jmol.AtomInfoParser
parses e.g.
parse(BufferedReader) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
Start the actual parsing.
parse(InputStream) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
Start the actual parsing.
parse(InputStream) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
parse(BufferedReader) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
parse(InputStream) - Method in class org.biojava3.alignment.aaindex.AAIndexFileParser
parse an inputStream that points to an AAINDEX database file
parse(String) - Method in class org.biojava3.core.sequence.location.InsdcParser
Main method for parsing a location from a String instance
parse(Reader) - Method in class org.biojava3.core.sequence.location.InsdcParser
Reader based version of the parse methods.
parse(Reader, Strand) - Method in class org.biojava3.core.sequence.location.InsdcParser
 
parse(<any>, ParseListener) - Method in interface org.biojava3.sequencing.io.fastq.FastqReader
Parse the specified input supplier.
parse(File) - Static method in class org.forester.go.etc.OntologizerResult
 
parse() - Method in class org.forester.go.OBOparser
 
parse() - Method in class org.forester.go.PfamToGoParser
 
parse() - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
parse() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
parse() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
 
parse() - Method in class org.forester.io.parsers.nexus.NexusCharactersParser
 
parse() - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
 
parse() - Method in class org.forester.io.parsers.nexus.PaupLogParser
 
parse() - Method in class org.forester.io.parsers.nhx.NHXParser
Parses the source set with setSource( final Object nhx_source ).
parse() - Method in interface org.forester.io.parsers.PhylogenyParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.AccessionParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.AnnotationParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.BinaryCharactersParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.BranchWidthParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.ColorParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.ConfidenceParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.DateParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.DistributionParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.DomainArchitectureParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.EventParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.IdentifierParser
 
parse(XmlElement) - Method in interface org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.PointParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.PropertyParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.ProteinDomainParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.ReferenceParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.SequenceParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.SequenceRelationParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.TaxonomyParser
 
parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.phylogenydata.UriParser
 
parse() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
parse() - Method in class org.forester.io.parsers.tol.TolParser
 
parse(Object) - Method in interface org.forester.phylogenyinference.DistanceMatrixParser
 
parse(Object) - Method in class org.forester.phylogenyinference.SymmetricalDistanceMatrixParser
 
parse(Object, String) - Static method in class org.forester.util.BasicTableParser
 
parse(Object, String, boolean) - Static method in class org.forester.util.BasicTableParser
 
parse(Object, String, boolean, String, boolean) - Static method in class org.forester.util.BasicTableParser
 
parseDouble(String) - Static method in class org.forester.util.ForesterUtil
 
parseFastqVariant(String) - Static method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Return the FASTQ sequence format variant with the specified name, if any.
parseGoIds(Object, String, String) - Static method in class org.forester.go.GoUtils
 
parseHeader(String, S) - Method in class org.biojava3.core.sequence.io.GenericFastaHeaderParser
Parse the header and set the values in the sequence
parseHeader(String, S) - Method in interface org.biojava3.core.sequence.io.template.FastaHeaderParserInterface
 
parseInt(String) - Static method in class org.forester.util.ForesterUtil
 
ParseListener - Interface in org.biojava3.sequencing.io.fastq
Low-level event based parser callback.
parseLocation(String, Strand) - Method in class org.biojava3.core.sequence.location.InsdcParser
 
parseMappingTable(File) - Static method in class org.forester.tools.PhylogenyDecorator
 
parseMultiXML(String) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
 
parseNext() - Method in class org.forester.io.parsers.nhx.NHXParser
 
parseNHX(String, PhylogenyNode, NHXParser.TAXONOMY_EXTRACTION, boolean) - Static method in class org.forester.io.parsers.nhx.NHXParser
 
parsePDBFile(InputStream) - Method in class org.biojava.bio.structure.io.PDBFileParser
parse a PDB file and return a datastructure implementing PDBStructure interface.
parsePDBFile(BufferedReader) - Method in class org.biojava.bio.structure.io.PDBFileParser
parse a PDB file and return a datastructure implementing PDBStructure interface.
parseRange(Matcher, Strand) - Method in class org.biojava3.core.sequence.location.InsdcParser
 
ParserBasedPhylogenyFactory - Class in org.forester.phylogeny.factories
 
ParserException - Exception in org.biojava3.core.exceptions
General abstraction of different parsing errors
ParserException(String) - Constructor for exception org.biojava3.core.exceptions.ParserException
 
ParserException(Exception) - Constructor for exception org.biojava3.core.exceptions.ParserException
 
ParserException(String, Exception) - Constructor for exception org.biojava3.core.exceptions.ParserException
 
ParserUtils - Class in org.forester.io.parsers
 
ParserUtils() - Constructor for class org.forester.io.parsers.ParserUtils
 
parseSingle(Matcher, Strand) - Method in class org.biojava3.core.sequence.location.InsdcParser
 
parseXmlFile(InputStream) - Method in class org.biojava.bio.structure.io.sifts.SiftsXMLParser
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_GAINS_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_GAINS_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_LOSSES_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_LOSSES_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_GAINS_BC - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_GAINS_BC - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_LOSSES_BC - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_LOSSES_BC - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_PRESENT_BC - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_PRESENT_BC - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing_old
 
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS - Static variable in class org.forester.application.surfacing
 
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS - Static variable in class org.forester.application.surfacing_old
 
PART_OF_STR - Static variable in interface org.forester.go.GoRelationship
 
PartitionRefiner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
PATTERN_SP_STYLE_TAXONOMY - Static variable in class org.forester.surfacing.SurfacingUtil
 
PaupLogParser - Class in org.forester.io.parsers.nexus
 
PaupLogParser() - Constructor for class org.forester.io.parsers.nexus.PaupLogParser
 
pccx - Class in org.forester.application
 
pccx() - Constructor for class org.forester.application.pccx
 
PDB_AUTHOR_ASSIGNMENT - Static variable in class org.biojava.bio.structure.io.PDBFileParser
Secondary strucuture assigned by the PDB author/
PDB_DIR - Static variable in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
the system property PDB_DIR can be used to configure the default location for PDB files.
PDB_DIR - Static variable in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
the system property PDB_DIR can be used to configure the default location for PDB files.
PDB_DIR - Static variable in class org.biojava.bio.structure.align.util.UserConfiguration
 
PDB_DIR - Static variable in class org.biojava.bio.structure.gui.util.PDBDirPanel
the system property PDB_DIR can be used to configure the default location for PDB files.
PDB_FILE_SERVER_PROPERTY - Static variable in class org.biojava.bio.structure.io.PDBFileReader
 
pdb_flag - Variable in class org.biojava.bio.structure.HetatomImpl
 
PDB_FORMAT - Static variable in class org.biojava.bio.structure.align.util.UserConfiguration
 
pdb_name - Variable in class org.biojava.bio.structure.HetatomImpl
 
PDB_SERVER_PROPERTY - Static variable in class org.biojava.bio.structure.PDBStatus
 
PDBCrystallographicInfo - Class in org.biojava.bio.structure
A class to hold crystallographic information about a PDB structure.
PDBCrystallographicInfo() - Constructor for class org.biojava.bio.structure.PDBCrystallographicInfo
 
PDBDirPanel - Class in org.biojava.bio.structure.gui.util
A class to define where a structure for the alignment is coming from
PDBDirPanel() - Constructor for class org.biojava.bio.structure.gui.util.PDBDirPanel
load the PDB files from a local directory
PDBFileParser - Class in org.biojava.bio.structure.io
This class implements the actual PDB file parsing.
PDBFileParser() - Constructor for class org.biojava.bio.structure.io.PDBFileParser
 
PDBFileReader - Class in org.biojava.bio.structure.io
The wrapper class for parsing a PDB file.
PDBFileReader() - Constructor for class org.biojava.bio.structure.io.PDBFileReader
 
PDBFilter - Interface in org.biojava.bio.structure.server
defines how a filter of PDB files has to behave
PDBHeader - Class in org.biojava.bio.structure
A class that contains PDB Header information.
PDBHeader() - Constructor for class org.biojava.bio.structure.PDBHeader
 
pdbId - Variable in class org.biojava.bio.structure.align.client.StructureName
 
PDBInstallation - Interface in org.biojava.bio.structure.server
Deprecated. 
pdbNumRangeRegex - Static variable in class org.biojava.bio.structure.StructureTools
Pattern to describe subranges.
PdbPair - Class in org.biojava.bio.structure.align.client
A pair for structure alignment
PdbPair(String, String) - Constructor for class org.biojava.bio.structure.align.client.PdbPair
 
PdbPairsMessage - Class in org.biojava.bio.structure.align.xml
 
PdbPairsMessage() - Constructor for class org.biojava.bio.structure.align.xml.PdbPairsMessage
 
PdbPairXMLConverter - Class in org.biojava.bio.structure.align.xml
 
PdbPairXMLConverter() - Constructor for class org.biojava.bio.structure.align.xml.PdbPairXMLConverter
 
PDBParseException - Exception in org.biojava.bio.structure.io
An exception during the parsing of a PDB file.
PDBParseException(String) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
Constructs a PDBParseException object.
PDBParseException(String, Throwable) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
Constructs a PDBParseException object.
PDBParseException(Throwable) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
Constructs a PDBParseException object.
PDBRecord - Interface in org.biojava.bio.structure
An interface implemented by all classes that represent PDB records
PDBServerPanel - Class in org.biojava.bio.structure.gui.util
A class to define where a structure for the alignment is coming from
PDBServerPanel() - Constructor for class org.biojava.bio.structure.gui.util.PDBServerPanel
load the PDB files from a local directory
PDBSRSReader - Class in org.biojava.bio.structure.io
reads a PDB file from a local SRS installation using getz Actually is the same as PDBFileReader, but instead of reading from a file stream, reads from a buffered stream.
PDBSRSReader() - Constructor for class org.biojava.bio.structure.io.PDBSRSReader
 
PDBStatus - Class in org.biojava.bio.structure
Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.
PDBStatus() - Constructor for class org.biojava.bio.structure.PDBStatus
 
PDBStatus.Status - Enum in org.biojava.bio.structure
Represents the status of PDB IDs.
PDBUploadPanel - Class in org.biojava.bio.structure.gui.util
A JPanel to upload 2 custom PDB files.
PDBUploadPanel() - Constructor for class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
PDBUploadPanel(boolean) - Constructor for class org.biojava.bio.structure.gui.util.PDBUploadPanel
 
PdbxEntityNonPoly - Class in org.biojava.bio.structure.io.mmcif.model
A bean for the Pdbx_entity_nonpoly category.
PdbxEntityNonPoly() - Constructor for class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
PdbxNonPolyScheme - Class in org.biojava.bio.structure.io.mmcif.model
A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.
PdbxNonPolyScheme() - Constructor for class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
PdbxPolySeqScheme - Class in org.biojava.bio.structure.io.mmcif.model
A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.
PdbxPolySeqScheme() - Constructor for class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
PDP_DOMAIN_IDENTIFIER - Static variable in class org.biojava.bio.structure.align.util.AtomCache
 
PDPDistanceMatrix - Class in org.biojava.bio.structure.domain.pdp
 
PDPDistanceMatrix() - Constructor for class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
PDPParameters - Class in org.biojava.bio.structure.domain.pdp
 
PDPParameters() - Constructor for class org.biojava.bio.structure.domain.pdp.PDPParameters
 
pdpprovider - Variable in class org.biojava.bio.structure.align.util.AtomCache
 
PDPProvider - Interface in org.biojava.bio.structure.domain
 
pearsonianSkewness() - Method in class org.forester.util.BasicDescriptiveStatistics
 
pearsonianSkewness() - Method in interface org.forester.util.DescriptiveStatistics
Determines relationship between the mean and the median.
PeptideProperties - Class in org.biojava3.aaproperties
This is an adaptor class which enable the ease of generating protein properties.
PeptideProperties() - Constructor for class org.biojava3.aaproperties.PeptideProperties
 
PeptideProperties.SingleLetterAACode - Enum in org.biojava3.aaproperties
Enumeration of 20 standard amino acid code
PeptidePropertiesImpl - Class in org.biojava3.aaproperties
This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
PeptidePropertiesImpl() - Constructor for class org.biojava3.aaproperties.PeptidePropertiesImpl
 
percentNucleotideSequence(String) - Static method in class org.biojava3.core.util.SequenceTools
 
percentOverlap(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Return percent overlap of two locations.
performBinning(double[], double, double, int) - Static method in class org.forester.util.BasicDescriptiveStatistics
 
performPairwiseComparisons(StringBuilder, boolean, DomainSimilarityCalculator.Detailedness, boolean, boolean, DomainSimilarity.DomainSimilaritySortField, PrintableDomainSimilarity.PRINT_OPTION, DomainSimilarity.DomainSimilarityScoring, Map<DomainId, List<GoId>>, Map<GoId, GoTerm>, GoNameSpace, Species[], int, List<GenomeWideCombinableDomains>, PairwiseDomainSimilarityCalculator, String, boolean, String, String, boolean, File, boolean) - Method in class org.forester.surfacing.PairwiseGenomeComparator
 
performPairwiseComparisonsJacknifed(Species[], int, List<GenomeWideCombinableDomains>, boolean, int, double, long) - Method in class org.forester.surfacing.PairwiseGenomeComparator
 
perfume - Class in org.forester.application
 
perfume() - Constructor for class org.forester.application.perfume
 
persistConfig(UserConfiguration) - Static method in class org.biojava.bio.structure.align.webstart.WebStartMain
 
PersistentConfig - Class in org.biojava.bio.structure.align.webstart
a class to store the config using the Java Web Start PersistenService.
PersistentConfig() - Constructor for class org.biojava.bio.structure.align.webstart.PersistentConfig
 
pfam2go_extractor - Class in org.forester.application
 
pfam2go_extractor() - Constructor for class org.forester.application.pfam2go_extractor
 
PFAM_FAMILY_ID_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
pfam_go - Class in org.forester.application
 
pfam_go() - Constructor for class org.forester.application.pfam_go
 
PFAM_INST - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
PFAM_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
PFAM_SERVER - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
PfamToGoMapping - Class in org.forester.go
 
PfamToGoMapping(DomainId, GoId) - Constructor for class org.forester.go.PfamToGoMapping
 
PfamToGoParser - Class in org.forester.go
 
PfamToGoParser(File) - Constructor for class org.forester.go.PfamToGoParser
 
Phe - Static variable in class org.biojava3.phylo.ResidueProperties
 
PHYLO_XML_END - Static variable in class org.forester.io.writers.PhylogenyWriter
 
PHYLO_XML_INTENDATION_BASE - Static variable in class org.forester.io.writers.PhylogenyWriter
 
PHYLO_XML_LOCATION - Static variable in class org.forester.util.ForesterConstants
 
PHYLO_XML_NAMESPACE_LINE - Static variable in class org.forester.io.writers.PhylogenyWriter
 
PHYLO_XML_REFERENCE - Static variable in class org.forester.util.ForesterConstants
 
PHYLO_XML_SUFFIX - Static variable in class org.forester.util.ForesterConstants
 
PHYLO_XML_VERSION - Static variable in class org.forester.util.ForesterConstants
 
PHYLO_XML_VERSION_ENCODING_LINE - Static variable in class org.forester.io.writers.PhylogenyWriter
 
PHYLO_XML_XSD - Static variable in class org.forester.util.ForesterConstants
 
PhylogeniesWebserviceClient - Interface in org.forester.archaeopteryx.webservices
 
PHYLOGENY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PHYLOGENY - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
Phylogeny - Class in org.forester.phylogeny
 
Phylogeny() - Constructor for class org.forester.phylogeny.Phylogeny
Default Phylogeny constructor.
PHYLOGENY_BRANCHLENGTH_UNIT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PHYLOGENY_DESCRIPTION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PHYLOGENY_IS_REROOTABLE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PHYLOGENY_IS_ROOTED_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PHYLOGENY_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PHYLOGENY_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PhylogenyBranch - Class in org.forester.phylogeny
 
PhylogenyBranch(PhylogenyNode, PhylogenyNode) - Constructor for class org.forester.phylogeny.PhylogenyBranch
 
PhylogenyBranch(PhylogenyNode, PhylogenyNode, boolean) - Constructor for class org.forester.phylogeny.PhylogenyBranch
 
PhylogenyData - Interface in org.forester.phylogeny.data
 
PhylogenyDataPhyloXmlParser - Interface in org.forester.io.parsers.phyloxml.phylogenydata
 
PhylogenyDataUtil - Class in org.forester.phylogeny.data
 
PhylogenyDataUtil() - Constructor for class org.forester.phylogeny.data.PhylogenyDataUtil
 
PhylogenyDecorator - Class in org.forester.tools
 
PhylogenyDecorator.FIELD - Enum in org.forester.tools
 
PhylogenyFactory - Interface in org.forester.phylogeny.factories
 
PhylogenyMethods - Class in org.forester.phylogeny
 
PhylogenyNode - Class in org.forester.phylogeny
 
PhylogenyNode() - Constructor for class org.forester.phylogeny.PhylogenyNode
Default constructor for PhylogenyNode.
PhylogenyNode(String) - Constructor for class org.forester.phylogeny.PhylogenyNode
 
PhylogenyNode(String, NHXParser.TAXONOMY_EXTRACTION) - Constructor for class org.forester.phylogeny.PhylogenyNode
 
PhylogenyNode(String, NHXParser.TAXONOMY_EXTRACTION, boolean) - Constructor for class org.forester.phylogeny.PhylogenyNode
Constructor for PhylogenyNode.
PhylogenyNodeI - Interface in org.forester.phylogeny
 
PhylogenyNodeIterator - Interface in org.forester.phylogeny.iterators
 
PhylogenyParser - Interface in org.forester.io.parsers
 
PhylogenyParserException - Exception in org.forester.io.parsers
 
PhylogenyParserException() - Constructor for exception org.forester.io.parsers.PhylogenyParserException
 
PhylogenyParserException(String) - Constructor for exception org.forester.io.parsers.PhylogenyParserException
 
PhylogenyWriter - Class in org.forester.io.writers
 
PhylogenyWriter() - Constructor for class org.forester.io.writers.PhylogenyWriter
 
PhylogenyWriter.FORMAT - Enum in org.forester.io.writers
 
phyloxml_converter - Class in org.forester.application
 
phyloxml_converter() - Constructor for class org.forester.application.phyloxml_converter
 
PhyloXmlDataFormatException - Exception in org.forester.io.parsers.phyloxml
 
PhyloXmlDataFormatException() - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
 
PhyloXmlDataFormatException(String) - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
 
PhyloXmlException - Exception in org.forester.io.parsers.phyloxml
 
PhyloXmlException() - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlException
 
PhyloXmlException(String) - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlException
 
PhyloXmlHandler - Class in org.forester.io.parsers.phyloxml
 
PhyloXmlMapping - Class in org.forester.io.parsers.phyloxml
 
PhyloXmlNodeWriter - Class in org.forester.io.writers
 
PhyloXmlNodeWriter() - Constructor for class org.forester.io.writers.PhyloXmlNodeWriter
 
PhyloXmlParser - Class in org.forester.io.parsers.phyloxml
 
PhyloXmlParser() - Constructor for class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
PhyloXmlUtil - Class in org.forester.io.parsers.phyloxml
 
PhyloXmlUtil() - Constructor for class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
PID(String, String) - Static method in class org.biojava3.phylo.Comparison
this is a gapped PID calculation
PID(String, String, int, int) - Static method in class org.biojava3.phylo.Comparison
 
pidColours - Static variable in class org.biojava3.phylo.ResidueProperties
 
pidThresholds - Static variable in class org.biojava3.phylo.ResidueProperties
 
pivot() - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
pivot() - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
plus(Structure, Matrix) - Static method in class org.biojava.bio.structure.Calc
calculate structure + Matrix coodinates ...
plus(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
C = A + B
plus() - Method in class org.biojava3.genome.parsers.gff.Location
Return location that is in same position on plus strand.
PLUS_MINUS - Static variable in interface org.forester.util.DescriptiveStatistics
 
plusEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
A = A + B
PMID_STR - Static variable in interface org.forester.go.GoXRef
 
Point - Interface in org.biojava3.core.sequence.location.template
Holds a single point part of a location
POINT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Point - Class in org.forester.phylogeny.data
 
Point(String, BigDecimal, BigDecimal) - Constructor for class org.forester.phylogeny.data.Point
 
Point(String, BigDecimal, BigDecimal, BigDecimal, String) - Constructor for class org.forester.phylogeny.data.Point
 
Point.Resolver<T extends Point> - Interface in org.biojava3.core.sequence.location.template
Used to resolve a position about a point
POINT_ALTITUDE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
POINT_ALTITUDE_UNIT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
POINT_GEODETIC_DATUM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
POINT_LATITUDE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
POINT_LONGITUDE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PointParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
polar - Static variable in class org.biojava3.phylo.ResidueProperties
 
PolymerType - Enum in org.biojava.bio.structure.io.mmcif.chem
Enumerates the classification of polymers.
polymerType - Variable in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
The associated PolymerType
polymerTypeFromString(String) - Static method in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
 
POLYNUCLEOTIDE_ONLY - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Convenience Set of polymer types classified as DNA.
populate(Sequence<C>) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Loops through the Compounds in a Sequence and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)
populate(String) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Loops through the chars in a String and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)
populateMaps() - Method in class org.biojava3.aaproperties.xml.ElementTable
Populate the Maps for quick retrieval
PositionInQueueXMLConverter - Class in org.biojava.bio.structure.align.xml
 
PositionInQueueXMLConverter() - Constructor for class org.biojava.bio.structure.align.xml.PositionInQueueXMLConverter
 
positionSelected(AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
positionSelected(AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
positionSelected(AlignedPosition) - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
 
positionSelected(AlignedPosition) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
positive - Static variable in class org.biojava3.phylo.ResidueProperties
 
POSITIVELY_REGULATES_STR - Static variable in interface org.forester.go.GoRelationship
 
postorderBranchColorAveragingExternalNodeBased(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
postOrderRelabelInternalNodes(Phylogeny, int) - Static method in class org.forester.util.ForesterUtil
 
PostOrderStackObject - Class in org.forester.phylogeny.iterators
 
PostOrderStackObject(PhylogenyNode, int) - Constructor for class org.forester.phylogeny.iterators.PostOrderStackObject
Creates a new PostOrderStackObject object.
PostorderTreeIterator - Class in org.forester.phylogeny.iterators
 
PostorderTreeIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.PostorderTreeIterator
 
postProcess(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
 
postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator) - Static method in class org.biojava.bio.structure.align.ce.CeCPMain
Circular permutation specific code to be run after the standard CE alignment
postProcessCompoundLists(List<List<T>>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
postProcessCompoundLists(List<List<NucleotideCompound>>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
 
postProcessCompoundLists(List<List<AminoAcidCompound>>) - Method in class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
Performs the trimming of stop codons and the conversion of a valid start amino acid to M
prefix(int) - Method in class org.biojava3.genome.parsers.gff.Location
The part of this location before the specified position.
prefix(Location) - Method in class org.biojava3.genome.parsers.gff.Location
The part of this location before the other location (not inclusive).
preorderPrint() - Method in class org.forester.phylogeny.PhylogenyNode
Prints to the console the subtree originating from this PhylogenyNode in preorder.
preOrderReId() - Method in class org.forester.phylogeny.Phylogeny
 
preOrderReId(int) - Method in class org.forester.phylogeny.Phylogeny
Resets the ID numbers of the Nodes of this Phylogeny in preorder, starting with i.
WARNING.
PreorderTreeIterator - Class in org.forester.phylogeny.iterators
 
PreorderTreeIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.PreorderTreeIterator
 
PreorderTreeIterator(PhylogenyNode) - Constructor for class org.forester.phylogeny.iterators.PreorderTreeIterator
 
prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
Rotate the Atoms/Groups so they are aligned for the 3D visualisation
PrepareIndexFile - Class in org.biojava.bio.structure.server
 
PrepareIndexFile() - Constructor for class org.biojava.bio.structure.server.PrepareIndexFile
 
prepareIndexFileForInstallation(FlatFileInstallation) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
prepare the index file for this installation
prepareIndexFileForInstallation(FlatFileInstallation) - Method in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
prepare the index file for this installation
PrepareMMcifIndexFile - Class in org.biojava.bio.structure.server
A class to index all files in a PDB installation
PrepareMMcifIndexFile() - Constructor for class org.biojava.bio.structure.server.PrepareMMcifIndexFile
 
preparePhylogeny(Phylogeny, DomainParsimonyCalculator, String, String, String, String) - Static method in class org.forester.surfacing.SurfacingUtil
 
PrettyXMLWriter - Class in org.biojava3.core.util
Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava3.core.util.PrettyXMLWriter
 
PRG_NAME - Static variable in class org.forester.application.surfacing
 
PRG_NAME - Static variable in class org.forester.application.surfacing_old
 
PRIME - Static variable in class org.biojava3.core.util.Hashcoder
The prime number used to multiply any calculated hashcode seed by i.e.
print(Graphics, PageFormat, int) - Method in class org.biojava.bio.structure.align.gui.JPrintPanel
 
PRINT - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
print(int, int) - Method in class org.biojava.bio.structure.jama.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class org.biojava.bio.structure.jama.Matrix
Print the matrix to the output stream.
print(NumberFormat, int) - Method in class org.biojava.bio.structure.jama.Matrix
Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class org.biojava.bio.structure.jama.Matrix
Print the matrix to the output stream.
print(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
print(String) - Method in interface org.biojava3.core.util.XMLWriter
Prints some textual content in an element.
print(Graphics, PageFormat, int) - Method in class org.forester.archaeopteryx.TreePanel
 
PrintableDomainSimilarity - Class in org.forester.surfacing
 
PrintableDomainSimilarity(CombinableDomains, double, double, double, double, double, int, int, int, SortedMap<Species, SpeciesSpecificDomainSimilariyData>, DomainSimilarity.DomainSimilaritySortField, boolean, boolean) - Constructor for class org.forester.surfacing.PrintableDomainSimilarity
If go_id_to_term_map not null, detailed GO information is written, only GO ids otherwise.
PrintableDomainSimilarity.PRINT_OPTION - Enum in org.forester.surfacing
 
printAllSpecies - Class in org.forester.application
 
printAllSpecies() - Constructor for class org.forester.application.printAllSpecies
 
printArray(Object[]) - Static method in class org.forester.util.ForesterUtil
 
printAttributeValue(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
printChars(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
printCountingMap(Map<String, Integer>) - Static method in class org.forester.util.ForesterUtil
 
printErrorMessage(String, String) - Static method in class org.forester.util.ForesterUtil
 
printExtNodes() - Method in class org.forester.phylogeny.Phylogeny
Prints descriptions of all external Nodes of this Phylogeny to System.out.
printHelp() - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
printHelp() - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
printHelp() - Method in class org.biojava.bio.structure.align.FarmJob
 
printHelp() - Method in class org.biojava.bio.structure.align.fatcat.FatCat
print the -h help text.
printHelp() - Method in interface org.biojava.bio.structure.align.StructureAlignment
Returns some documentation on the command line arguments for this algorithm.
println(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
println(String) - Method in interface org.biojava3.core.util.XMLWriter
Prints some textual content, terminated with a newline character.
printMatrix(Matrix) - Method in class org.biojava.bio.structure.SVDSuperimposer
Simple debug method to print a Matrix object on System.out.
printProgramInformation(String, String, String) - Static method in class org.forester.util.ForesterUtil
 
printProgramInformation(String, String, String, String, String) - Static method in class org.forester.util.ForesterUtil
 
printRaw(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
 
printRaw(String) - Method in interface org.biojava3.core.util.XMLWriter
Send raw data to the stream.
printSameOrder - Class in org.forester.application
 
printSameOrder() - Constructor for class org.forester.application.printSameOrder
 
printTimeStamps - Static variable in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
printWarningMessage(String, String) - Static method in class org.forester.util.ForesterUtil
 
printXMLEQRInferPositions(PrettyXMLWriter, AFPChain, int, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
 
printXMLHeader(PrettyXMLWriter, AFPChain) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
 
Pro - Static variable in class org.biojava3.phylo.ResidueProperties
 
process(String[]) - Method in class org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
 
process(String[]) - Method in interface org.biojava.bio.structure.align.ce.UserArgumentProcessor
Process user arguments that have been provided from the command line
process() - Method in class org.biojava.bio.structure.io.FastaStructureParser
Parses the fasta file and loads it into memory.
process() - Method in class org.biojava3.core.sequence.io.FastaGeneWriter
 
process() - Method in class org.biojava3.core.sequence.io.FastaReader
The parsing is done in this method
process() - Method in class org.biojava3.core.sequence.io.FastaWriter
 
process(String) - Method in interface org.biojava3.core.sequence.io.util.IOUtils.ReaderProcessor
 
process(File, double, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava3.genome.homology.GFF3FromUniprotBlastHits
 
process(LinkedHashMap<String, ArrayList<String>>, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava3.genome.homology.GFF3FromUniprotBlastHits
 
process(File, File, File, double, double, boolean, boolean) - Method in class org.biojava3.genome.query.OutputHitsGFF
 
process(String, String) - Method in class org.biojava3.genome.uniprot.UniprotToFasta
Convert a Uniprot sequence file to a fasta file.
process(Phylogeny, DistanceMatrix) - Method in class org.biojava3.phylo.CheckTreeAccuracy
 
process() - Method in class org.biojava3.phylo.TreeConstructor
 
process(Phylogeny, DistanceMatrix) - Method in class org.forester.application.CheckTreeAccuracy
 
processInstructions(PhylogeniesWebserviceClient, Phylogeny) - Static method in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
processNucleotides(File, String, File) - Method in class org.biojava3.genome.util.SplitFasta
 
processReader(BufferedReader, IOUtils.ReaderProcessor) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
Takes in a reader and a processor, reads every line from the given file and then invokes the processor.
processUnknownCompound(C, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Since bit encoding only supports a finite number of bases it is more than likely when processing sequence you will encounter a compound which is not covered by the encoding e.g.
ProfeatProperties - Class in org.biojava3.aaproperties.profeat
This is an adaptor class which enable the ease of generating profeat properties.
ProfeatProperties() - Constructor for class org.biojava3.aaproperties.profeat.ProfeatProperties
 
ProfeatPropertiesImpl - Class in org.biojava3.aaproperties.profeat
 
ProfeatPropertiesImpl() - Constructor for class org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
 
profile - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
Profile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure for the results of sequence alignment.
Profile.StringFormat - Enum in org.biojava3.alignment.template
List of output formats.
ProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an Aligner for a pair of Profiles.
ProfileProfileScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an algorithm which computes a score for a pairing of alignment profiles.
ProfileView<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure for a view of sequence alignment.
ProgessListenerStub - Class in org.biojava3.phylo
 
ProgessListenerStub() - Constructor for class org.biojava3.phylo.ProgessListenerStub
 
programMessage(String, String) - Static method in class org.forester.util.ForesterUtil
 
progress(Object, String, int) - Method in interface org.biojava3.phylo.NJTreeProgressListener
 
progress(Object, String, int, int) - Method in interface org.biojava3.phylo.NJTreeProgressListener
 
progress(Object, String, int) - Method in class org.biojava3.phylo.ProgessListenerStub
 
progress(Object, String, int, int) - Method in class org.biojava3.phylo.ProgessListenerStub
 
proline - Static variable in class org.biojava3.phylo.ResidueProperties
 
PropertiesMap - Class in org.forester.phylogeny.data
 
PropertiesMap() - Constructor for class org.forester.phylogeny.data.PropertiesMap
 
PROPERTY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Property - Class in org.forester.phylogeny.data
 
Property(String, String, String, String, Property.AppliesTo) - Constructor for class org.forester.phylogeny.data.Property
 
Property(String, String, String, String, Property.AppliesTo, String) - Constructor for class org.forester.phylogeny.data.Property
 
Property.AppliesTo - Enum in org.forester.phylogeny.data
 
PROPERTY_APPLIES_TO - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PROPERTY_DATATYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PROPERTY_REF - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PROPERTY_UNIT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
PropertyParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
propHash - Static variable in class org.biojava3.phylo.ResidueProperties
 
Protein - Interface in org.forester.surfacing
 
PROTEIN_ONLY - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Convenience Set of polymer types classified as protein.
ProteinCountsBasedPairwiseDomainSimilarityCalculator - Class in org.forester.surfacing
 
ProteinCountsBasedPairwiseDomainSimilarityCalculator() - Constructor for class org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator
 
proteinCreator(SequenceCreatorInterface<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
ProteinDomain - Class in org.forester.phylogeny.data
 
ProteinDomain(String, int, int) - Constructor for class org.forester.phylogeny.data.ProteinDomain
 
ProteinDomain(String, int, int, double) - Constructor for class org.forester.phylogeny.data.ProteinDomain
 
ProteinDomain(String, int, int, String) - Constructor for class org.forester.phylogeny.data.ProteinDomain
 
ProteinDomain(String, int, int, String, double) - Constructor for class org.forester.phylogeny.data.ProteinDomain
 
ProteinDomainParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
ProteinId - Class in org.forester.surfacing
 
ProteinId(String) - Constructor for class org.forester.surfacing.ProteinId
 
ProteinModification - Interface in org.biojava3.protmod
This interface defines information about a specific protein modification.
ProteinModificationIdentifier - Class in org.biojava3.protmod.structure
Identify attachment modification in a 3-D structure.
ProteinModificationIdentifier() - Constructor for class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
ProteinModificationImpl - Class in org.biojava3.protmod
This class contains information about a specific protein modification.
ProteinModificationImpl.Builder - Class in org.biojava3.protmod
Uses Builder pattern to build a ProteinModification.
ProteinModificationImpl.Builder(String, ModificationCategory, ModificationOccurrenceType, ModificationCondition) - Constructor for class org.biojava3.protmod.ProteinModificationImpl.Builder
 
ProteinModificationImpl.Builder(ProteinModification) - Constructor for class org.biojava3.protmod.ProteinModificationImpl.Builder
Create a Builder from an existing ProteinModification.
ProteinModificationRegistry - Class in org.biojava3.protmod
This class serves as a instance registry by maintaining a pool of ProteinModification instances.
ProteinModificationRegistry() - Constructor for class org.biojava3.protmod.ProteinModificationRegistry
 
ProteinModificationXmlReader - Class in org.biojava3.protmod.io
 
ProteinSequence - Class in org.biojava3.core.sequence
The representation of a ProteinSequence
ProteinSequence(String) - Constructor for class org.biojava3.core.sequence.ProteinSequence
Create a protein from a string
ProteinSequence(String, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.ProteinSequence
Create a protein from a string with a user defined set of amino acids
ProteinSequence(ProxySequenceReader<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.ProteinSequence
A protein sequence where the storage of the sequence is somewhere else.
ProteinSequence(ProxySequenceReader<AminoAcidCompound>, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.ProteinSequence
A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.
ProteinSequenceCreator - Class in org.biojava3.core.sequence.io
Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.
ProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.ProteinSequenceCreator
 
ProxySequenceReader<C extends Compound> - Interface in org.biojava3.core.sequence.template
 
put(Double, Color) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
Adds a gradient endpoint at the specified position.
put(K, V) - Method in class org.biojava3.core.util.SoftHashMap
Here we put the key, value pair into the HashMap using a SoftValue object.
putAll(Map<? extends Double, ? extends Color>) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 

Q

Q - Static variable in class org.biojava.bio.structure.secstruc.SecStruc
constant for electrostatic energy
Q - Static variable in class org.biojava3.aaproperties.Constraints
 
qr() - Method in class org.biojava.bio.structure.jama.Matrix
QR Decomposition
QRDecomposition - Class in org.biojava.bio.structure.jama
QR Decomposition.
QRDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.QRDecomposition
QR Decomposition, computed by Householder reflections.
quality(String) - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this listener of a quality line.
QualityFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.features
DNA Sequences produced by modern sequencers usually have quality informaion attached to them.
QualityFeature(String, String) - Constructor for class org.biojava3.core.sequence.features.QualityFeature
 
qualityScore(char) - Method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Convert the specified quality in ASCII format to a quality score.
qualityScores(Fastq) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Return the quality scores from the specified FASTQ formatted sequence.
qualityScores(Fastq, int[]) - Static method in class org.biojava3.sequencing.io.fastq.FastqTools
Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
QuantityFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.features
It is common to have a numerical value or values associated with a feature.
QuantityFeature(String, String) - Constructor for class org.biojava3.core.sequence.features.QuantityFeature
 
QUERY_PLACEHOLDER - Static variable in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
 
Queue - Class in org.forester.datastructures
 
Queue() - Constructor for class org.forester.datastructures.Queue
This created a new, empty Queue object.
quickSort(String[], int, int) - Static method in class org.biojava.bio.structure.align.gui.SystemInfo
Stripped-down QuickSort.

R

R - Static variable in class org.biojava3.aaproperties.Constraints
 
radiansPerDegree - Static variable in class org.biojava.bio.structure.Calc
Radians per degree.
RAINBOW_GRADIENT - Static variable in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
RAINBOW_INTENSITY_GRADIENT - Static variable in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
random(int, int) - Static method in class org.biojava.bio.structure.jama.Matrix
Generate matrix with random elements
randomize(long) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
randomizeSpecies(int, int, Phylogeny) - Static method in class org.forester.development.DevelopmentTools
Sets the species names of the external Nodes of Phylogeny t to a random positive integer number between (and including) min and max.
randomPick(Collection<Number>) - Static method in class org.biojava.bio.structure.align.util.CollectionTools
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
 
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
rank() - Method in class org.biojava.bio.structure.jama.Matrix
Matrix rank
rank() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
Effective numerical matrix rank
RasmolCommandListener - Class in org.biojava.bio.structure.align.gui.jmol
a utility class that listens to Ramsol script commands in the @link BiojavaJmol class
RasmolCommandListener(JmolPanel, JTextField) - Constructor for class org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener
 
RasmolCommandListener - Class in org.biojava.bio.structure.gui
Deprecated.
use org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener instead
RasmolCommandListener(JmolPanel, JTextField) - Constructor for class org.biojava.bio.structure.gui.RasmolCommandListener
Deprecated.
 
REACTOME_STR - Static variable in interface org.forester.go.GoXRef
 
read(BufferedReader) - Static method in class org.biojava.bio.structure.jama.Matrix
Read a matrix from a stream.
read() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Reads a single character.
read(char[], int, int) - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Reads characters into a portion of an array.
read() - Method in class org.biojava3.core.util.UncompressInputStream
 
read(byte[], int, int) - Method in class org.biojava3.core.util.UncompressInputStream
 
read(String) - Static method in class org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
Read a file into a FeatureList.
read(String) - Static method in class org.biojava3.genome.parsers.gff.GeneMarkGTFReader
Read a file into a FeatureList.
read(String) - Static method in class org.biojava3.genome.parsers.gff.GFF3Reader
Read a file into a FeatureList.
read(File) - Method in interface org.biojava3.sequencing.io.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified file.
read(URL) - Method in interface org.biojava3.sequencing.io.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified url.
read(InputStream) - Method in interface org.biojava3.sequencing.io.fastq.FastqReader
Read zero or more FASTQ formatted sequences from the specified input stream.
readDistanceMatrix(File) - Method in class org.forester.sdi.RIO
 
readFasta(InputStream) - Static method in class org.biojava3.data.sequence.SequenceUtil
Reads fasta sequences from inStream into the list of FastaSequence objects
readFastaDNASequence(File, boolean) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
readFastaDNASequence(InputStream) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
Read a fasta DNA sequence
readFastaDNASequence(File) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
 
readFastaProteinSequence(File) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
Read a fasta file containing amino acids with setup that would handle most cases.
readFastaProteinSequence(InputStream) - Static method in class org.biojava3.core.sequence.io.FastaReaderHelper
Read a fasta file containing amino acids with setup that would handle most cases.
readLine() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Reads a line of text.
ready() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Tells whether this stream is ready to be read.
rebuildAFPChain(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLParser
replace the PDB res nums with atom positions:
recalculateNumberOfExternalDescendants(boolean) - Method in class org.forester.phylogeny.Phylogeny
(Re)counts the number of children for each PhylogenyNode of this Phylogeny.
RED_BLUE_GRADIENT - Static variable in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
ReducedChemCompProvider - Class in org.biojava.bio.structure.io.mmcif
Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.
ReducedChemCompProvider() - Constructor for class org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider
 
reduceFragments(List<FragmentPair>, FragmentPair, Matrix) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
In helices often many similar fragments can be found.
reduceInitialFragments() - Method in class org.biojava.bio.structure.align.StrucAligParameters
if this is set to false, the time spent to joint the initial fragments (step 2) is increased.
REFERENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Reference - Class in org.forester.phylogeny.data
 
Reference(String) - Constructor for class org.forester.phylogeny.data.Reference
 
Reference(String, String) - Constructor for class org.forester.phylogeny.data.Reference
 
REFERENCE_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
REFERENCE_DOI_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
ReferenceParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
refExists(String) - Method in class org.forester.phylogeny.data.PropertiesMap
 
refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
Refinement procedure based on superposition and dynamic programming.
Refine - Class in org.biojava.bio.structure.io.mmcif.model
 
Refine() - Constructor for class org.biojava.bio.structure.io.mmcif.model.Refine
 
reformat(File, String, File, String, File, double, String, List<PfamToGoMapping>) - Static method in class org.forester.go.etc.MetaOntologizer
 
register(ProteinModification) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
Register a new ProteinModification.
registerProteinModificationFromXml(InputStream) - Static method in class org.biojava3.protmod.io.ProteinModificationXmlReader
Read protein modifications from XML file and register them.
REGULATES_STR - Static variable in interface org.forester.go.GoRelationship
 
RELEASE - Static variable in class org.forester.util.ForesterConstants
 
reloadFromFile() - Method in class org.biojava.bio.structure.domain.SerializableCache
 
remainder() - Method in class org.biojava3.genome.parsers.gff.LocIterator
Get portion of bounding location that has not yet been retrieved by next() method.
remark800toPDB(StringBuffer) - Method in class org.biojava.bio.structure.Site
Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.
remark800toPDB() - Method in class org.biojava.bio.structure.Site
Provides REMARK 800 section pertaining to the site as a string.
RemoteDomainProvider - Class in org.biojava.bio.structure.domain
 
RemoteDomainProvider() - Constructor for class org.biojava.bio.structure.domain.RemoteDomainProvider
 
RemoteDomainProvider(boolean) - Constructor for class org.biojava.bio.structure.domain.RemoteDomainProvider
initialize this provider with caching enabled
RemoteHmmerScan - Class in org.biojava3.ws.hmmer
Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
RemoteHmmerScan() - Constructor for class org.biojava3.ws.hmmer.RemoteHmmerScan
 
RemotePairwiseAlignmentOutputProperties - Interface in org.biojava3.ws.alignment
RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.
RemotePairwiseAlignmentProperties - Interface in org.biojava3.ws.alignment
RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.
RemotePairwiseAlignmentService - Interface in org.biojava3.ws.alignment
This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
RemotePDPProvider - Class in org.biojava.bio.structure.domain
A class that provided PDP assignments that are loaded from a remote web server
RemotePDPProvider() - Constructor for class org.biojava.bio.structure.domain.RemotePDPProvider
 
RemotePDPProvider(boolean) - Constructor for class org.biojava.bio.structure.domain.RemotePDPProvider
 
RemoteScopInstallation - Class in org.biojava.bio.structure.scop
A class that fetches information about SCOP from a remote data-source.
RemoteScopInstallation() - Constructor for class org.biojava.bio.structure.scop.RemoteScopInstallation
 
remove() - Method in class org.biojava.bio.structure.AtomIterator
does nothing.
remove() - Method in class org.biojava.bio.structure.GroupIterator
does nothing .
remove(Object) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
remove() - Method in class org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator
 
remove(Object) - Method in class org.biojava3.core.util.SoftHashMap
 
remove() - Method in class org.biojava3.genome.parsers.gff.LocIterator
Unsupported.
remove() - Method in class org.forester.phylogeny.iterators.ChildNodeIteratorForward
Not supported.
remove() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator
Not supported.
remove() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator
Not supported.
remove() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator
Not supported.
remove() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator
Not supported.
removeAlgorithm(String) - Static method in class org.biojava.bio.structure.align.StructureAlignmentFactory
Removes the specified algorithm from the list of options
removeAlignedSequence(S) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Remove a sequence
removeAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Removes given parameter
removeCDS(String) - Method in class org.biojava3.core.sequence.TranscriptSequence
Remove a CDS or coding sequence from the transcript sequence
removeChildNode(int) - Method in class org.forester.phylogeny.PhylogenyNode
 
removeChildNode(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
 
removeExon(String) - Method in class org.biojava3.core.sequence.GeneSequence
Remove the exon sequence
removeFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Remove a feature from the sequence
removeGaps(ProteinSequence) - Static method in class org.biojava.bio.structure.io.StructureSequenceMatcher
Removes all gaps ('-') from a protein sequence
removeGaps(T[][]) - Static method in class org.biojava.bio.structure.io.StructureSequenceMatcher
Creates a new list consisting of all columns of gapped where no row contained a null value.
removeGeneSequence(String) - Method in class org.biojava3.core.sequence.ChromosomeSequence
 
removeIntron(String) - Method in class org.biojava3.core.sequence.GeneSequence
Remove the intron by accession
removeMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
remove a single consumer from the parser
removeMMcifConsumer(MMcifConsumer) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
removeNode(PhylogenyNode, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
removeNote(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
removeOutputOption(BlastOutputParameterEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Removes given parameter
removeOverlappingDomains(int, boolean, Protein) - Static method in class org.forester.surfacing.SurfacingUtil
Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ ignored
removeProgessListener(NJTreeProgressListener) - Method in class org.biojava3.phylo.TreeConstructor
 
removeSequence(int) - Method in class org.forester.development.BasicMsa
 
removeSuffix(String) - Static method in class org.forester.util.ForesterUtil
 
removeTranscript(String) - Method in class org.biojava3.core.sequence.GeneSequence
Remove the transcript sequence from the gene
removeWhiteSpace(String) - Static method in class org.forester.util.ForesterUtil
Removes all white space from String s.
render(double, double, Graphics2D, TreePanel, boolean) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
render(double, double, Graphics2D, TreePanel, boolean) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
This can be used to render phylogeny data as graphics (for example, display of the domain structure).
RenderableDomainArchitecture - Class in org.forester.archaeopteryx.phylogeny.data
 
RenderableDomainArchitecture(DomainArchitecture) - Constructor for class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
RenderablePhylogenyData - Interface in org.forester.archaeopteryx.phylogeny.data
 
RenderStyle - Enum in org.biojava3.structure.gui
 
repaint() - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
repaint() - Method in interface org.biojava3.structure.gui.StructureViewer
 
repeatDescription(String) - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this parse listener of a repeat description line.
REPLACE_UNDERSCORES_DEFAULT - Static variable in class org.forester.io.parsers.nhx.NHXParser
 
replaceIllegalNhCharacters(String) - Static method in class org.forester.util.ForesterUtil
 
replaceIllegalNhxCharacters(String) - Static method in class org.forester.util.ForesterUtil
 
replaceIllegalXmlCharacters(String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil
 
RepresentativeXMLConverter - Class in org.biojava.bio.structure.align.xml
 
RepresentativeXMLConverter() - Constructor for class org.biojava.bio.structure.align.xml.RepresentativeXMLConverter
 
requestingAlignmentsFromServer(int) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
requestingAlignmentsFromServer(int) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
 
requestingAlignmentsFromServer(int) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
requestNextStructure(StructureListener) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
requestNextStructure(StructureListener) - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
requestUserConfig() - Static method in class org.biojava.bio.structure.align.webstart.WebStartMain
 
reRoot(int) - Method in class org.forester.phylogeny.Phylogeny
Places the root of this Phylogeny on the parent branch of the PhylogenyNode with a corresponding ID.
reRoot(PhylogenyBranch) - Method in class org.forester.phylogeny.Phylogeny
Places the root of this Phylogeny on Branch b.
reRoot(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
Places the root of this Phylogeny on the parent branch PhylogenyNode n.
reRoot(PhylogenyNode, double) - Method in class org.forester.phylogeny.Phylogeny
 
RescoreRefiner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.
reset() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
reset() - Method in interface org.biojava.bio.structure.align.ce.ConfigStrucAligParams
Set the parameters to the default.
reset() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
reset() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
reset() - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
reset() - Method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
 
reset() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
reset() - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
 
reset() - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
 
reset() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Resets the stream to the most recent mark.
reset() - Method in class org.biojava3.core.util.CRC64Checksum
 
reset() - Method in class org.forester.phylogeny.iterators.ChildNodeIteratorForward
Resets the iterator.
reset() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator
DOCUMENT ME!
reset() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator
Resets the iterator.
reset() - Method in interface org.forester.phylogeny.iterators.PhylogenyNodeIterator
 
reset() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator
DOCUMENT ME!
reset() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator
 
reset() - Method in class org.forester.sdi.ORcount
 
resetAnchors() - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
resetDisplay() - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
RESID_STR - Static variable in interface org.forester.go.GoXRef
 
residueNumber - Variable in class org.biojava.bio.structure.HetatomImpl
 
ResidueNumber - Class in org.biojava.bio.structure
Everything that is needed to uniquely describe a residue position
ResidueNumber() - Constructor for class org.biojava.bio.structure.ResidueNumber
 
ResidueNumber(String, Integer, Character) - Constructor for class org.biojava.bio.structure.ResidueNumber
 
ResidueProperties - Class in org.biojava3.phylo
 
ResidueType - Enum in org.biojava.bio.structure.io.mmcif.chem
Enumerates the possible classifications of residues.
resizeArray(Object, int) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
Reallocates an array with a new size, and copies the contents of the old array to the new array.
resizeInnerPanel(String) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
resolve(T) - Method in interface org.biojava3.core.sequence.location.template.Point.Resolver
 
ResourceManager - Class in org.biojava.bio.structure.align.util
A class that manages the Strings that are defined in the spice.properties file.
ResourceManager() - Constructor for class org.biojava.bio.structure.align.util.ResourceManager
 
reverse(int) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
 
reverse(int) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
reverse(int, int) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
reverse(int) - Method in interface org.biojava3.core.sequence.location.template.Point
Returns the equivalent position on the reverse strand
ReversedSequenceView<C extends Compound> - Class in org.biojava3.core.sequence.views
For a given sequence this class will return the base at the reversed position i.e.
ReversedSequenceView(Sequence<C>) - Constructor for class org.biojava3.core.sequence.views.ReversedSequenceView
 
reverseSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).
RG - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
RG1 - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
rio - Class in org.forester.application
 
rio() - Constructor for class org.forester.application.rio
 
RIO - Class in org.forester.sdi
 
RIO() - Constructor for class org.forester.sdi.RIO
Default constructor.
RIOn - Class in org.forester.sdi
 
RIOn() - Constructor for class org.forester.sdi.RIOn
 
rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.
rmsdThr - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
rmsdThrJoin - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
RNA_ONLY - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Convenience Set of polymer types classified as RNA.
rnaAminoAcidTranslator(RNAToAminoAcidTranslator) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
rnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
RNACompoundSet - Class in org.biojava3.core.sequence.compound
 
RNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.RNACompoundSet
 
rnaCreator(SequenceCreatorInterface<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
RNASequence - Class in org.biojava3.core.sequence
RNASequence where RNACompoundSet are the allowed values
RNASequence(String) - Constructor for class org.biojava3.core.sequence.RNASequence
Create a RNA sequence from a String
RNASequence(ProxySequenceReader<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.RNASequence
Create a RNA aequence from a proxy reader
RNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.RNASequence
Create a RNA sequence from a string with a user defined RNA compound set
RNASequence(ProxySequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.RNASequence
Create a RNA sequence from a proxy reader and user defined RNA compound set
RNASequenceCreator - Class in org.biojava3.core.sequence.io
Used to create a RNA sequence
RNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.io.RNASequenceCreator
 
RnaSequenceView - Class in org.biojava3.core.sequence.views
Attempts to do on the fly translation of RNA by not requesting the compounds until asked.
RnaSequenceView(Sequence<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.views.RnaSequenceView
 
RnaSequenceView(Sequence<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.views.RnaSequenceView
 
RNAToAminoAcidTranslator - Class in org.biojava3.core.sequence.transcription
Takes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list of Sequence which hold AminoAcidCompound.
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean) - Constructor for class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
 
RonnConstraint - Class in org.biojava3.ronn
A collection of various constrain values used by RONN
RonnConstraint() - Constructor for class org.biojava3.ronn.RonnConstraint
 
RonnConstraint.Threshold - Enum in org.biojava3.ronn
 
rotate(Atom, double[][]) - Static method in class org.biojava.bio.structure.Calc
rotate a single atom aroud a rotation matrix.
rotate(Structure, double[][]) - Static method in class org.biojava.bio.structure.Calc
Rotate a structure.
rotate(Group, double[][]) - Static method in class org.biojava.bio.structure.Calc
rotate a structure .
rotate(Atom, Matrix) - Static method in class org.biojava.bio.structure.Calc
Rotate an atom around a Matrix object.
rotate(Group, Matrix) - Static method in class org.biojava.bio.structure.Calc
Rotate a group object.
rotate(Structure, Matrix) - Static method in class org.biojava.bio.structure.Calc
Rotate a structure object.
rotateHue(Color, float) - Static method in class org.biojava.bio.structure.gui.util.color.ColorUtils
 
round(double, int) - Static method in class org.forester.util.ForesterUtil
 
ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
roundToDecimals(double, int) - Static method in class org.biojava3.aaproperties.Utils
Returns a value with the desired number of decimal places.
roundToInt(double) - Static method in class org.forester.util.ForesterUtil
Rounds d to an int.
roundToInt(float) - Static method in class org.forester.util.ForesterUtil
 
run() - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
run() - Method in class org.biojava.bio.structure.align.FarmJob
 
run() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalc
 
run() - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
run() - Method in class org.biojava.bio.structure.align.gui.GUIFarmJobRunnable
 
run() - Method in class org.biojava.bio.structure.gui.util.AlignmentCalc
 
run() - Method in class org.biojava.bio.structure.io.mmcif.AllChemCompProvider
Do the actual loading of the dictionary in a thread.
run() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
Deprecated.
 
run(String[]) - Static method in class org.biojava3.aaproperties.CommandPrompt
 
run() - Method in class org.biojava3.phylo.TreeConstructor
 
run() - Method in class org.forester.archaeopteryx.UrlTreeReader
 
runOptimization(int) - Method in class org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer
run the optimization
runPairwiseScorers(List<PairwiseSequenceScorer<S, C>>) - Static method in class org.biojava3.alignment.Alignments
Factory method to run a list of scorers concurrently.

S

S - Static variable in class org.biojava3.aaproperties.Constraints
 
s_min - Variable in class org.biojava.bio.structure.domain.pdp.CutValues
 
sampleStandardDeviation() - Method in class org.forester.util.BasicDescriptiveStatistics
 
sampleStandardDeviation() - Method in interface org.forester.util.DescriptiveStatistics
 
sampleStandardUnit(double) - Method in class org.forester.util.BasicDescriptiveStatistics
 
sampleStandardUnit(double, double, double) - Static method in class org.forester.util.BasicDescriptiveStatistics
Computes the sample standard unit (z-score).
sampleStandardUnit(double) - Method in interface org.forester.util.DescriptiveStatistics
 
sampleVariance() - Method in class org.forester.util.BasicDescriptiveStatistics
 
sampleVariance() - Method in interface org.forester.util.DescriptiveStatistics
 
SandboxStyleStructureProvider - Class in org.biojava.bio.structure.io
The "Sandbox" style of organizing files is to have a directory structure like below, i.e.
SandboxStyleStructureProvider() - Constructor for class org.biojava.bio.structure.io.SandboxStyleStructureProvider
 
SangerFastqReader - Class in org.biojava3.sequencing.io.fastq
Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqReader() - Constructor for class org.biojava3.sequencing.io.fastq.SangerFastqReader
 
SangerFastqWriter - Class in org.biojava3.sequencing.io.fastq
Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter() - Constructor for class org.biojava3.sequencing.io.fastq.SangerFastqWriter
 
SANITIZE - Static variable in class org.forester.tools.PhylogenyDecorator
 
sanitizeString(String) - Static method in class org.forester.util.ForesterUtil
 
SankoffParsimony<STATE_TYPE> - Class in org.forester.phylogenyinference
 
SankoffParsimony() - Constructor for class org.forester.phylogenyinference.SankoffParsimony
 
save(UserConfiguration) - Method in class org.biojava.bio.structure.align.webstart.PersistentConfig
writes the configuration
SAVE_ALIGNMENT_XML - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
SAX_FEATURES_VALIDATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
SAX_FEATURES_VALIDATION - Static variable in class org.forester.io.parsers.tol.TolParser
 
SCALE_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
ScaleableMatrixPanel - Class in org.biojava.bio.structure.gui
A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.
ScaleableMatrixPanel() - Constructor for class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
ScaleableMatrixPanel.GradientRenderer - Class in org.biojava.bio.structure.gui
A renderer for the the gradient dropdown menu at the top of scaleableMatrixPanes.
ScaleableMatrixPanel.GradientRenderer() - Constructor for class org.biojava.bio.structure.gui.ScaleableMatrixPanel.GradientRenderer
 
scaleAdd(float, Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
 
scaleColours - Static variable in class org.biojava3.phylo.ResidueProperties
 
ScaledSubstitutionMatrix - Class in org.biojava3.alignment.aaindex
The biojava-alignment module represents substitution matrices with short values.
ScaledSubstitutionMatrix() - Constructor for class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
scan(ProteinSequence) - Method in interface org.biojava3.ws.hmmer.HmmerScan
 
scan(ProteinSequence) - Method in class org.biojava3.ws.hmmer.RemoteHmmerScan
 
scan(ProteinSequence, URL) - Method in class org.biojava3.ws.hmmer.RemoteHmmerScan
Scans a protein sequence for Pfam profile matches.
SchemaGenerator - Class in org.biojava3.aaproperties.xml
 
SchemaGenerator(String) - Constructor for class org.biojava3.aaproperties.xml.SchemaGenerator
 
SCOP_DOWNLOAD - Static variable in class org.biojava.bio.structure.scop.ScopInstallation
 
SCOPAutoSuggestProvider - Class in org.biojava.bio.structure.align.gui.autosuggest
 
SCOPAutoSuggestProvider() - Constructor for class org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
ScopCategory - Enum in org.biojava.bio.structure.scop
The various categories provided by SCOP.
ScopDatabase - Interface in org.biojava.bio.structure.scop
General API how to interact with SCOP
ScopDescription - Class in org.biojava.bio.structure.scop
Contains data from dir.des.scop.txt_1.75
ScopDescription() - Constructor for class org.biojava.bio.structure.scop.ScopDescription
 
ScopDescriptions - Class in org.biojava.bio.structure.scop.server
 
ScopDescriptions() - Constructor for class org.biojava.bio.structure.scop.server.ScopDescriptions
 
ScopDomain - Class in org.biojava.bio.structure.scop
Container for the information for a domain.
ScopDomain() - Constructor for class org.biojava.bio.structure.scop.ScopDomain
 
ScopDomains - Class in org.biojava.bio.structure.scop.server
 
ScopDomains() - Constructor for class org.biojava.bio.structure.scop.server.ScopDomains
 
scopDownloadURL - Variable in class org.biojava.bio.structure.scop.ScopInstallation
 
ScopFactory - Class in org.biojava.bio.structure.scop
Controls the global ScopDatabase being used.
ScopFactory() - Constructor for class org.biojava.bio.structure.scop.ScopFactory
 
scopIDregex - Static variable in class org.biojava.bio.structure.align.util.AtomCache
 
ScopInstallation - Class in org.biojava.bio.structure.scop
This class provides access to the SCOP protein structure classification.
ScopInstallation(String) - Constructor for class org.biojava.bio.structure.scop.ScopInstallation
Create a new SCOP installation.
ScopInstallation() - Constructor for class org.biojava.bio.structure.scop.ScopInstallation
Create a new SCOP installation, downloading the file to "the right place".
ScopInstallationInstance - Class in org.biojava.bio.structure.gui.util
 
ScopNode - Class in org.biojava.bio.structure.scop
 
ScopNode() - Constructor for class org.biojava.bio.structure.scop.ScopNode
 
ScopNodes - Class in org.biojava.bio.structure.scop.server
 
ScopNodes() - Constructor for class org.biojava.bio.structure.scop.server.ScopNodes
 
ScopSelectPanel - Class in org.biojava.bio.structure.gui.util
 
ScopSelectPanel() - Constructor for class org.biojava.bio.structure.gui.util.ScopSelectPanel
 
ScopSelectPanel(boolean) - Constructor for class org.biojava.bio.structure.gui.util.ScopSelectPanel
 
scopVersion - Variable in class org.biojava.bio.structure.scop.ScopInstallation
 
score - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
score() - Method in class org.biojava3.genome.parsers.gff.Feature
Get score.
scoreMatrices - Static variable in class org.biojava3.phylo.ResidueProperties
 
ScoreMatrix - Class in org.biojava3.phylo
 
Scorer - Interface in org.biojava3.alignment.template
Defines an algorithm which computes a score.
scores - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
scoresToRanges(float[], float) - Static method in class org.biojava3.ronn.Jronn
Convert raw scores to ranges.
SCORING_STRATEGY - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
ScoringMethodForExternalNode - Interface in org.forester.pccx
 
scoringStrategy - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
scroll - Variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
sdi - Class in org.forester.application
 
sdi() - Constructor for class org.forester.application.sdi
 
SDI - Class in org.forester.sdi
 
SDI(Phylogeny, Phylogeny) - Constructor for class org.forester.sdi.SDI
Constructor which sets the gene tree and the species tree to be compared.
sdi_r - Class in org.forester.application
 
sdi_r() - Constructor for class org.forester.application.sdi_r
 
SDIdirectory - Class in org.forester.sdi
 
SDIdirectory() - Constructor for class org.forester.sdi.SDIdirectory
 
SDIR - Class in org.forester.sdi
 
SDIR() - Constructor for class org.forester.sdi.SDIR
Default contructor which creates an "empty" object..
SDIse - Class in org.forester.sdi
 
SDIse(Phylogeny, Phylogeny) - Constructor for class org.forester.sdi.SDIse
Constructor which sets the gene tree and the species tree to be compared.
searchData(String, Phylogeny, boolean, boolean) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
searchDataLogicalAnd(String[], Phylogeny, boolean, boolean) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing
 
SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing_old
 
SecStruc - Class in org.biojava.bio.structure.secstruc
Assign secondary structure to a Structure object.
SecStruc() - Constructor for class org.biojava.bio.structure.secstruc.SecStruc
 
SecStrucGroup - Class in org.biojava.bio.structure.secstruc
 
SecStrucGroup() - Constructor for class org.biojava.bio.structure.secstruc.SecStrucGroup
 
SEED - Static variable in class org.biojava3.core.util.Hashcoder
An initial value for a hashCode, to which we add contributions from fields.
Segment - Class in org.biojava.bio.structure.domain.pdp
 
Segment() - Constructor for class org.biojava.bio.structure.domain.pdp.Segment
 
SegmentComparator - Class in org.biojava.bio.structure.domain.pdp
 
SegmentComparator() - Constructor for class org.biojava.bio.structure.domain.pdp.SegmentComparator
 
SELECT_EQR - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
selectByAttribute(String, String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that include the specified attribute key/value pair.
selectByAttribute(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that include the specified attribute key.
selectByGroup(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that have the specified group id, as defined by the group() method of the features.
selectByType(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that are of the specified type, as defined by the type() method of the features.
selectByUserData(String, Object) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that include the specified key/value pair in their userMap().
selectByUserData(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that include the specified key in their userMap().
selectElements(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
 
Selection - Interface in org.biojava3.structure.gui
 
SelectionImpl - Class in org.biojava3.structure.gui
 
SelectionImpl() - Constructor for class org.biojava3.structure.gui.SelectionImpl
 
selectionLocked() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
selectionLocked() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
selectionLocked() - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
 
selectionLocked() - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
selectionUnlocked() - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
selectionUnlocked() - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
selectionUnlocked() - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
 
selectionUnlocked() - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
selectOverlapping(String, Location, boolean) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a list of all features that overlap the specified location on the specified sequence.
selectParentElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
 
SelectPDBPanel - Class in org.biojava.bio.structure.align.gui
A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
SelectPDBPanel() - Constructor for class org.biojava.bio.structure.align.gui.SelectPDBPanel
 
SelectPDBPanel(boolean) - Constructor for class org.biojava.bio.structure.align.gui.SelectPDBPanel
 
selectSingleElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
 
sendAFPChainToServer(String, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Converts given sequence to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Converts given GenBank GID to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Sends the Blast request via the Put command of the CGI-BIN interface.
sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentService
Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentService
Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
sendDeleteRequest(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Sends a delete request for given request id.
sendMultiAFPChainToServer(String, String, String) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
sendMultiAFPChainToServer(String, String, String, String) - Static method in class org.biojava.bio.structure.align.client.JFatCatClient
 
sendResultsToServer(List<String>) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
sentResultsToServer(int, String) - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
sentResultsToServer(int, String) - Method in interface org.biojava.bio.structure.align.events.AlignmentProgressListener
 
sentResultsToServer(int, String) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
SEPARATOR - Static variable in interface org.forester.surfacing.BinaryDomainCombination
 
seqArraySize(int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
 
seqFont - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
seqname() - Method in class org.biojava3.genome.parsers.gff.Feature
Get the sequence name.
seqname() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get the sequence name.
SeqRes2AtomAligner - Class in org.biojava.bio.structure.io
Aligns the SEQRES residues to the ATOM residues.
SeqRes2AtomAligner() - Constructor for class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
SEQRESRECORD - Static variable in interface org.biojava.bio.structure.AminoAcid
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
Sequence<C extends Compound> - Interface in org.biojava3.core.sequence.template
Main interface for defining a collection of Compounds and accessing them using biological indexes
sequence(String) - Method in interface org.biojava3.sequencing.io.fastq.ParseListener
Notify this parse listener of a sequence line.
Sequence - Interface in org.forester.development
 
SEQUENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Sequence - Class in org.forester.phylogeny.data
 
Sequence() - Constructor for class org.forester.phylogeny.data.Sequence
 
SEQUENCE_ACCESSION - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
SEQUENCE_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
SEQUENCE_CONSERVATION - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_DOMAIN_ARCHITECURE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_LOCATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_MOL_SEQ - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_SYMBOL - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_SYMBOL_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
SEQUENCE_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
SEQUENCE_TYPES - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
sequenceAndQualityLengthsMatch() - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
SequenceAsStringHelper<C extends Compound> - Class in org.biojava3.core.sequence.storage
This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.
SequenceAsStringHelper() - Constructor for class org.biojava3.core.sequence.storage.SequenceAsStringHelper
 
SequenceComparator - Class in org.biojava3.core.sequence
Used to sort sequences
SequenceComparator() - Constructor for class org.biojava3.core.sequence.SequenceComparator
 
SequenceCreatorInterface<C extends Compound> - Interface in org.biojava3.core.sequence.io.template
 
SequenceDisplay - Class in org.biojava.bio.structure.gui
A sequence display that can show the results of a protein structure alignment.
SequenceDisplay(StructurePairAligner) - Constructor for class org.biojava.bio.structure.gui.SequenceDisplay
 
sequenceEquality(Sequence<C>, Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
A case-sensitive manner of comparing two sequence objects together.
sequenceEqualityIgnoreCase(Sequence<C>, Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
A case-insensitive manner of comparing two sequence objects together.
SequenceFileProxyLoader<C extends Compound> - Class in org.biojava3.core.sequence.loader
This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.
SequenceFileProxyLoader(File, SequenceParserInterface, long, int, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
SequenceLengthError - Error in org.biojava3.core.exceptions
Currently not used
SequenceLengthError(String) - Constructor for error org.biojava3.core.exceptions.SequenceLengthError
 
SequenceLocation<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.location
A location in a sequence that keeps a reference to its parent sequence
SequenceLocation(int, int, S) - Constructor for class org.biojava3.core.sequence.location.SequenceLocation
 
SequenceMixin - Class in org.biojava3.core.sequence.template
Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way.
SequenceMixin() - Constructor for class org.biojava3.core.sequence.template.SequenceMixin
 
SequenceMixin.SequenceIterator<C extends Compound> - Class in org.biojava3.core.sequence.template
A basic sequence iterator which iterates over the given Sequence by biological index.
SequenceMixin.SequenceIterator(Sequence<C>) - Constructor for class org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator
 
SequenceMouseListener - Class in org.biojava.bio.structure.gui.util
a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events
SequenceMouseListener(SequenceDisplay) - Constructor for class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
SequenceOptimizationHints - Class in org.biojava3.core.sequence
A static class that provides optimization hints for memory or performance handling of sequence data.
SequenceOptimizationHints() - Constructor for class org.biojava3.core.sequence.SequenceOptimizationHints
 
SequenceOptimizationHints.SequenceCollection - Enum in org.biojava3.core.sequence
 
SequenceOptimizationHints.SequenceUsage - Enum in org.biojava3.core.sequence
 
SequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure for the results of pairwise sequence alignment.
SequenceParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
SequenceParserInterface - Interface in org.biojava3.core.sequence.io.template
 
SequenceProxyView<C extends Compound> - Class in org.biojava3.core.sequence.template
 
SequenceProxyView() - Constructor for class org.biojava3.core.sequence.template.SequenceProxyView
 
SequenceProxyView(Sequence<C>) - Constructor for class org.biojava3.core.sequence.template.SequenceProxyView
 
SequenceProxyView(Sequence<C>, Integer, Integer) - Constructor for class org.biojava3.core.sequence.template.SequenceProxyView
Main constructor for working with SequenceProxyViews
SequenceReader<C extends Compound> - Interface in org.biojava3.core.sequence.template
 
SequenceRelation - Class in org.forester.phylogeny.data
 
SequenceRelation() - Constructor for class org.forester.phylogeny.data.SequenceRelation
 
SequenceRelation.SEQUENCE_RELATION_TYPE - Enum in org.forester.phylogeny.data
 
SequenceRelationParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
SequenceScalePanel - Class in org.biojava.bio.structure.gui.util
A class that draws a Sequence as a rectangle, a scale display over it.
SequenceScalePanel(int) - Constructor for class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
SequenceTools - Class in org.biojava3.core.util
 
SequenceTools() - Constructor for class org.biojava3.core.util.SequenceTools
 
SequenceUtil - Class in org.biojava3.data.sequence
Utility class for operations on sequences
SequenceView<C extends Compound> - Interface in org.biojava3.core.sequence.template
 
seqWeight - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
Ser - Static variable in class org.biojava3.phylo.ResidueProperties
 
SerializableCache<K,V> - Class in org.biojava.bio.structure.domain
A class that provides all that is necessary to create a Serializable Cache
SerializableCache(String) - Constructor for class org.biojava.bio.structure.domain.SerializableCache
set cacheFileName to null to disable caching
serialize(File) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
serializedCache - Variable in class org.biojava.bio.structure.domain.SerializableCache
 
serialVersionUID - Static variable in class org.biojava.bio.structure.align.gui.ChooseDirAction
 
serialVersionUID - Static variable in exception org.biojava.bio.structure.io.PDBParseException
 
serialVersionUID - Static variable in exception org.biojava.bio.structure.StructureException
 
serialVersionUID - Static variable in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
 
serialVersionUID - Static variable in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties
 
serialVersionUID - Static variable in class org.forester.archaeopteryx.FontChooser
 
set(int, int, double) - Method in class org.biojava.bio.structure.jama.Matrix
Set a single element.
setA(float) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setAAIndexProvider(AAIndexProvider) - Static method in class org.biojava3.alignment.aaindex.AAindexFactory
 
setAbsorpt_coefficient_mu(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setAbsorpt_correction_T_max(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setAbsorpt_correction_T_min(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setAbsorpt_correction_type(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setAbsorpt_process_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setAcc(String) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setAcceptedAtomNames(String[]) - Method in class org.biojava.bio.structure.io.FileParsingParameters
by default the parser will read in all atoms (unless using the CAonly switch).
setAccession(AccessionID) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setAccession(AccessionID) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setAccession(Accession) - Method in class org.forester.phylogeny.data.Sequence
 
setAccession(String) - Method in class org.forester.surfacing.BasicProtein
 
setAfpAftIndex(int[][]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpBefIndex(int[][]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAFPChain(AFPChain) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
 
setAFPChain(AFPChain) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
setAfpChain(AFPChain) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
setAfpChainLen(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpChainList(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpChainTwiBin(double[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpChainTwiList(double[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpChainTwiNum(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpDisCut(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setAfpDisCut0(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setAfpIndex(int[][]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAfpSet(List<AFP>) - Method in class org.biojava.bio.structure.align.model.AFPChain
Set the set of AFPs for this alignment.
setAlgorithm(StructureAlignment) - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
setAlgorithmName(String) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setAlgorithmName(String) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAligMap(List<AlignedPosition>) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
setAligMat(AligMatEl[][]) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setAligMat(int, int, AligMatEl) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setAligMat(AligMatEl[][]) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setAlign_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setAlign_se1(int[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setAlign_se1(int[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setAlign_se2(int[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setAlign_se2(int[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setAlignementOption(String, String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
This method forwards to NCBIQBlastAlignmentProperties.setAlignmentOption(BlastAlignmentParameterEnum, String).
setAlignementOption(String, String) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties
Method to set the value for a specific alignment parameter using a key to store in a map.
setAlignmentNumber(int) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Set the number of alignments to fetch
setAlignmentOption(BlastAlignmentParameterEnum, String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the value of specified parameter
setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the alignment output format to get from the QBlast service
setAlignments(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
we only keep the first alternative...
setAlignPairs(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setAlignScore(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlignScoreUpdate(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlignSeqRes(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
setAliLenth(Integer) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setAllNodesToNotCollapse() - Method in class org.forester.phylogeny.Phylogeny
Sets all Nodes of this Phylogeny to not-collapsed.
setAllowDomainsToBeIgnored(boolean) - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
 
setAllowNonUniqueQuery(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setAlnbeg1(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlnbeg2(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlnLength(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlnseq1(char[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlnseq2(char[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlnsymb(char[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setAlpha(float) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setAltAligNumber(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
setAlternativeAlignment(AlternativeAlignment) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
 
setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
setAltitude(BigDecimal) - Method in class org.forester.phylogeny.data.Distribution
 
setAltLoc(Character) - Method in interface org.biojava.bio.structure.Atom
get set alternate Location.
setAltLoc(Character) - Method in class org.biojava.bio.structure.AtomImpl
set alternate Location.
setAminoacid(List<AminoAcidComposition>) - Method in class org.biojava3.aaproperties.xml.AminoAcidCompositionTable
 
setAminoType(Character) - Method in interface org.biojava.bio.structure.AminoAcid
set the name of the AA, in single letter code .
setAminoType(Character) - Method in class org.biojava.bio.structure.AminoAcidImpl
set the name of the AA, in single letter code .
setAnchors(int[]) - Method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Sets the starting list of anchors before running the alignment routine.
setAngleDiff(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setAniso_B(String[][]) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setArrowCursor() - Method in class org.forester.archaeopteryx.MainPanel
 
setAssignments(Map<String, String>) - Method in class org.biojava.bio.structure.domain.AssignmentXMLSerializer
 
setAsym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setAsym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setAtcc(String) - Method in class org.biojava.bio.structure.Compound
 
setAtomCaThreshold(int) - Method in class org.biojava.bio.structure.io.FileParsingParameters
the maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
setAtomGroups(List<Group>) - Method in interface org.biojava.bio.structure.Chain
Set all groups that have been specified in the ATOM section of this chain .
setAtomGroups(List<Group>) - Method in class org.biojava.bio.structure.ChainImpl
Set all groups that have been specified in the ATOM section of this chain .
setAtomicNumber(int) - Method in class org.biojava3.aaproperties.xml.Element
 
setAtomLinkages(Set<StructureAtomLinkage>) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
Set atom linkages
setAtomLinkages(Set<StructureAtomLinkage>) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
setAtomName(String) - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
setAtoms(Atom[]) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
setAtoms(List<Atom>) - Method in interface org.biojava.bio.structure.Group
Set the atoms of this group.
setAtoms(List<Atom>) - Method in class org.biojava.bio.structure.HetatomImpl
set the atoms of this group
setAuth_asym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setAuth_atom_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setAuth_comp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setAuth_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setAuth_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setAuth_seq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setAuth_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setAuth_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setAuthority(String) - Method in class org.forester.phylogeny.data.Taxonomy
 
setAuthorList(List<Author>) - Method in class org.biojava.bio.structure.JournalArticle
 
setAuthors(String) - Method in class org.biojava.bio.structure.PDBHeader
 
setAutoFetch(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setAutoFetch(boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
Does the cache automatically download files that are missing from the local installation from the PDB FTP site?
setAutoFetch(boolean) - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
setAutoFetch(boolean) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
setAutoFetch(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
 
setAutoFetch(boolean) - Method in interface org.biojava.bio.structure.io.StructureIOFile
Tell the parser to fetch missing PDB files from the FTP server automatically.
setAutoFetch(boolean) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
Deprecated.
tell the parser to fetch missing mmCif files from the RCSB FTP server automatically.
setAutoSuggestProvider(AutoSuggestProvider) - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
setB(float) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setB_iso_max(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setB_iso_mean(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setB_iso_min(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setB_iso_or_equiv(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setB_iso_or_equiv_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setBadRmsd(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setBeta(float) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setBetweenCompounds(boolean) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setBinaryCharacters(BinaryCharacters) - Method in class org.forester.phylogeny.data.NodeData
 
setBioAssemblyFallback(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
Set bioAssemblyFallback to true, to download the original PDB file in cases that a biological assembly file is not available.
setBioAssemblyId(int) - Method in class org.biojava.bio.structure.io.PDBFileReader
Sets the ID of the biological assembly to be loaded.
setBioBegin(Integer) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setBioEnd(Integer) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setBioEnd(Integer) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
setBiol_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setBiologicalAssembly(boolean) - Method in interface org.biojava.bio.structure.Structure
Sets a flag to indicate if this structure is a biological assembly
setBiologicalAssembly(boolean) - Method in class org.biojava.bio.structure.StructureImpl
Sets a flag to indicate if this structure is a biological assembly
setBiologicalUnit(String) - Method in class org.biojava.bio.structure.Compound
 
setBioStart(Integer) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
 
setBlastAdvancedOptions(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
This method is to be used if a request is to use non-default values at submission.
setBlastDatabase(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the database to be used with blastall
setBlastExpect(double) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the EXPECT parameter to be use with blastall
setBlastFromToPosition(int, int) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the QUERY_FROM and QUERY_TO parameters to be use by blast.
setBlastGapCosts(int, int) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the GAPCOSTS parameter
setBlastMatrix(BlastMatrixEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the value for the MATRIX parameter to use for blastall
setBlastProgram(BlastProgramEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the program to be used with blastall
setBlastWordSize(int) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
Sets the WORD_SIZE parameter to be use with blastall
setBlock2Afp(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockGap(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockNum(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockNumClu(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockNumIni(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockNumSpt(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockResList(int[][][]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockResSize(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockRmsd(double[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockRotationMatrix(Matrix[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockScore(double[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockShiftVector(Atom[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setBlockSize(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setbondLengthTolerance(double) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
setBootstrapConfidence(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method.
setBranchColor(BranchColor) - Method in class org.forester.phylogeny.data.BranchData
 
setBranchColorValue(PhylogenyNode, Color) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
setBranchData(BranchData) - Method in class org.forester.phylogeny.PhylogenyNode
 
setBranchWidth(BranchWidth) - Method in class org.forester.phylogeny.data.BranchData
 
setBranchWidthValue(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method
setC(float) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setC(Atom) - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
setCA(Atom) - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
setCa1(Atom[]) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setCa1(Atom[]) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
setCa1(Atom[]) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
setCa1Length(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setCa2(Atom[]) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
setCa2(Atom[]) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
setCa2Length(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setCache(AtomCache) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setCacheLocation(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
setCacheSize(int) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
setCacheSize(int) - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
set how many structures should be kept in memory - for quicker access
setCalculationTime(long) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setCalculationTime(long) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setCallbackFunction(String, String) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
setCartn_x(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setCartn_x_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setCartn_y(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setCartn_y_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setCartn_z(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setCartn_z_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setCategory(ScopCategory) - Method in class org.biojava.bio.structure.scop.ScopDescription
 
setCategory(ModificationCategory) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
 
setCell(String) - Method in class org.biojava.bio.structure.Compound
 
setCellColor(ContinuousColorMapper) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
setCellColor(ContinuousColorMapper) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
setCellLine(String) - Method in class org.biojava.bio.structure.Compound
 
setCellularLocation(String) - Method in class org.biojava.bio.structure.Compound
 
setCenter1(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setCenter2(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setChain(Chain) - Method in interface org.biojava.bio.structure.Group
Sets the back-reference to its parent Chain.
setChain(Chain) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
setChain(Chain) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
setChain(Chain) - Method in class org.biojava.bio.structure.HetatomImpl
Sets the back-reference to its parent Chain.
setChain1(String) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setChain2(String) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setChainId(String) - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
setChainID(String) - Method in interface org.biojava.bio.structure.Chain
get and set the name of this chain (Chain id in PDB file ).
setChainID(String) - Method in class org.biojava.bio.structure.ChainImpl
get and set the name of this chain (Chain id in PDB file ).
setChainId(List<String>) - Method in class org.biojava.bio.structure.Compound
Sets the list of chain IDs.
setChainId(Character) - Method in class org.biojava.bio.structure.DBRef
The chain ID of the corresponding chain.
setChainId(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setChainId(String) - Method in class org.biojava.bio.structure.ResidueNumber
 
setChainId(String) - Method in class org.biojava3.protmod.structure.StructureGroup
 
setChainID1(String) - Method in class org.biojava.bio.structure.SSBond
 
setChainID2(String) - Method in class org.biojava.bio.structure.SSBond
 
setChainInfoFile(File) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
setChainLen(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setChainRmsd(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
The RMSD of the chain of AFPs.
setChains(List<Chain>) - Method in class org.biojava.bio.structure.Compound
 
setChains(List<Chain>) - Method in interface org.biojava.bio.structure.Structure
set the chains of a structure, if this is a NMR structure, this will only set model 0.
setChains(int, List<Chain>) - Method in interface org.biojava.bio.structure.Structure
set the chains for a model
setChains(List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
 
setChains(int, List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
 
setCharacter(int, String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
setCharacter(int, String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
setChemComp(ChemComp) - Method in interface org.biojava.bio.structure.Group
Set the Chemical Component that closer describes this group.
setChemComp(ChemComp) - Method in class org.biojava.bio.structure.HetatomImpl
 
setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
 
setChild1(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the first child PhylogenyNode of this PhylogenyNode to n.
setChild2(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the second child PhylogenyNode of this PhylogenyNode to n.
setChildNode(int, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
Inserts PhylogenyNode n at the specified position i into the list of child nodes.
setChildren(List<Integer>) - Method in class org.biojava.bio.structure.scop.ScopNode
 
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava3.core.sequence.features.AbstractFeature
Set the children features
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Set the children features
setChromosomeNumber(int) - Method in class org.biojava3.core.sequence.ChromosomeSequence
 
setCircular(boolean) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setClassId(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setClassification(String) - Method in class org.biojava.bio.structure.PDBHeader
 
setClassificationId(String) - Method in class org.biojava.bio.structure.scop.ScopDescription
 
setClassificationId(String) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setCluster(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
set the number of the cluster this alignment belongs to.
setCluster(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setCol(short) - Method in class org.biojava.bio.structure.align.helper.IndexPair
 
setCollapse(boolean) - Method in class org.forester.phylogeny.PhylogenyNode
Sets whether this PhylogenyNode should be drawn as collapsed.
setColor(Color) - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
setColor(Color) - Method in interface org.biojava3.structure.gui.StructureViewer
Apply this color to the current Selection
setColorMap(Map<String, Color>) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
setColorSpace(ColorSpace, LinearColorInterpolator.InterpolationDirection[]) - Method in class org.biojava.bio.structure.gui.util.color.LinearColorInterpolator
Sets the ColorSpace to use for interpolation.
setColorSpace(ColorSpace) - Method in class org.biojava.bio.structure.gui.util.color.LinearColorInterpolator
 
setCols(List<AminoAcidCompound>) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setComment(String) - Method in class org.forester.go.BasicGoTerm
 
setCommonName(String) - Method in class org.forester.phylogeny.data.Taxonomy
 
setComp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
setComp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
setCompoundAt(char, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Converts from char to Compound and sets it at the given biological index
setCompoundAt(C, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
Sets the compound at the specified biological index
setCompounds(List<Compound>) - Method in interface org.biojava.bio.structure.Structure
set the compounts
setCompounds(List<Compound>) - Method in class org.biojava.bio.structure.StructureImpl
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Class is immutable & so this is unsupported
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Unsupported
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setCompoundSet(CompoundSet<C>) - Method in interface org.biojava3.core.sequence.template.SequenceReader
 
setCompoundSet(CompoundSet<NucleotideCompound>) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
setCondition(ModificationCondition) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
 
setConfidence(Confidence) - Method in class org.forester.phylogeny.data.Annotation
 
setConfidence(Confidence) - Method in class org.forester.phylogeny.data.Event
 
setConfidence(Confidence) - Method in class org.forester.phylogeny.Phylogeny
 
setConfidence(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method.
setConfidence(PhylogenyNode, double, String) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method.
setConn(Double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setConnections(List<Map<String, Integer>>) - Method in interface org.biojava.bio.structure.Structure
sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
setConnections(List<Map<String, Integer>>) - Method in class org.biojava.bio.structure.StructureImpl
 
setContacts(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setContents(String) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
setContents(String) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
setContents(String) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
Once the sequence is retrieved set the contents and make sure everything this is valid
setContents(String) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
setContents(List<C>) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
 
setContents(String) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
Class is immutable & so this is unsupported
setContents(String) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
 
setContents(String) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Unsupported
setContents(String) - Method in interface org.biojava3.core.sequence.template.SequenceReader
 
setContents(String) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
 
setContig(int) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
 
setCoords(double[]) - Method in interface org.biojava.bio.structure.Atom
set the coordinates.
setCoords(double[]) - Method in class org.biojava.bio.structure.AtomImpl
the coordinates.
setCopiedAndPastedNodes(Set<PhylogenyNode>) - Method in class org.forester.archaeopteryx.MainPanel
 
setCorrelation_coeff_Fo_to_Fc(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setCorrelation_coeff_Fo_to_Fc_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setCovered(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setCPPoint(Integer) - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
setCreate_co(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setCrystallographicInfo(PDBCrystallographicInfo) - Method in interface org.biojava.bio.structure.Structure
Sets crystallographic information for this structure
setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.bio.structure.StructureImpl
Sets crystallographic information for this structure
setCrystals_number(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setCut_sites(int[]) - Method in class org.biojava.bio.structure.domain.pdp.CutSites
 
setCuts(int, int[], AlignerHelper.Last[][], AlignerHelper.Cut[]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setCutsPerSection(int) - Method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Sets the number of cuts added to each section during each pass.
setData(TreeSet<String>) - Method in class org.biojava.bio.structure.scop.server.TreeSetStringWrapper
 
setDatabase(String) - Method in class org.biojava.bio.structure.DBRef
Specifies the database value.
setDatabase(String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
 
setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setDate(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
setDate(Date) - Method in class org.forester.phylogeny.data.NodeData
 
setDate_original(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
setDb_align_beg(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setDb_align_end(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setDb_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setDb_name(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setDbAccession(String) - Method in class org.biojava.bio.structure.DBRef
Sequence database accession code.
setDbIdCode(String) - Method in class org.biojava.bio.structure.DBRef
Sequence database identification code.
setDBRefs(List<DBRef>) - Method in interface org.biojava.bio.structure.Structure
set the list of database references for this structure
setDBRefs(List<DBRef>) - Method in class org.biojava.bio.structure.StructureImpl
 
setDbSeqBegin(int) - Method in class org.biojava.bio.structure.DBRef
Initial sequence number of the database seqment.
setDbSeqEnd(int) - Method in class org.biojava.bio.structure.DBRef
The begin of the sequence position in the database
setDcl(Integer) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setDebug(boolean) - Method in class org.biojava.bio.structure.align.StructurePairAligner
set the debug flag
setDebug(boolean) - Method in class org.biojava.bio.structure.domain.SerializableCache
 
setDEBUG(boolean) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
 
setDefault() - Method in class org.biojava.bio.structure.align.gui.ParameterGUI
 
setDefault() - Method in class org.biojava.bio.structure.io.FileParsingParameters
 
setDefaultCutsPerSection(int) - Static method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
Sets the default number of cuts added to each section during each pass.
setDefaultExtensionPenalty(short) - Static method in class org.biojava3.alignment.SimpleGapPenalty
Sets the default gap extension penalty.
setDefaultOpenPenalty(short) - Static method in class org.biojava3.alignment.SimpleGapPenalty
Sets the default gap open penalty.
setDefaultText(String) - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
 
setDefinition(String) - Method in class org.forester.go.BasicGoTerm
 
setDensityCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDepDate(Date) - Method in class org.biojava.bio.structure.PDBHeader
 
setDesc(String) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setDesc(String) - Method in class org.forester.phylogeny.data.Annotation
 
setDesc(String) - Method in class org.forester.phylogeny.data.Date
 
setDescription(String) - Method in class org.biojava.bio.structure.PDBHeader
 
setDescription(String) - Method in class org.biojava.bio.structure.scop.ScopDescription
 
setDescription(String) - Method in class org.biojava.bio.structure.Site
sets the REMARK 800 description of the site
setDescription(String) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setDescription(String) - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
setDescription(String) - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Sets the description of this matrix.
setDescription(String) - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
setDescription(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature
 
setDescription(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Set the description that can be used to describe the feature
setDescription(String) - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
setDescription(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setDescription(String) - Method in interface org.biojava3.core.sequence.template.Compound
 
setDescription(String) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
setDescription(String) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
setDescription(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
 
setDescription(String) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
setDescription(String) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
setDescription(String) - Method in class org.forester.phylogeny.data.Distribution
 
setDescription(String) - Method in class org.forester.phylogeny.Phylogeny
 
setDescription(String) - Method in class org.forester.surfacing.BasicProtein
 
setDescription(String) - Method in class org.forester.surfacing.MappingResults
 
setDescription2(String) - Method in class org.biojava.bio.structure.align.model.AFPChain
Set the textual description for protein 2.
setDescriptionNumber(int) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the number of descriptions to fetch
setDescriptor(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setDetailedness(DomainSimilarityCalculator.Detailedness) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
setDetails(String) - Method in class org.biojava.bio.structure.Compound
 
setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setDiagonalDistance(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDiagonalDistance2(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDirectionTowards(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch
 
setDisCut(Double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setDisFilter(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setDisplayDomainNames(boolean) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
setDisSmooth(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setDist(int[][]) - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
setDist1(double[][]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setDist1(double[][]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setDist2(double[][]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setDist2(double[][]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setDisTable1(Matrix) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setDisTable2(Matrix) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setDistance(double) - Method in class org.biojava.bio.structure.secstruc.DistEn
 
setDistanceIncrement(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setDistanceMatrix(Matrix) - Method in class org.biojava.bio.structure.align.model.AFPChain
A matrix with ca1length rows and ca2length columns.
setDistanceMatrix(Matrix) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
The distance matrix this alignment is based on
setDistanceToParent(double) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the length of the branch leading to the _parent of this PhylogenyNode to double d.
setDistanceToParent(double) - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
setDistanceUnit(String) - Method in class org.forester.phylogeny.Phylogeny
 
setDistribution(Distribution) - Method in class org.forester.phylogeny.data.NodeData
 
setDNAType(DNASequence.DNAType) - Method in class org.biojava3.core.sequence.DNASequence
 
setDoAngleCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDoDensityCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDoDistanceCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDoi(String) - Method in class org.biojava.bio.structure.JournalArticle
Set the value of doi
setDoi(String) - Method in class org.forester.phylogeny.data.Reference
 
setDomainArchitecture(DomainArchitecture) - Method in class org.forester.phylogeny.data.Sequence
 
setDomainId(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setDomainProvider(DomainProvider) - Static method in class org.biojava.bio.structure.domain.DomainProviderFactory
 
setDomains(SortedSet<HmmerDomain>) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setDomainsIgnoredDueToEval(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setDomainsIgnoredDueToEval(int) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setDomainsIgnoredDueToIndividualScoreCutoff(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setDomainsIgnoredDueToIndividualScoreCutoff(int) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setDoRMSCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setDownloadAll(boolean) - Method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
By default this provider will download only some of the ChemComp files.
setDuplications(int) - Method in class org.forester.phylogeny.data.Event
 
setDVar(Double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setEcNums(List<String>) - Method in class org.biojava.bio.structure.Compound
 
setEditorList(List<Author>) - Method in class org.biojava.bio.structure.JournalArticle
 
setElement(Element) - Method in interface org.biojava.bio.structure.Atom
set element of the atom name, e.g.
setElement(Element) - Method in class org.biojava.bio.structure.AtomImpl
 
setElement(List<Element>) - Method in class org.biojava3.aaproperties.xml.ElementTable
 
setEmail(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Set the email for QBlast.
setEnd(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
setEnd(Point) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setEnergy(double) - Method in class org.biojava.bio.structure.secstruc.DistEn
 
setEnergy(double) - Method in class org.biojava.bio.structure.secstruc.HBond
 
setEngineered(String) - Method in class org.biojava.bio.structure.Compound
 
setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setEntityId(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
setEquivalent(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
setEvalCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setEvalue(Float) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setEValueMaximum(double) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setEValueMaximum(double) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setEvCode(String) - Method in class org.biojava.bio.structure.Site
sets the REMARK 800 EVIDENCE CODE for the site.
setEvent(Event) - Method in class org.forester.phylogeny.data.NodeData
 
setEvidence(String) - Method in class org.forester.phylogeny.data.Annotation
 
setExpectedExecutionTime(long) - Method in class org.biojava3.ws.alignment.qblast.BlastJob
 
setExpressionSystem(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemAtccNumber(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemCell(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemCellLine(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemCellularLocation(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemGene(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemOrgan(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemOrganelle(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemOtherDetails(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemPlasmid(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemStrain(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemTaxId(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemTissue(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemVariant(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemVector(String) - Method in class org.biojava.bio.structure.Compound
 
setExpressionSystemVectorType(String) - Method in class org.biojava.bio.structure.Compound
 
setExtensionPenalty(short) - Method in class org.biojava3.alignment.SimpleGapPenalty
 
setExtensionPenalty(short) - Method in interface org.biojava3.alignment.template.GapPenalty
Sets penalty given when an already open gap elongates by a single element
setFamilyId(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setFarmJob(FarmJob) - Method in class org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener
 
setFatCatOutput(boolean) - Method in class org.biojava.bio.structure.align.gui.MySaveFileListener
 
setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setFetchCurrent(boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation.
setFetchCurrent(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation.
setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
setFile1(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setFile2(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setFileFormat(String) - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
setFileLocation(String) - Static method in class org.biojava.bio.structure.io.sifts.SiftsMappingProvider
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.LocalCacheStructureProvider
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.PDBFileParser
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.PDBFileReader
 
setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
 
setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.bio.structure.io.StructureIOFile
Set the parameters that should be used for file parsing
setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.bio.structure.io.StructureProvider
Set the parameters that should be used for file parsing
setFileParsingParams(FileParsingParameters) - Method in class org.biojava.bio.structure.align.util.AtomCache
 
setFilePath(File) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
setFlexible(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setFocusAfpList(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setFocusAfpn(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setFocusRes1(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setFocusRes2(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setFocusResn(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setFoldId(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setFont(Font) - Method in class org.forester.archaeopteryx.FontChooser
 
setFormula(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setFormula(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the residue formula.
setFormula_weight(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setFormula_weight(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setFragCompat(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setFragLen(Integer) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setFragLen(int) - Method in class org.biojava.bio.structure.align.model.AFP
 
setFragLenSq(int) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setFragment(String) - Method in class org.biojava.bio.structure.Compound
 
setFragmentLength(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setFragmentMiniDistance(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.align.StructurePairAligner
 
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
setFragScore(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setFrom(Integer) - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
setFromFtp(JCheckBox) - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
setFullName(String) - Method in interface org.biojava.bio.structure.Atom
set full name of atom e.g.
setFullName(String) - Method in class org.biojava.bio.structure.AtomImpl
set full name of atom e.g.
setGamma(float) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setGapCreate(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setGapExtCol(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setGapExtCol(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setGapExtend(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setGapExtend(Short) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
setGapExtension(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setGapExtension(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setGapExtRow(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setGapExtRow(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setGapLen(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setGapOpen(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setGapOpen(Short) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
setGapOpen(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setGapOpenCol(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setGapOpenCol(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setGapOpenRow(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setGapOpenRow(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setGapPenalty(GapPenalty) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Sets the gap penalties.
setGene(String) - Method in class org.biojava.bio.structure.Compound
 
setGeneLosses(int) - Method in class org.forester.phylogeny.data.Event
 
setGeodeticDatum(String) - Method in class org.forester.phylogeny.data.Distribution
 
setGoAnnotationOutput(DomainSimilarityCalculator.GoAnnotationOutput) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
setGoIdToTermMap(Map<GoId, GoTerm>) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
setGoNamespaceLimit(GoNameSpace) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
setGoSubsets(List<GoSubset>) - Method in class org.forester.go.BasicGoTerm
 
setGroup(Group) - Method in interface org.biojava.bio.structure.Atom
Sets the back-reference to its parent Group.
setGroup(Group) - Method in class org.biojava.bio.structure.AtomImpl
 
setGroup_PDB(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setGroups(List<Group>) - Method in class org.biojava.bio.structure.Site
 
setGroups(Set<StructureGroup>) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
setGroups(Set<StructureGroup>) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
setGuessRootedness(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser
 
setH(Atom) - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
setHeader(Compound) - Method in interface org.biojava.bio.structure.Chain
Set the Header from the PDB file.
setHeader(Compound) - Method in class org.biojava.bio.structure.ChainImpl
Set the Header from the PDB file.
setHeader(Map<String, Object>) - Method in interface org.biojava.bio.structure.Structure
Deprecated. 
setHeader(Map<String, Object>) - Method in class org.biojava.bio.structure.StructureImpl
set the Header data.
setHeaderOnly(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
Parse only the PDB file header out of the files
setHeaderVars(String) - Method in class org.biojava.bio.structure.Compound
 
setHetero(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
setHetero(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setHmmAcc(String) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setHmmDesc(String) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setHmmFrom(Integer) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setHmmName(String) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setHmmTo(Integer) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setIclose(int[]) - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
setId(long) - Method in class org.biojava.bio.structure.align.model.AFP
 
setId(long) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setId(long) - Method in class org.biojava.bio.structure.AtomImpl
Set the Hibernate database ID.
setId(Long) - Method in interface org.biojava.bio.structure.Chain
Set the ID used by Hibernate.
setId(Long) - Method in class org.biojava.bio.structure.ChainImpl
Set the ID used by Hibernate.
setId(Long) - Method in class org.biojava.bio.structure.Compound
set the ID used by Hibernate
setId(Long) - Method in class org.biojava.bio.structure.DBRef
Set the ID used by Hibernate.
setId(String) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
setId(long) - Method in class org.biojava.bio.structure.HetatomImpl
the Hibernate database ID
setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
 
setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setId(Long) - Method in interface org.biojava.bio.structure.Structure
set the ID used by Hibernate
setId(Long) - Method in class org.biojava.bio.structure.StructureImpl
set the ID used by Hibernate
setId(String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
 
setId(String) - Method in class org.biojava3.ws.alignment.qblast.BlastJob
 
setIdbnsBegin(char) - Method in class org.biojava.bio.structure.DBRef
Insertion code of initial residue of the segment, if PDB is the reference.
setIdbnsEnd(char) - Method in class org.biojava.bio.structure.DBRef
Insertion code of the ending residue of the segment, if PDB is the reference.
setIdCode(String) - Method in class org.biojava.bio.structure.DBRef
Set the idCode for this entry.
setIdCode(String) - Method in class org.biojava.bio.structure.PDBHeader
The PDB code for this protein structure.
setIdentifier(Identifier) - Method in class org.forester.phylogeny.data.Taxonomy
 
setIdentifier(Identifier) - Method in class org.forester.phylogeny.Phylogeny
 
setIdentifier(int, String) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
setIdentifier(int, String) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
setIdentifier(int, String) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
setIdentifier(int, String) - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
setIdentity(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setIdxlist(List<int[]>) - Method in class org.biojava.bio.structure.align.helper.JointFragments
Stores the alignment between the residues of several fragments.
setIgnoreDufs(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setIgnoreDufs(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setIgnoreEngulfedDomains(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
To ignore domains which are completely engulfed by domains (individual ones or stretches of overlapping ones) with better support values.
setIgnoreEngulfedDomains(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
To ignore domains which are completely engulfed by domains (individual ones or stretches of overlapping ones) with better support values.
setIgnoreQuotes(boolean) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
 
setIgnoreQuotes(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser
 
setIgnoreVirusLikeIds(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setIgnoreVirusLikeIds(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setIndentPhyloxml(boolean) - Method in class org.forester.io.writers.PhylogenyWriter
 
setIndex(int) - Method in class org.biojava.bio.structure.align.helper.GapArray
 
setIndicator(byte) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the _indicator value of this PhylogenyNode to i.
setIndicatorsToZero() - Method in class org.forester.phylogeny.Phylogeny
Sets the indicators of all Nodes of this Phylogeny to 0.
setIndividualDomainScoreCutoffs(Map<String, String>) - Method in class org.forester.io.parsers.HmmPfamOutputParser
Sets the individual domain score cutoff values (for example, gathering thresholds from Pfam).
setIndividualScoreCutoffs(Map<String, Double>) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
Sets the individual score cutoff values (for example, gathering thresholds from Pfam).
setInitialized(boolean) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
setInitialK(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setInitials(String) - Method in class org.biojava.bio.structure.Author
 
setInputMatrixType(SymmetricalDistanceMatrixParser.InputMatrixType) - Method in class org.forester.phylogenyinference.SymmetricalDistanceMatrixParser
 
setInsCode(Character) - Method in class org.biojava.bio.structure.ResidueNumber
 
setInsCode(Character) - Method in class org.biojava3.protmod.structure.StructureGroup
 
setInsCode1(String) - Method in class org.biojava.bio.structure.SSBond
 
setInsCode2(String) - Method in class org.biojava.bio.structure.SSBond
 
setInsertBegin(char) - Method in class org.biojava.bio.structure.DBRef
Initial insertion code of the PDB sequence segment.
setInsertEnd(char) - Method in class org.biojava.bio.structure.DBRef
Ending insertion code of the PDB sequence segment.
setInterpolationDirection(int, LinearColorInterpolator.InterpolationDirection) - Method in class org.biojava.bio.structure.gui.util.color.LinearColorInterpolator
 
setInterpolator(ColorInterpolator) - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
setIoTime(long) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setIoTime(long) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setIsAminoAcid(boolean) - Method in class org.biojava3.protmod.structure.StructureGroup
 
setIsotopes(List<Isotope>) - Method in class org.biojava3.aaproperties.xml.Element
 
setIsPublished(Boolean) - Method in class org.biojava.bio.structure.JournalArticle
Sets the publication state of a JournalArticle - TO BE PUBLISHED == false
setJclose(int[]) - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
setJmolPanel(JmolPanel) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
setJoinFast(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setJoinPlo(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setJoinRMSCutoff(double) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setJournalArticle(JournalArticle) - Method in interface org.biojava.bio.structure.Structure
set the associated publication as defined by the JRNL records in a PDB file.
setJournalArticle(JournalArticle) - Method in class org.biojava.bio.structure.StructureImpl
set the associated publication as defined by the JRNL records in a PDB file.
setJournalName(String) - Method in class org.biojava.bio.structure.JournalArticle
 
setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics) - Method in class org.forester.surfacing.BasicCombinableDomains
 
setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics) - Method in interface org.forester.surfacing.CombinableDomains
This is to set descriptive statistics for the confidence (i.e.
setKeyDomainCount(int) - Method in class org.forester.surfacing.BasicCombinableDomains
 
setKeyDomainCount(int) - Method in interface org.forester.surfacing.CombinableDomains
Sets how many times the key domain is present in a given species genome.
setKeyDomainProteinsCount(int) - Method in class org.forester.surfacing.BasicCombinableDomains
 
setKeyDomainProteinsCount(int) - Method in interface org.forester.surfacing.CombinableDomains
Sets how many proteins with the key domain are present in a given species genome.
setLabel_alt_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setLabel_asym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setLabel_atom_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setLabel_comp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setLabel_entity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setLabel_seq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setLatitude(BigDecimal) - Method in class org.forester.phylogeny.data.Distribution
 
setLcmp(int) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setLcmp(int) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setLength(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setLength(int) - Method in class org.biojava.bio.structure.gui.util.CoordManager
 
setLength1(int) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setLength2(int) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setLineLength(int) - Method in class org.biojava3.core.sequence.io.FastaGeneWriter
 
setLineLength(int) - Method in class org.biojava3.core.sequence.io.FastaWriter
 
setLineSeparator(String) - Method in class org.biojava3.core.sequence.io.FastaWriter
Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
setLink(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the linked PhylogenyNode of this PhylogenyNode to n.
setLoadChemCompInfo(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
Sets if chemical component defintions should be loaded from the web
setLocation(SequenceLocation<S, C>) - Method in class org.biojava3.core.sequence.features.AbstractFeature
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
setLocation(SequenceLocation<S, C>) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
The new location for this feature.
setLocation(String) - Method in class org.forester.phylogeny.data.Sequence
 
setLocationInAlignment(Location) - Method in interface org.biojava3.alignment.template.MutableAlignedSequence
Sets the position of the AlignedSequence to the given Location (start, gaps, end).
setLongitude(BigDecimal) - Method in class org.forester.phylogeny.data.Distribution
 
setLongName(String) - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
setLongName(String) - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
setLongName(String) - Method in interface org.biojava3.core.sequence.template.Compound
 
setLongName(String) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
setLongName(String) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
setLookAndFeel() - Static method in class org.biojava.bio.structure.align.webstart.AligUIManager
 
setLowercaseToNull(ProteinSequence, Object[]) - Static method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator.
setLs_d_res_high(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_d_res_low(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_number_parameters(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_number_reflns_all(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_number_reflns_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_number_reflns_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_number_restraints(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_percent_reflns_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_percent_reflns_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_R_factor_all(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_R_factor_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_R_factor_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_R_factor_R_free_error(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_R_factor_R_free_error_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_R_factor_R_work(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_redundancy_reflns_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_wR_factor_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setLs_wR_factor_R_work(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setM(Matrix) - Method in class org.biojava.bio.structure.align.model.AFP
 
setMappingSequence(String) - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
 
setMass(double) - Method in class org.biojava3.aaproperties.xml.Element
 
setMass(double) - Method in class org.biojava3.aaproperties.xml.Isotope
 
setMatMatrix(double[][]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setMatMatrix(double[][]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setMatrix(Matrix) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
sets the distance matrix to be displayed
setMatrix(Matrix) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Set a submatrix.
setMatrix(short[][]) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setMax(short) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setMax(BigDecimal) - Method in class org.forester.phylogeny.data.Date
 
setMaxAllowedOverlap(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setMaxAllowedOverlap(int) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setMaxAtoms(int) - Method in class org.biojava.bio.structure.io.FileParsingParameters
the maximum numbers of atoms to load in a protein structure (prevents memory overflows)
setMaxGap(int) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setMaxGapFrag(int) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setMaxGapSize(Integer) - Method in class org.biojava.bio.structure.align.ce.CeParameters
Set the Max gap size parameter.
setMaxGapSize(int) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
CE specific parameter: set the Max gap size parameter G (during AFP extension).
setMaxIter(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setMaxIterations(int) - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
setMaxNrIterationsForOptimization(int) - Method in class org.biojava.bio.structure.align.ce.CeParameters
Set the maximum nr of times the (slow) optimiziation of alignment should iterate.
setMaxNrSuggestions(int) - Method in interface org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider
set the maximum number of suggestions to return
setMaxNrSuggestions(int) - Method in class org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
setMaxNrSuggestions(int) - Method in class org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
setMaxOptRMSD(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
set the maximum RMSD cutoff to be applied during alignment optimization.
setMaxOptRMSD(Double) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
(jCE specific): maximum RMSD that shall be calculated for the alignment.
setMaxPenalty(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setMaxrefine(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setMaxTra(Integer) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
set the maximum number of Twists that are allowed...
setMaxTra(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
Set the maximum number of Twists that are allowed...
setMethod(String) - Method in class org.biojava.bio.structure.align.xml.PdbPairsMessage
 
setMethod(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setMethod(String) - Method in class org.biojava.bio.structure.PDBHeader
 
setMethod_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
 
setMin(short) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setMin(BigDecimal) - Method in class org.forester.phylogeny.data.Date
 
setMinLen(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setMisCut(int) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setMisLen(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setMisScore(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setMod_type(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
setModDate(Date) - Method in class org.biojava.bio.structure.PDBHeader
 
setModel(int, List<Chain>) - Method in interface org.biojava.bio.structure.Structure
a convenience function if one wants to edit and replace the models in a structure.
setModel(int, List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
 
setModelNumber(int) - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
setModification(ProteinModification) - Method in interface org.biojava3.protmod.structure.ModifiedCompound
 
setModification(ProteinModification) - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
setMolecularSequence(String) - Method in class org.forester.phylogeny.data.Sequence
 
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
setMolecularWeight(Float) - Method in interface org.biojava3.core.sequence.template.Compound
 
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
setMolId(String) - Method in class org.biojava.bio.structure.Compound
Set the mol id value.
setMolName(String) - Method in class org.biojava.bio.structure.Compound
 
setMon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
setMon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setMon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setMon_nstd_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setMon_nstd_parent_comp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setMutation(String) - Method in class org.biojava.bio.structure.Compound
 
setN(Atom) - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
setName(String) - Method in interface org.biojava.bio.structure.Atom
set trimmed version of atom name, e.g.
setName(String) - Method in class org.biojava.bio.structure.AtomImpl
trimmed version of atom name, e.g.
setName(String) - Method in interface org.biojava.bio.structure.Chain
Deprecated.
replaced by Chain.setChainID(String)
setName(String) - Method in class org.biojava.bio.structure.ChainImpl
 
setName(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AuditAuthor
 
setName(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setName(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
 
setName(String) - Method in class org.biojava.bio.structure.scop.ScopDescription
 
setName(String) - Method in interface org.biojava.bio.structure.Structure
set biological name of Structure .
setName(String) - Method in class org.biojava.bio.structure.StructureImpl
set biological name of Structure.
setName(String) - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
setName(String) - Method in class org.biojava3.aaproperties.xml.Element
 
setName(String) - Method in class org.biojava3.aaproperties.xml.Isotope
 
setName(String) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setName(String) - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
 
setName(String) - Method in interface org.biojava3.alignment.template.SubstitutionMatrix
Sets the name (short description) of this matrix.
setName(String) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setName(String) - Method in class org.forester.phylogeny.data.Sequence
 
setName(String) - Method in class org.forester.phylogeny.Phylogeny
Sets the name of this Phylogeny to s.
setName(String) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the name of this node.
setName(String) - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
setName(String) - Method in class org.forester.surfacing.BasicProtein
 
setName1(String) - Method in class org.biojava.bio.structure.align.client.PdbPair
 
setName1(String) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setName2(String) - Method in class org.biojava.bio.structure.align.client.PdbPair
 
setName2(String) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setnAtom(int) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
setnAtom(int) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
setNaturalPos(Integer) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setNclose(int) - Method in class org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
 
setNcuts(int) - Method in class org.biojava.bio.structure.domain.pdp.CutSites
 
setNdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setNdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setNdom(Integer) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setNeutronsNum(int) - Method in class org.biojava3.aaproperties.xml.Isotope
 
setNmr(boolean) - Method in interface org.biojava.bio.structure.Structure
set NMR flag.
setNmr(boolean) - Method in class org.biojava.bio.structure.StructureImpl
 
setNodeCount(int) - Static method in class org.forester.phylogeny.PhylogenyNode
Sets the total number of all Nodes created so far to i (int).
setNodeId(int) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the ID of this PhylogenyNode to i (int).
setNodeIdentifier(Identifier) - Method in class org.forester.phylogeny.data.NodeData
 
setNormAlignScore(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setNotesList(ArrayList<String>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setNotObserved(Boolean) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setNrAlignments(int) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setNrCPUs(int) - Method in class org.biojava.bio.structure.align.gui.AlignmentCalc
does not do anything here...
setNrCPUs(int) - Method in class org.biojava.bio.structure.align.gui.AlignmentCalcDB
 
setNrCPUs(int) - Method in interface org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable
 
setNreported(Integer) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setNseg(int) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
setNullValue(String) - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
 
setNum(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
setNum(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
 
setNumRes(String) - Method in class org.biojava.bio.structure.Compound
 
setO(Atom) - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
setOccupancy(double) - Method in interface org.biojava.bio.structure.Atom
set occupancy.
setOccupancy(double) - Method in class org.biojava.bio.structure.AtomImpl
 
setOccupancy(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setOccupancy_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setOccupancy_max(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOccupancy_min(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOccurrenceType(ModificationOccurrenceType) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
 
setOne_letter_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setOpenPenalty(short) - Method in class org.biojava3.alignment.SimpleGapPenalty
 
setOpenPenalty(short) - Method in interface org.biojava3.alignment.template.GapPenalty
Sets penalty given when a deletion or insertion gap first opens
setOptAln(int[][][]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setOptLen(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setOptLength(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
The length of the optimal alignment.
setOptRmsd(double[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setOrgan(String) - Method in class org.biojava.bio.structure.Compound
 
setOrganelle(String) - Method in class org.biojava.bio.structure.Compound
 
setOrganismCommon(String) - Method in class org.biojava.bio.structure.Compound
 
setOrganismScientific(String) - Method in class org.biojava.bio.structure.Compound
 
setOrganismTaxId(String) - Method in class org.biojava.bio.structure.Compound
 
setOriginal(Group) - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
setOriginalHeader(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setORmsdThr(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
Set the Original RMSD threshold from which the alignment optimization is started
setOutFile(SynchronizedOutFile) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setOutFile(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setOutputDir(File) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setOutputFormat(BlastOutputFormatEnum) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the stream output format to get from the QBlast service

If HTML format is selected, also adds the following parameters (which are removed if another output format is chosen):

setOutputOption(String, String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
This method forwards to NCBIQBlastOutputProperties.setOutputOption(BlastOutputParameterEnum, String).
setOutputOption(BlastOutputParameterEnum, String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
Sets the value of specified output parameter
setOutputOption(String, String) - Method in interface org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
Method to set the value for a specific output parameter using a key to store in a map.
setOutputPDB(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
When writing the results to a file, don;t write as XML but write aligned PDB file
setOverall_FOM_free_R_set(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOverall_FOM_work_R_set(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOverall_SU_B(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOverall_SU_ML(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOverall_SU_R_Cruickshank_DPI(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setOverall_SU_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setP1(int) - Method in class org.biojava.bio.structure.align.model.AFP
 
setP2(int) - Method in class org.biojava.bio.structure.align.model.AFP
 
setPaintDefaults(Graphics2D) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
set some default rendering hints, like text antialiasing on
setPair(PdbPair) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava3.alignment.template.MutableProfilePair
Sets both Profiles of the pair.
setPair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava3.alignment.template.MutableSequencePair
Sets both AlignedSequences of the pair.
setPairs(SortedSet<PdbPair>) - Method in class org.biojava.bio.structure.align.xml.PdbPairsMessage
 
setParameter(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
setParameter(double) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.AbstractStructureAlignment
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.BioJavaStructureAlignment
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.CallableStructureAlignment
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.ce.CeMain
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.ce.CeSideChainMain
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.fatcat.FatCatFlexible
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.fatcat.FatCatRigid
 
setParameters(ConfigStrucAligParams) - Method in class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
setParameters(ConfigStrucAligParams) - Method in interface org.biojava.bio.structure.align.StructureAlignment
Set the default parameters for this algorithm to use
setParams(FarmJobParameters) - Method in class org.biojava.bio.structure.align.FarmJob
 
setParams(StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
set the parameters to be used for the algorithm
setParent(Group) - Method in interface org.biojava.bio.structure.Atom
Deprecated.
replaced by Atom.setGroup(Group)
setParent(Group) - Method in class org.biojava.bio.structure.AtomImpl
 
setParent(Structure) - Method in interface org.biojava.bio.structure.Chain
Set the back-reference to its parent Structure.
setParent(Structure) - Method in class org.biojava.bio.structure.ChainImpl
Set the back-reference to its parent Structure.
setParent(Structure) - Method in class org.biojava.bio.structure.DBRef
Set the structure object that this DBRef relates to.
setParent(Chain) - Method in interface org.biojava.bio.structure.Group
Deprecated.
setParent(Chain) - Method in class org.biojava.bio.structure.HetatomImpl
Set the back-reference (to its parent Chain)
setParent(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the _parent PhylogenyNode of this PhylogenyNode to n.
setParent(PhylogenyNode) - Method in interface org.forester.phylogeny.PhylogenyNodeI
 
setParentDNASequence(AbstractSequence, Integer, Integer) - Method in class org.biojava3.core.sequence.ProteinSequence
A Protein sequence can be stand alone or loaded from a transcript sequence.
setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava3.core.sequence.features.AbstractFeature
A feature can be the child or contained by a parent feature.
setParentFeature(FeatureInterface<S, C>) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Set the parent feature
setParentSequence(AbstractSequence<C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setParentSunid(int) - Method in class org.biojava.bio.structure.scop.ScopNode
 
setParseCAOnly(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
the flag if only the C-alpha atoms of the structure should be parsed.
setParseSecStruc(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
a flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e.
setPartner(int) - Method in class org.biojava.bio.structure.secstruc.HBond
 
setPath(IndexPair[]) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setPath(IndexPair[]) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setPath(String) - Method in class org.biojava.bio.structure.align.util.AtomCache
Set the path that is used to cache PDB files.
setPath(String) - Method in class org.biojava.bio.structure.io.LocalCacheStructureProvider
directory where to find PDB files
setPath(String) - Static method in class org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider
making sure we use the same path for the PDB installation as is used by the PdbFileReader
setPath(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
 
setPath(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
directory where to find PDB files
setPath(String) - Method in class org.biojava.bio.structure.io.SandboxStyleStructureProvider
directory where to find PDB files
setPath(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
Set path to file / connection string to db.
setPathSize(int) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setPathSize(int) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setPathToParent(boolean) - Method in class org.forester.phylogeny.PhylogenyNode
 
setPdb1(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
setPdb1(String) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setPdb2(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
setPdb2(String) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
setPdb_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setPdb_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setPdb_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setPdb_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setPdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setPdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setPdb_strand_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setPdb_strand_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setPdbAln(String[][][]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setPdbccId(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the Protein Data Bank Chemical Component ID.
setPdbccName(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the Protein Data Bank Chemical Component name.
setPDBCode(String) - Method in interface org.biojava.bio.structure.Group
Deprecated.
replaced by Group.setResidueNumber(ResidueNumber)
setPDBCode(String) - Method in class org.biojava.bio.structure.HetatomImpl
Deprecated.
replaced by HetatomImpl.setResidueNumber(ResidueNumber)
setPDBCode(String) - Method in interface org.biojava.bio.structure.server.StructureEvent
 
setPDBCode(String) - Method in class org.biojava.bio.structure.server.StructureEventImpl
 
setPDBCode(String) - Method in interface org.biojava.bio.structure.Structure
set PDB code of structure .
setPDBCode(String) - Method in class org.biojava.bio.structure.StructureImpl
set PDB code of structure .
setPdbDirectorySplit(boolean) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).
setPdbDirectorySplit(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).
setPdbDirectorySplit(boolean) - Method in interface org.biojava.bio.structure.io.StructureIOFile
The PDB files are organized hierarchically (as on the PDB - FTP server.
setPDBDirField(JTextField) - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
setPdbDirSplit(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setPdbDirSplit(boolean) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setPdbFilePath(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
mandatory argument to set the location of PDB files.
setPdbFilePath(String) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setPdbFilePath(String) - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
setPDBFlag(boolean) - Method in interface org.biojava.bio.structure.Group
flag if group has 3D data .
setPDBFlag(boolean) - Method in class org.biojava.bio.structure.HetatomImpl
flag if group has 3D data.
setPDBHeader(PDBHeader) - Method in interface org.biojava.bio.structure.Structure
the the header information for this PDB file
setPDBHeader(PDBHeader) - Method in class org.biojava.bio.structure.StructureImpl
 
setPdbId(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setPdbId(String) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setPDBInfoFile(File) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
Deprecated.
 
setPDBInstallation(PDBInstallation) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
setPDBInstallation(PDBInstallation) - Method in interface org.biojava.bio.structure.server.StructureServer
Deprecated.
 
setPDBline(String) - Method in interface org.biojava.bio.structure.Atom
Deprecated.
replaced by PDBRecord.toPDB()
setPDBline(String) - Method in class org.biojava.bio.structure.AtomImpl
Deprecated. 
setPDBName(String) - Method in class org.biojava.bio.structure.AminoAcidImpl
set three character name of AminoAcid.
setPDBName(String) - Method in interface org.biojava.bio.structure.Group
Set the PDB 3 letter name for this group.
setPDBName(String) - Method in class org.biojava.bio.structure.HetatomImpl
set three character name of Group .
setPDBName(String) - Method in class org.biojava3.protmod.structure.StructureGroup
 
setPDBResidueNumber(ResidueNumber) - Method in class org.biojava3.protmod.structure.StructureGroup
 
setPdbResName(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setPdbResNum(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setPDBresnum1(String[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
setPDBresnum2(String[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
setPDBserial(int) - Method in interface org.biojava.bio.structure.Atom
set PDB atom number.
setPDBserial(int) - Method in class org.biojava.bio.structure.AtomImpl
set PDB atom number.
setPdbSplit(JCheckBox) - Method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
setPdbx_align_begin(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setPdbx_ambiguous_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_auth_seq_align_beg(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_auth_seq_align_end(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_blank_PDB_chainid_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
setPdbx_CASP_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
setPdbx_data_cutoff_high_absF(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_data_cutoff_high_rms_absF(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_data_cutoff_low_absF(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_db_accession(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setPdbx_db_accession(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_db_align_beg_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_db_align_end_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_description(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setPdbx_descriptor(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
setPdbx_ec(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setPdbx_formal_charge(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setPdbx_formal_charge(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_fragment(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setPdbx_ideal_coordinates_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_ideal_coordinates_missing_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_initial_date(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_isotropic_thermal_model(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_keywords(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
setPdbx_ls_cross_valid_method(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_ls_sigma_F(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_ls_sigma_I(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_method_to_determine_struct(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_model_coordinates_db_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_model_coordinates_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_model_coordinates_missing_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_model_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
setPdbx_model_type_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
setPdbx_modified(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
setPdbx_modified_date(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_mutation(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setPdbx_number_of_molecules(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setPdbx_ordinal(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AuditAuthor
 
setPdbx_overall_ESU_R(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_overall_ESU_R_Free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_overall_phase_error(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_PDB_id_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_PDB_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setPdbx_PDB_model_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setPdbx_processing_site(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_R_Free_selection_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_refine_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_release_status(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_replaced_by(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_replaces(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_seq_align_beg_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_seq_align_end_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_seq_one_letter_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
 
setPdbx_solvent_ion_probe_radii(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_solvent_shrinkage_radii(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_solvent_vdw_probe_radii(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_starting_model(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_stereochem_target_val_spec_case(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_stereochemistry_target_values(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setPdbx_strand_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setPdbx_subcomponent_list(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_synonyms(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdbx_type(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPdpprovider(PDPProvider) - Method in class org.biojava.bio.structure.align.util.AtomCache
 
setPercId(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
setPermutationSize(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setPmid(String) - Method in class org.biojava.bio.structure.JournalArticle
Set the value of pmid
setPolymerType(PolymerType) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setPos(int, int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
setPos1(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setPos1(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
setPos2(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setPos2(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
setPosition(int) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
setPreferredSize() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
setPrintCE(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
Display the output string in CE style
setPrintConnections(boolean) - Method in class org.biojava.bio.structure.io.FileConvert
enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.
setPrintFatCat(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setPrintXML(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setProbability(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setProfile(Profile<S, C>) - Method in class org.biojava3.alignment.GuideTree.Node
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava3.alignment.NeedlemanWunsch
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava3.alignment.SimpleProfileProfileAligner
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava3.alignment.SmithWaterman
 
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
 
setProfile(Profile<S, C>) - Method in interface org.biojava3.alignment.template.GuideTreeNode
Stores the given profile.
setProfileFuture(Future<ProfilePair<S, C>>) - Method in class org.biojava3.alignment.GuideTree.Node
 
setProfileFuture(Future<ProfilePair<S, C>>) - Method in interface org.biojava3.alignment.template.GuideTreeNode
Stores the given profile future.
setProgram(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
setProgram_version(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
setProperties(Map<String, Object>) - Method in interface org.biojava.bio.structure.Group
properties of this amino acid.
setProperties(Map<String, Object>) - Method in class org.biojava.bio.structure.HetatomImpl
properties of this amino acid.
setProperties(LinkedHashMap<String, String>) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
 
setProperties(PropertiesMap) - Method in class org.forester.phylogeny.data.Annotation
 
setProperties(PropertiesMap) - Method in class org.forester.phylogeny.data.NodeData
 
setProperty(String, Object) - Method in interface org.biojava.bio.structure.Group
set a single property .
setProperty(String, Object) - Method in class org.biojava.bio.structure.HetatomImpl
set a single property .
setProxySequenceReader(SequenceReader<C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Very important method that allows external mappings of sequence data and features.
setPsimodId(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the PSI-MOD ID.
setPsimodName(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the PSI-MOD name.
setPublicationDate(int) - Method in class org.biojava.bio.structure.JournalArticle
 
setPublished(boolean) - Method in class org.biojava.bio.structure.JournalArticle
 
setPublisher(String) - Method in class org.biojava.bio.structure.JournalArticle
 
setPvalue(Double) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setPx(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setQualities(List<Number>) - Method in class org.biojava3.core.sequence.features.QualityFeature
 
setQuantities(List<Number>) - Method in class org.biojava3.core.sequence.features.QuantityFeature
 
setQuery(S) - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
Sets the query Sequence.
setQuery(Profile<S, C>) - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
Sets the query Profile.
setQuery(Profile<S, C>) - Method in interface org.biojava3.alignment.template.MutableProfilePair
Sets the first Profile of the pair.
setQuery(AlignedSequence<S, C>) - Method in interface org.biojava3.alignment.template.MutableSequencePair
Sets the first AlignedSequence of the pair.
setRandomize(boolean) - Method in class org.forester.phylogenyinference.FitchParsimony
 
setRandomize(boolean) - Method in class org.forester.phylogenyinference.SankoffParsimony
 
setRandomNumberSeed(long) - Method in class org.forester.phylogenyinference.FitchParsimony
 
setRandomNumberSeed(long) - Method in class org.forester.phylogenyinference.SankoffParsimony
 
setRanges(List<String>) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setRank(String) - Method in class org.forester.phylogeny.data.Taxonomy
 
setRecordAdditionalAttachments(boolean) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
setRecordType(String) - Method in interface org.biojava.bio.structure.AminoAcid
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
setRecordType(String) - Method in class org.biojava.bio.structure.AminoAcidImpl
 
setRecordUnidentifiableCompounds(boolean) - Method in class org.biojava3.protmod.structure.ProteinModificationIdentifier
 
setReduceInitialFragments(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setRef(String) - Method in class org.biojava.bio.structure.JournalArticle
Set the value of the ref.
setRef(String) - Method in class org.forester.phylogeny.data.Annotation
 
setRef_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setRefChainId(String) - Method in class org.biojava.bio.structure.Compound
Returns the ref chain id value.
setReference(Reference) - Method in class org.forester.phylogeny.data.NodeData
 
setRefn(String) - Method in class org.biojava.bio.structure.JournalArticle
Set the value of the refn
setRenderingFactorWidth(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
setRenderingHeight(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
setRenderingHeight(double) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
 
setReplaces(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
setReplaceUnderscores(boolean) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
 
setReplaceUnderscores(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser
 
setRerootable(boolean) - Method in class org.forester.phylogeny.Phylogeny
 
setResidId(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the RESID ID.
setResidName(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the RESID name.
setResidueAt(int, char) - Method in class org.forester.development.AminoAcidSequence
 
setResidueName(String) - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
Including insertion code
setResidueNumber(String) - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
setResidueNumber(ResidueNumber) - Method in interface org.biojava.bio.structure.Group
sets the ResidueNumber for this Group
setResidueNumber(String, Integer, Character) - Method in interface org.biojava.bio.structure.Group
Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.
setResidueNumber(ResidueNumber) - Method in class org.biojava.bio.structure.HetatomImpl
 
setResidueNumber(String, Integer, Character) - Method in class org.biojava.bio.structure.HetatomImpl
 
setResidueNumber(int) - Method in class org.biojava3.protmod.structure.StructureGroup
 
setResidues(List<SiftsResidue>) - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
setResidueType(ResidueType) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setResNames(String) - Method in class org.biojava.bio.structure.Compound
 
setResnum1(String) - Method in class org.biojava.bio.structure.SSBond
 
setResnum2(String) - Method in class org.biojava.bio.structure.SSBond
 
setResolution(float) - Method in class org.biojava.bio.structure.PDBHeader
 
setResScore(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setReturnGainLossMatrix(boolean) - Method in class org.forester.phylogenyinference.DolloParsimony
 
setReturnGainLossMatrix(boolean) - Method in class org.forester.phylogenyinference.FitchParsimony
 
setReturnGainLossMatrix(boolean) - Method in class org.forester.phylogenyinference.SankoffParsimony
 
setReturnInternalStates(boolean) - Method in class org.forester.phylogenyinference.DolloParsimony
 
setReturnInternalStates(boolean) - Method in class org.forester.phylogenyinference.FitchParsimony
 
setReturnInternalStates(boolean) - Method in class org.forester.phylogenyinference.SankoffParsimony
 
setReturnType(HmmPfamOutputParser.ReturnType) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setReturnType(HmmscanPerDomainTableParser.ReturnType) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
 
setRms(double) - Method in class org.biojava.bio.structure.align.helper.JointFragments
 
setRms(double) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
the rms in the structurally equivalent regions
setRms(double) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setRmsd(double) - Method in class org.biojava.bio.structure.align.model.AFP
 
setRmsdCut(Double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
The cutoff to be used during AFP detection
setRmsdThr(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setRmsdThrJoin(Double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setRoot(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
 
setRooted(boolean) - Method in class org.forester.phylogeny.Phylogeny
Sets whether this Phylogeny is rooted or not.
setRot(Matrix) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setRow(short) - Method in class org.biojava.bio.structure.align.helper.IndexPair
 
setRow(String, int) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
setRows(List<AminoAcidCompound>) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setRunBackground(boolean) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setSaturation(float) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
Deprecated.
setSaturation(float) - Method in class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
 
setSaveOutputDir(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setScale(float) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
setScale(float) - Method in class org.biojava.bio.structure.gui.util.CoordManager
 
setScale(float) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
setScale(int) - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
setScale(int) - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
 
setScalevalue(float) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
Deprecated.
setScalevalue(double) - Method in class org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper
 
setScientificName(String) - Method in class org.forester.phylogeny.data.Taxonomy
 
setScientificName(PhylogenyNode, String) - Static method in class org.forester.phylogeny.PhylogenyMethods
 
setScopDatabase(ScopDatabase) - Static method in class org.biojava.bio.structure.scop.ScopFactory
 
setScopDescription(List<ScopDescription>) - Method in class org.biojava.bio.structure.scop.server.ScopDescriptions
 
setScopDomain(List<ScopDomain>) - Method in class org.biojava.bio.structure.scop.server.ScopDomains
 
setScopDownloadURL(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
setScopId(String) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setScopNode(List<ScopNode>) - Method in class org.biojava.bio.structure.scop.server.ScopNodes
 
setScopVersion(String) - Method in class org.biojava.bio.structure.scop.ScopInstallation
 
setScore(double) - Method in class org.biojava.bio.structure.align.model.AFP
 
setScore(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
 
setScore(float) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
 
setScore(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
setScore(double) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
setScore(double) - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
setScore(Float) - Method in class org.biojava3.ws.hmmer.HmmerResult
 
setScorePoint(int, int, short, short, short, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScorePoint(int, int, short, short, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, short, short, short[], boolean, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, int[], short, short, short[], boolean, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, int, int, int, short, short, short[], boolean, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, short, short[], boolean, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, int[], short, short[], boolean, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, int, int, int, short, short[], boolean, short[][][]) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, short, short, short[], boolean, short[][][], int[], int) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, int, int, int, short, short, short[], boolean, short[][][], int[], int) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, short, short[], boolean, short[][][], int[], int) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoreVector(int, int, int, int, short, short[], boolean, short[][][], int[], int) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setScoringStrategy(Integer) - Method in class org.biojava.bio.structure.align.ce.CeParameters
Set the scoring strategy to use.
setSecretion(String) - Method in class org.biojava.bio.structure.Compound
 
setSecStruc(Map<String, String>) - Method in interface org.biojava.bio.structure.AminoAcid
Specifies the secondary structure as a Map.
setSecStruc(Map<String, String>) - Method in class org.biojava.bio.structure.AminoAcidImpl
set the secondary structure data for this amino acid.
setSeedFragmentLength(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setSeedRmsdCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setSegId(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
setSegments(List<Segment>) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
setSegments(List<SiftsSegment>) - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
setSelectedAlignmentPos(int) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
 
setSelectedAlignmentPos(int) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
setSelection(Selection) - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
setSelection(List<AtomInfo>) - Method in interface org.biojava3.structure.gui.Selection
 
setSelection(List<AtomInfo>) - Method in class org.biojava3.structure.gui.SelectionImpl
 
setSelection(Selection) - Method in interface org.biojava3.structure.gui.StructureViewer
 
setSeparatorSequence(String) - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
 
setSeq_align_beg(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setSeq_align_end(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
setSeq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
 
setSeq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
 
setSeqBegin(int) - Method in class org.biojava.bio.structure.DBRef
Initial sequence number of the PDB sequence segment.
setSeqEnd(int) - Method in class org.biojava.bio.structure.DBRef
Ending sequence number of the PDB sequence segment.
setSeqNum(Integer) - Method in class org.biojava.bio.structure.ResidueNumber
 
setSeqResGroups(List<Group>) - Method in interface org.biojava.bio.structure.Chain
Set the list of SeqResGroups for this chain.
setSeqResGroups(List<Group>) - Method in class org.biojava.bio.structure.ChainImpl
Set the list of SeqResGroups for this chain.
setSeqResName(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
setSequence(Sequence) - Method in class org.forester.phylogeny.data.NodeData
 
setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
 
setSequences(List<AlignedSequence<S, C>>) - Method in interface org.biojava3.alignment.template.MutableProfile
Sets entirely new set of AlignedSequences.
setSequenceScore(Double) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setSequenceUsage(SequenceOptimizationHints.SequenceUsage) - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
 
setSequentialAlignment(boolean) - Method in class org.biojava.bio.structure.align.model.AFPChain
Set whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.
setSeqWeight(double) - Method in class org.biojava.bio.structure.align.ce.CeParameters
Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
setSerNum(int) - Method in class org.biojava.bio.structure.SSBond
get serial number of this SSBOND in PDB file
setServer(String) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setServer(String) - Method in class org.biojava.bio.structure.domain.RemotePDPProvider
 
setServer(String) - Method in class org.biojava.bio.structure.scop.RemoteScopInstallation
 
setShortAlign(boolean) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setShortDescription(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature
 
setShortDescription(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Set the short description that can be used to describe the feature
setShortName(String) - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
setShortName(String) - Method in class org.biojava3.core.sequence.compound.CodonCompound
 
setShortName(String) - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
setShortName(String) - Method in interface org.biojava3.core.sequence.template.Compound
 
setShortName(String) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
setShortName(String) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
setShow3d(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setShowAFPRanges(boolean) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setShowAFPRanges(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setShowDBresult(String) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setShowMenu(boolean) - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
setSimCount(Integer) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setSimilarity(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setSiteID(String) - Method in class org.biojava.bio.structure.Site
 
setSites(List<Site>) - Method in interface org.biojava.bio.structure.Structure
 
setSites(List<Site>) - Method in class org.biojava.bio.structure.StructureImpl
 
setSize(int) - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
setSolvent_model_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setSolvent_model_param_bsol(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setSolvent_model_param_ksol(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
 
setSource(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature
Set the feature source
setSource(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Change the source of the FeatureInterface.
setSource(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
Added support for the source of this sequence for GFF3 export
setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
 
setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusCharactersParser
 
setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
 
setSource(Object) - Method in class org.forester.io.parsers.nexus.PaupLogParser
 
setSource(Object) - Method in class org.forester.io.parsers.nhx.NHXParser
This sets the source to be parsed.
setSource(Object) - Method in interface org.forester.io.parsers.PhylogenyParser
 
setSource(Object) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
setSource(Object) - Method in class org.forester.io.parsers.tol.TolParser
 
setSource(String) - Method in class org.forester.phylogeny.data.Annotation
 
setSpaceGroup(String) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setSparse(int) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setSpeciations(int) - Method in class org.forester.phylogeny.data.Event
 
setSpeciesId(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setSpeciesOrder(List<Species>) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
setSplit(boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
Is the organization of files within the directory split, as on the PDB FTP servers, or are all files contained in one directory.
setSplit(boolean) - Method in class org.biojava.bio.structure.align.util.UserConfiguration
 
setSqFrom(Integer) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setSqTo(Integer) - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
setSrc_method(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setSSBonds(List<SSBond>) - Method in interface org.biojava.bio.structure.Structure
set the list of SSBonds for this structure
setSSBonds(List<SSBond>) - Method in class org.biojava.bio.structure.StructureImpl
set the list of SSBonds for this structure
setStandard(boolean) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setStart(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
setStart(Point) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setStartPage(String) - Method in class org.biojava.bio.structure.JournalArticle
 
setStartTimestamp(long) - Method in class org.biojava3.ws.alignment.qblast.BlastJob
 
setState(int, int, S) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
setState(String, int, S) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
setState(String, String, S) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
setState(int, int, S) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
setState(String, int, S) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
setState(String, String, S) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
setStateAt(int, byte) - Method in class org.forester.development.AminoAcidSequence
 
setStatus(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
setSteps(int[], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava3.alignment.routines.AlignerHelper
Sets the alignment path following the list of anchors.
setSteps(AlignerHelper.Last[][][], boolean, int[], AlignerHelper.Last, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setSteps(AlignerHelper.Last[][][], short[][][], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setSteps(AlignerHelper.Last[][][], int[], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava3.alignment.routines.AlignerHelper
 
setStepSize(int) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setStoreEmptySeqRes(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
 
setStoringScoreMatrix(boolean) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.
setStrain(String) - Method in class org.biojava.bio.structure.Compound
 
setStrand(Strand) - Method in class org.biojava3.core.sequence.GeneSequence
 
setStrand(Strand) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setStrictSCOP(boolean) - Method in class org.biojava.bio.structure.align.util.AtomCache
When strictSCOP is enabled, SCOP domain identifiers (eg 'd1gbga_') are matched literally to the SCOP database.
setStringSequence(String) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
 
setStruct(Struct) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
 
setStruct(Struct) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
 
setStruct(Struct) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
setStructure(Structure) - Method in class org.biojava.bio.structure.align.gui.jmol.JmolPanel
 
setStructure(Structure) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
setStructure(Structure) - Method in class org.biojava.bio.structure.gui.BiojavaJmol
 
setStructure(Structure) - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
setStructure(Structure) - Method in interface org.biojava3.structure.gui.StructureViewer
 
setStructure1(Structure) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
setStructure1(Structure) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
setStructure2(Structure) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
setStructure2(Structure) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
setStructureAlignmentJmol(StructureAlignmentJmol) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
 
setStyle(RenderStyle) - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
setStyle(RenderStyle) - Method in interface org.biojava3.structure.gui.StructureViewer
Apply this style to the current selection
setSubLocations(List<Location>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.bio.structure.align.ce.CeParameters
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
setSubstitutionMatrix(SubstitutionMatrix<C>) - Method in class org.biojava3.alignment.template.AbstractMatrixAligner
Sets the substitution matrix.
setSumExtNodes(int) - Method in class org.forester.phylogeny.PhylogenyNode
Sets the total number of external Nodes originating from this PhylogenyNode to i (int).
setSumOfFailures(int) - Method in class org.forester.surfacing.MappingResults
 
setSumOfSuccesses(int) - Method in class org.forester.surfacing.MappingResults
 
setSunID(int) - Method in class org.biojava.bio.structure.scop.ScopDescription
 
setSunid(Integer) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setSunid(int) - Method in class org.biojava.bio.structure.scop.ScopNode
 
setSuperfamilyId(int) - Method in class org.biojava.bio.structure.scop.ScopDomain
 
setSurname(String) - Method in class org.biojava.bio.structure.Author
 
setSwissprotId(String) - Method in interface org.biojava.bio.structure.Chain
Set the Swissprot id of this chain.
setSwissprotId(String) - Method in class org.biojava.bio.structure.ChainImpl
set the Swissprot id of this chains .
setSymbol(String) - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
setSymbol(String) - Method in class org.biojava3.aaproperties.xml.Element
 
setSymbol(String) - Method in class org.forester.phylogeny.data.Sequence
 
setSynonyms(List<String>) - Method in class org.biojava.bio.structure.Compound
 
setSynthetic(String) - Method in class org.biojava.bio.structure.Compound
 
setSystematicName(String) - Method in class org.biojava3.protmod.ProteinModificationImpl.Builder
Set the systematic name.
setT(double[]) - Method in class org.biojava.bio.structure.align.model.AFP
 
setTabPane(JTabbedPane) - Method in class org.biojava.bio.structure.align.gui.DBSearchGUI
 
setTarget(S) - Method in class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner
Sets the target Sequence.
setTarget(Profile<S, C>) - Method in class org.biojava3.alignment.template.AbstractProfileProfileAligner
Sets the target Profile.
setTarget(Profile<S, C>) - Method in interface org.biojava3.alignment.template.MutableProfilePair
Sets the second Profile of the pair.
setTarget(AlignedSequence<S, C>) - Method in interface org.biojava3.alignment.template.MutableSequencePair
Sets the second AlignedSequence of the pair.
setTaxonomy(TaxonomyID) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setTaxonomy(Taxonomy) - Method in class org.forester.phylogeny.data.NodeData
 
setTaxonomyCode(String) - Method in class org.forester.phylogeny.data.Taxonomy
 
setTaxonomyCode(PhylogenyNode, String) - Static method in class org.forester.phylogeny.PhylogenyMethods
Convenience method to set the taxonomy code of a phylogeny node.
setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION) - Method in class org.forester.io.parsers.nhx.NHXParser
 
setTechnique(String) - Method in class org.biojava.bio.structure.PDBHeader
 
setTempFactor(double) - Method in interface org.biojava.bio.structure.Atom
get set temp factor .
setTempFactor(double) - Method in class org.biojava.bio.structure.AtomImpl
 
setText(String) - Method in class org.biojava.bio.structure.align.gui.AlignmentTextPanel
 
setText(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
 
setText(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
setTextField(JTextField) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
setThreadPool(ThreadPoolExecutor) - Static method in class org.biojava3.core.util.ConcurrencyTools
Sets thread pool to any given ThreadPoolExecutor to allow use of an alternative execution style.
setThreadPoolCPUsAvailable(int) - Static method in class org.biojava3.core.util.ConcurrencyTools
Sets thread pool to reserve a given number of processor cores for foreground or other use.
setThreadPoolCPUsFraction(float) - Static method in class org.biojava3.core.util.ConcurrencyTools
Sets thread pool to a given fraction of the available processors.
setThreadPoolDefault() - Static method in class org.biojava3.core.util.ConcurrencyTools
Sets thread pool to default of 1 background thread for each processor core.
setThreadPoolSingle() - Static method in class org.biojava3.core.util.ConcurrencyTools
Sets thread pool to a single background thread.
setThreadPoolSize(int) - Static method in class org.biojava3.core.util.ConcurrencyTools
Sets thread pool to given size.
setThreads(int) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setThree_letter_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setTime(int) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setTissue(String) - Method in class org.biojava.bio.structure.Compound
 
setTitle(String) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
setTitle(String) - Method in class org.biojava.bio.structure.Compound
 
setTitle(String) - Method in class org.biojava.bio.structure.gui.BiojavaJmol
 
setTitle(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
setTitle(String) - Method in class org.biojava.bio.structure.JournalArticle
Set the value of title
setTitle(String) - Method in class org.biojava.bio.structure.PDBHeader
 
setTitle(String) - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
setTMScore(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setTo(Integer) - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
setTool(String) - Method in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Set the tool identifier for QBlast.
setTorsionPenalty(double) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
setTotalLength(int) - Method in class org.forester.phylogeny.data.DomainArchitecture
 
setTotalLenIni(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setTotalLenOpt(int) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setTotalRmsdIni(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
this is the init-RMSD, not the final RMSD after refinement.
setTotalRmsdOpt(double) - Method in class org.biojava.bio.structure.align.model.AFPChain
The RMSD of the final alignment.
setTraceFlag(boolean) - Method in class org.biojava.bio.structure.secstruc.BigSqrt
 
setTrans(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setTree(Phylogeny) - Method in class org.forester.sdi.DistanceCalculator
Sets the rooted Phylogeny t for which the mean distance to the root and its variance and standard deviation are calculated.
setTreeAndExtNodes(Phylogeny, ArrayList<PhylogenyNode>) - Method in class org.forester.sdi.DistanceCalculator
Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated.
setTreeAndExtNodes(Phylogeny, Vector<PhylogenyNode>) - Method in class org.forester.sdi.DistanceCalculator
Sets the rooted Phylogeny t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated.
setTryAllCPs(Boolean) - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
setTwi(int[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setTwistedGroups(Group[]) - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
 
setType(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
setType(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
setType(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
setType(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
setType(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature
Set the feature type
setType(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
Change the type of this feature.
setType(String) - Method in class org.forester.phylogeny.data.Annotation
 
setType(String) - Method in class org.forester.phylogeny.data.BinaryCharacters
 
setType(String) - Method in class org.forester.phylogeny.data.Confidence
 
setType(String) - Method in class org.forester.phylogeny.data.Sequence
 
setType(String) - Method in class org.forester.phylogeny.Phylogeny
 
setType_symbol(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
 
setUncertain(boolean) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
setUniProtAccessionId(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setUniprotbaseURL(String) - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
setUniprotDirectoryCache(String) - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
setUniProtPos(Integer) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setUniProtResName(String) - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
setUnit(String) - Method in class org.forester.phylogeny.data.Date
 
setUnitv(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setUnknown(boolean) - Method in class org.biojava3.core.sequence.location.SimplePoint
 
setUpdateRemediatedFiles(boolean) - Method in class org.biojava.bio.structure.io.FileParsingParameters
A flag if local files should be replaced with the latest version of remediated PDB files.
setUri(Uri) - Method in class org.forester.phylogeny.data.Annotation
 
setUri(Uri) - Method in class org.forester.phylogeny.data.Sequence
 
setUri(Uri) - Method in class org.forester.phylogeny.data.Taxonomy
 
setUsed(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
setUsedAtomNames(String[]) - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
setUseLast(boolean) - Method in class org.forester.phylogenyinference.FitchParsimony
This sets whether to use the first or last state in the sorted states at the undecided internal nodes.
setUseLast(boolean) - Method in class org.forester.phylogenyinference.SankoffParsimony
This sets whether to use the first or last state in the sorted states at the undecided internal nodes.
setUserCollection(Collection<Object>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
setUsername(String) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setUserObject(Object) - Method in class org.biojava3.core.sequence.features.AbstractFeature
Allow the user to associate an object with the feature.
setUserObject(Object) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
 
setValidateAgainstSchema(String) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
setValidateAgainstSchema(String) - Method in class org.forester.io.parsers.tol.TolParser
 
setValue(int) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
 
setValue(int) - Method in class org.biojava.bio.structure.align.helper.GapArray
 
setValue(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement
[Careful, this does not call "new String(...)"]
setValue(Color) - Method in class org.forester.phylogeny.data.BranchColor
 
setValue(double) - Method in class org.forester.phylogeny.data.Confidence
 
setValue(BigDecimal) - Method in class org.forester.phylogeny.data.Date
 
setValue(String) - Method in class org.forester.phylogeny.data.Reference
 
setValue(int, int, double) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
setValue(int, int, double) - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
setValue(int, int, E) - Method in class org.forester.util.BasicTable
 
setValue(IDENTIFIER_TYPE, IDENTIFIER_TYPE, VALUE_TYPE) - Method in class org.forester.util.GeneralTable
 
setVariant(String) - Method in class org.biojava.bio.structure.Compound
 
setVerbose(boolean) - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
setVerbose(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
 
setVerbose(boolean) - Method in class org.forester.phylogenyinference.NeighborJoining
 
setVersion(String) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
setVolume(String) - Method in class org.biojava.bio.structure.JournalArticle
 
setWaitCursor() - Method in class org.forester.archaeopteryx.MainPanel
 
setWaitForAlignments(boolean) - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
 
setWinSize(Integer) - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
setX(double) - Method in interface org.biojava.bio.structure.Atom
Set the X coordinate.
setX(double) - Method in class org.biojava.bio.structure.AtomImpl
 
setXcoord(float) - Method in class org.forester.phylogeny.PhylogenyNode
Used for drawing of Trees.
setXSecondary(float) - Method in class org.forester.phylogeny.PhylogenyNode
 
setY(double) - Method in interface org.biojava.bio.structure.Atom
Set the Y coordinate.
setY(double) - Method in class org.biojava.bio.structure.AtomImpl
 
setYcoord(float) - Method in class org.forester.phylogeny.PhylogenyNode
Used for drawing of Trees.
setYSecondary(float) - Method in class org.forester.phylogeny.PhylogenyNode
 
setZ(double) - Method in interface org.biojava.bio.structure.Atom
Set the Z coordinate.
setZ(double) - Method in class org.biojava.bio.structure.AtomImpl
 
setZ(int) - Method in class org.biojava.bio.structure.PDBCrystallographicInfo
 
setZippedInputstream(boolean) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
setZippedInputstream(boolean) - Method in class org.forester.io.parsers.tol.TolParser
 
setZoom(int) - Method in class org.biojava3.structure.gui.JmolViewerImpl
 
setZoom(int) - Method in interface org.biojava3.structure.gui.StructureViewer
Set the Zoom level
shift(Structure, Atom) - Static method in class org.biojava.bio.structure.Calc
shift a structure with a vector.
shift(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
Shift a vector.
shift(Group, Atom) - Static method in class org.biojava.bio.structure.Calc
Shift a Group with a vector.
shiftAtAlignmentLocation(Location, int) - Method in interface org.biojava3.alignment.template.MutableAlignedSequence
Slides a part of the AlignedSequence.
shiftAtSequenceLocation(Location, int) - Method in interface org.biojava3.alignment.template.MutableAlignedSequence
Slides a part of the AlignedSequence.
shiftCA2(AFPChain, Atom[], Matrix, Atom, Group[]) - Static method in class org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
only shift CA positions.
shin - Class in org.forester.application
 
shin() - Constructor for class org.forester.application.shin
 
Shin - Class in org.forester.sdi
 
Shin() - Constructor for class org.forester.sdi.Shin
 
ShortSegmentRemover - Class in org.biojava.bio.structure.domain.pdp
 
ShortSegmentRemover() - Constructor for class org.biojava.bio.structure.domain.pdp.ShortSegmentRemover
 
show(BufferedReader, UserConfiguration) - Method in class org.biojava.bio.structure.align.gui.DBResultTable
 
show(File, UserConfiguration) - Method in class org.biojava.bio.structure.align.gui.DBResultTable
 
show(URL, UserConfiguration) - Method in class org.biojava.bio.structure.align.gui.DBResultTable
 
showAboutDialog() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
show some info about this gui
showAFPRanges - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
showAlignmentGUI() - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.bio.structure.align.ce.GuiWrapper
 
showAlignmentImage(AFPChain, Atom[], Atom[], StructureAlignmentJmol) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
 
showAlignmentImage(AFPChain, String) - Static method in class org.biojava.bio.structure.align.gui.DisplayAFP
 
showAlternative(int) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
 
showCompound() - Method in class org.biojava.bio.structure.Compound
 
showConsole(boolean) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
showDialog() - Method in class org.biojava.bio.structure.align.gui.AboutDialog
 
showDialog() - Static method in class org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
 
showDialog() - Method in class org.biojava.bio.structure.align.gui.HelpDialog
 
showDialog() - Method in class org.biojava.bio.structure.align.gui.SystemInfo
 
showDialog(Component, String) - Method in class org.forester.archaeopteryx.FontChooser
 
showDistanceMatrix(int) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
 
showDocument(URL) - Static method in class org.biojava.bio.structure.align.webstart.BrowserOpener
open a URL in the browser that was used to launch SPICE
showDocument(String) - Static method in class org.biojava.bio.structure.align.webstart.BrowserOpener
open a URL in the browser that was used to launch SPICE
showDocument(URL) - Static method in class org.biojava.bio.structure.align.webstart.JNLPProxy
 
showHeader() - Method in class org.biojava.bio.structure.Compound
Print some debug statements to System.out
ShowPDBIDListener - Class in org.biojava.bio.structure.align.gui
 
ShowPDBIDListener() - Constructor for class org.biojava.bio.structure.align.gui.ShowPDBIDListener
 
showSource() - Method in class org.biojava.bio.structure.Compound
 
showSuggest() - Method in class org.biojava.bio.structure.align.gui.autosuggest.JAutoSuggest
Force the suggestions to be displayed (Useful for buttons e.g.
showSystemInfo() - Static method in class org.biojava.bio.structure.align.gui.MenuCreator
 
showUrl(String) - Method in class org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
 
shuffle(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.
shutdown() - Static method in class org.biojava3.core.util.ConcurrencyTools
Disables new tasks from being submitted and closes the thread pool cleanly.
shutdownAndAwaitTermination() - Static method in class org.biojava3.core.util.ConcurrencyTools
Closes the thread pool.
SIDE_CHAIN_ANGLE_SCORING - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
SIDE_CHAIN_SCORING - Static variable in class org.biojava.bio.structure.align.ce.CeParameters
 
sideChainScoringType - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
SiftsEntity - Class in org.biojava.bio.structure.io.sifts
 
SiftsEntity() - Constructor for class org.biojava.bio.structure.io.sifts.SiftsEntity
 
SiftsEntity(String, String) - Constructor for class org.biojava.bio.structure.io.sifts.SiftsEntity
 
SiftsMappingProvider - Class in org.biojava.bio.structure.io.sifts
 
SiftsMappingProvider() - Constructor for class org.biojava.bio.structure.io.sifts.SiftsMappingProvider
 
SiftsResidue - Class in org.biojava.bio.structure.io.sifts
 
SiftsResidue() - Constructor for class org.biojava.bio.structure.io.sifts.SiftsResidue
 
SiftsSegment - Class in org.biojava.bio.structure.io.sifts
 
SiftsSegment() - Constructor for class org.biojava.bio.structure.io.sifts.SiftsSegment
 
SiftsSegment(String, String, String) - Constructor for class org.biojava.bio.structure.io.sifts.SiftsSegment
 
SiftsXMLParser - Class in org.biojava.bio.structure.io.sifts
 
SiftsXMLParser() - Constructor for class org.biojava.bio.structure.io.sifts.SiftsXMLParser
 
SigEva - Class in org.biojava.bio.structure.align.fatcat.calc
 
SigEva() - Constructor for class org.biojava.bio.structure.align.fatcat.calc.SigEva
 
SIMILARITY_COLOR - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements a data structure for a Sequence within an alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>) - Constructor for class org.biojava3.alignment.SimpleAlignedSequence
Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava3.alignment.SimpleAlignedSequence
Creates an AlignedSequence for the given Sequence in a local alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>) - Constructor for class org.biojava3.alignment.SimpleAlignedSequence
Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava3.alignment.SimpleAlignedSequence
Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
SimpleDomain - Class in org.forester.surfacing
 
SimpleDomain(String) - Constructor for class org.forester.surfacing.SimpleDomain
 
SimpleGapPenalty - Class in org.biojava3.alignment
Implements a data structure for the gap penalties used during a sequence alignment routine.
SimpleGapPenalty() - Constructor for class org.biojava3.alignment.SimpleGapPenalty
Creates a new set of gap penalties using the defaults.
SimpleGapPenalty(short, short) - Constructor for class org.biojava3.alignment.SimpleGapPenalty
Creates a new set of gap penalties.
SimpleLocation - Class in org.biojava3.core.sequence.location
Very basic implementation of the Location interface which defines a series of simple constructors.
SimpleLocation(int, int) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(int, int, Strand) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, AccessionID) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, AccessionID) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, boolean) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(int, int, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
 
SimpleMMcifConsumer - Class in org.biojava.bio.structure.io.mmcif
A MMcifConsumer implementation that build a in-memory representation of the content of a mmcif file as a BioJava Structure object.
SimpleMMcifConsumer() - Constructor for class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
 
SimpleMMcifParser - Class in org.biojava.bio.structure.io.mmcif
A simple mmCif file parser
SimpleMMcifParser() - Constructor for class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
SimpleMutableMsa - Class in org.forester.development
 
SimpleMutableMsa(String[], String[]) - Constructor for class org.forester.development.SimpleMutableMsa
 
SimplePoint - Class in org.biojava3.core.sequence.location
Basic implementation of the Point interface.
SimplePoint() - Constructor for class org.biojava3.core.sequence.location.SimplePoint
 
SimplePoint(int) - Constructor for class org.biojava3.core.sequence.location.SimplePoint
 
SimplePoint(int, boolean, boolean) - Constructor for class org.biojava3.core.sequence.location.SimplePoint
 
SimpleProfile<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements a data structure for the results of sequence alignment.
SimpleProfile(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava3.alignment.SimpleProfile
Creates a pair profile for the given already aligned sequences.
SimpleProfile(S) - Constructor for class org.biojava3.alignment.SimpleProfile
Creates a profile from a single sequence.
SimpleProfile(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava3.alignment.SimpleProfile
Creates a pair profile for the given sequences.
SimpleProfile(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava3.alignment.SimpleProfile
Creates a pair profile for the given profiles.
SimpleProfilePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements a data structure for the results of the alignment of a pair of Profiles.
SimpleProfilePair(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava3.alignment.SimpleProfilePair
Creates a pair profile for the given profiles.
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements a simple (naive) Aligner for a pair of Profiles.
SimpleProfileProfileAligner() - Constructor for class org.biojava3.alignment.SimpleProfileProfileAligner
Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
SimpleProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment.
SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.SimpleProfileProfileAligner
Prepares for a profile-profile alignment run concurrently.
SimpleSequencePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Implements a data structure for the results of pairwise sequence alignment.
SimpleSequencePair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava3.alignment.SimpleSequencePair
Creates a pair profile for the given already aligned sequences.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava3.alignment.SimpleSequencePair
Creates a pair profile for the given sequences with a global alignment.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava3.alignment.SimpleSequencePair
Creates a pair profile for the given sequences with a local alignment.
SimpleStructureServer - Class in org.biojava.bio.structure.server
Deprecated. 
SimpleStructureServer() - Constructor for class org.biojava.bio.structure.server.SimpleStructureServer
Deprecated.
 
SimpleSubstitutionMatrix<C extends Compound> - Class in org.biojava3.alignment
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SimpleSubstitutionMatrix() - Constructor for class org.biojava3.alignment.SimpleSubstitutionMatrix
Creates a substitution matrix using the defaults (BLOSUM 62).
SimpleSubstitutionMatrix(CompoundSet<C>, File) - Constructor for class org.biojava3.alignment.SimpleSubstitutionMatrix
Creates a substitution matrix by reading in a file.
SimpleSubstitutionMatrix(CompoundSet<C>, Reader, String) - Constructor for class org.biojava3.alignment.SimpleSubstitutionMatrix
Creates a substitution matrix by parsing some input.
SimpleSubstitutionMatrix(CompoundSet<C>, String, String) - Constructor for class org.biojava3.alignment.SimpleSubstitutionMatrix
Creates a substitution matrix by parsing a String.
SimpleSubstitutionMatrix(CompoundSet<C>, short, short) - Constructor for class org.biojava3.alignment.SimpleSubstitutionMatrix
Creates an identity substitution matrix from match and replace values.
SingleCompoundSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet).
SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Public constructor to be used with String based constructor
SingleCompoundSequenceReader(C, CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
Build the object with a compound rather than a String
SingularValueDecomposition - Class in org.biojava.bio.structure.jama
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.SingularValueDecomposition
Construct the singular value decomposition.
Site - Class in org.biojava.bio.structure
Holds the data of sites presented in PDB files.
Site() - Constructor for class org.biojava.bio.structure.Site
 
Site(String, List<Group>) - Constructor for class org.biojava.bio.structure.Site
 
site2 - Variable in class org.biojava.bio.structure.domain.pdp.CutValues
 
size() - Method in interface org.biojava.bio.structure.Group
getnumber of atoms.
size() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
SIZE - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
size() - Method in class org.biojava.bio.structure.HetatomImpl
getnumber of atoms.
size() - Method in interface org.biojava.bio.structure.Structure
return number of Chains in this Structure.
size(int) - Method in interface org.biojava.bio.structure.Structure
return number of chains of model.
size() - Method in class org.biojava.bio.structure.StructureImpl
return number of chains , if NMR return number of chains of first model .
size(int) - Method in class org.biojava.bio.structure.StructureImpl
return number of chains of model.
size() - Method in class org.biojava3.core.util.FlatFileCache
 
size() - Method in class org.biojava3.core.util.SoftHashMap
 
skalarProduct(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
skalar product.
skip(long) - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
Skips characters.
skip(long) - Method in class org.biojava3.core.util.UncompressInputStream
 
slider - Variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
SLIDER_STEPS - Static variable in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
small - Static variable in class org.biojava3.phylo.ResidueProperties
 
smartAdapter - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
 
smartAdapter - Static variable in class org.biojava3.structure.gui.JmolViewerImpl
 
SmithWaterman<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).
SmithWaterman() - Constructor for class org.biojava3.alignment.SmithWaterman
Before running a pairwise local sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
SmithWaterman(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava3.alignment.SmithWaterman
Prepares for a pairwise local sequence alignment.
SmithWaterman3Daligner - Class in org.biojava.bio.structure.align.seq
provides a 3D superimposition based on the sequence alignment
SmithWaterman3Daligner() - Constructor for class org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
 
SmithWaterman3DParameters - Class in org.biojava.bio.structure.align.seq
 
SmithWaterman3DParameters() - Constructor for class org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
 
SmithWatermanUserArgumentProcessor - Class in org.biojava.bio.structure.align.seq
 
SmithWatermanUserArgumentProcessor() - Constructor for class org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor
 
SoftHashMap<K,V> - Class in org.biojava3.core.util
A in memory cache using soft references.
SoftHashMap() - Constructor for class org.biojava3.core.util.SoftHashMap
 
SoftHashMap(int) - Constructor for class org.biojava3.core.util.SoftHashMap
 
SolexaFastqReader - Class in org.biojava3.sequencing.io.fastq
Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqReader() - Constructor for class org.biojava3.sequencing.io.fastq.SolexaFastqReader
 
SolexaFastqWriter - Class in org.biojava3.sequencing.io.fastq
Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter() - Constructor for class org.biojava3.sequencing.io.fastq.SolexaFastqWriter
 
solve(Matrix) - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
Solve A*X = B
solve(Matrix) - Method in class org.biojava.bio.structure.jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class org.biojava.bio.structure.jama.QRDecomposition
Least squares solution of A*X = B
solveTranspose(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Solve X*A = B, which is also A'*X' = B'
sortAfps(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
 
sortByStart() - Method in class org.biojava3.genome.parsers.gff.FeatureList
Create a new list that is ordered by the starting index of the features' locations.
source() - Method in class org.biojava3.genome.parsers.gff.Feature
Get source (aka method).
Species - Interface in org.forester.surfacing
 
SPECIES_NAME - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
SPECIES_SEPARATOR - Static variable in class org.forester.surfacing.PrintableDomainSimilarity
 
splice(DNASequence) - Method in class org.biojava3.genome.parsers.gff.FeatureList
Concatenate successive portions of the specified sequence using the feature locations in the list.
SplitFasta - Class in org.biojava3.genome.util
Utility to write each Fasta entry to a unique file
SplitFasta() - Constructor for class org.biojava3.genome.util.SplitFasta
 
sqrt(BigInteger) - Method in class org.biojava.bio.structure.secstruc.BigSqrt
Get square root
sqrt(BigDecimal) - Method in class org.biojava.bio.structure.secstruc.BigSqrt
Get square root
SqrtColorMapper - Class in org.biojava.bio.structure.gui.util.color
Performs a sqrt transform on input before passing the values off to another colorMapper.
SqrtColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.bio.structure.gui.util.color.SqrtColorMapper
Creates a new SqrtColorMapper.
SSBond - Class in org.biojava.bio.structure
A simple bean to store disulfid bridge information, the SSBOND records in the PDB files.
SSBond() - Constructor for class org.biojava.bio.structure.SSBond
 
ssHash - Static variable in class org.biojava3.phylo.ResidueProperties
 
STANDARD - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
standardAASet - Static variable in class org.biojava3.aaproperties.PeptideProperties
Contains the 20 standard AA code in a set
StandardAminoAcid - Class in org.biojava.bio.structure
A class that provides a set of standard amino acids.
standardErrorOfMean() - Method in class org.forester.util.BasicDescriptiveStatistics
 
standardErrorOfMean() - Method in interface org.forester.util.DescriptiveStatistics
 
StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> - Class in org.biojava3.alignment
 
StandardRescoreRefiner(Alignments.PairInProfileScorerType, Alignments.ProfileProfileAlignerType) - Constructor for class org.biojava3.alignment.StandardRescoreRefiner
 
start() - Method in class org.biojava3.genome.parsers.gff.Location
Get starting index (origin 0).
start() - Method in class org.forester.archaeopteryx.ArchaeopteryxA
 
start() - Method in class org.forester.archaeopteryx.ArchaeopteryxE
 
StartCodonSequence - Class in org.biojava3.core.sequence
Used to map the start codon feature on a gene
StartCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava3.core.sequence.StartCodonSequence
 
startDocument() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
 
startDocument() - Method in class org.forester.io.parsers.tol.TolXmlHandler
 
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.structure.align.webstart.ConfigXMLHandler
 
startElement(String, String, String, Attributes) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
 
startElement(String, String, String, Attributes) - Method in class org.forester.io.parsers.tol.TolXmlHandler
 
startingAlignment(String, Atom[], String, Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
 
startsAfter(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location starts after the other location starts.
startsBefore(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Check if this location starts before other location starts.
StartupParameters - Class in org.biojava.bio.structure.align.ce
a simple bean that contains the parameters that can get set at startup
StartupParameters() - Constructor for class org.biojava.bio.structure.align.ce.StartupParameters
 
stateChanged(ChangeEvent) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
 
stateChanged(ChangeEvent) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
StatusDisplay - Class in org.biojava.bio.structure.align.gui.aligpanel
 
StatusDisplay() - Constructor for class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
stop() - Method in interface org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider
Interrupt searching for suggestions
stop() - Method in class org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
 
stop() - Method in class org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
 
STOP - Static variable in class org.biojava3.phylo.ResidueProperties
 
StopCodonSequence - Class in org.biojava3.core.sequence
Used to map the stop codon sequence on a gene
StopCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava3.core.sequence.StopCodonSequence
 
storeParameters() - Method in class org.biojava.bio.structure.align.gui.ParameterGUI
 
STRAND - Static variable in class org.biojava.bio.structure.io.PDBFileParser
Strand secondary structure assignment.
Strand - Enum in org.biojava3.core.sequence
Provides a way of representing the strand of a sequence, location hit or feature.
strand - Static variable in class org.biojava3.phylo.ResidueProperties
 
strandmax - Static variable in class org.biojava3.phylo.ResidueProperties
 
strandmin - Static variable in class org.biojava3.phylo.ResidueProperties
 
StrCompAlignment - Class in org.biojava.bio.structure.align.pairwise
 
StrCompAlignment(int, int) - Constructor for class org.biojava.bio.structure.align.pairwise.StrCompAlignment
 
stream(<any>, StreamListener) - Method in interface org.biojava3.sequencing.io.fastq.FastqReader
Stream the specified input supplier.
StreamBasedMsaFactory - Interface in org.forester.development
 
StreamListener - Interface in org.biojava3.sequencing.io.fastq
Event based parser callback.
STRING_LIMIT - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
stringArrayToString(String[]) - Static method in class org.forester.util.ForesterUtil
 
StringManipulationHelper - Class in org.biojava3.core.util
A utility class for common String manipulation tasks.
StringProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader
An example of a ProxySequenceReader that is created from a String.
StringProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
strip - Class in org.forester.application
 
strip() - Constructor for class org.forester.application.strip
 
StrucAligParameters - Class in org.biojava.bio.structure.align
A class that contains all the parameters of the structure alignment algorithm.
StrucAligParameters() - Constructor for class org.biojava.bio.structure.align.StrucAligParameters
 
Struct - Class in org.biojava.bio.structure.io.mmcif.model
a bean to contain the data of the _struct lines
Struct() - Constructor for class org.biojava.bio.structure.io.mmcif.model.Struct
 
StructAsym - Class in org.biojava.bio.structure.io.mmcif.model
Contains the data for _struct_asym
StructAsym() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructAsym
 
StructKeywords - Class in org.biojava.bio.structure.io.mmcif.model
 
StructKeywords() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructKeywords
 
StructRef - Class in org.biojava.bio.structure.io.mmcif.model
A class to containt the _struct_ref field data
StructRef() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructRef
 
StructRefSeq - Class in org.biojava.bio.structure.io.mmcif.model
 
StructRefSeq() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
 
Structure - Interface in org.biojava.bio.structure
Interface for a structure object.
StructureAlignment - Interface in org.biojava.bio.structure.align
 
StructureAlignmentDisplay - Class in org.biojava.bio.structure.align.gui
 
StructureAlignmentDisplay() - Constructor for class org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
 
StructureAlignmentFactory - Class in org.biojava.bio.structure.align
 
StructureAlignmentFactory() - Constructor for class org.biojava.bio.structure.align.StructureAlignmentFactory
 
StructureAlignmentJmol - Class in org.biojava.bio.structure.align.gui.jmol
A class that provides a simple GUI for Jmol
StructureAlignmentJmol() - Constructor for class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
StructureAlignmentJmol(AFPChain, Atom[], Atom[]) - Constructor for class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
StructureAlignmentOptimizer - Class in org.biojava.bio.structure.align.fatcat.calc
 
StructureAlignmentOptimizer(int, int, Atom[], int, int, Atom[], int, int[][]) - Constructor for class org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer
optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues
StructureAtom - Class in org.biojava3.protmod.structure
Everything that is needed to uniquely describe a atom.
StructureAtom(StructureGroup, String) - Constructor for class org.biojava3.protmod.structure.StructureAtom
 
StructureAtomLinkage - Class in org.biojava3.protmod.structure
 
StructureAtomLinkage(StructureAtom, StructureAtom, double) - Constructor for class org.biojava3.protmod.structure.StructureAtomLinkage
 
StructureAtomXMLConverter - Class in org.biojava3.protmod.io
 
StructureAtomXMLConverter() - Constructor for class org.biojava3.protmod.io.StructureAtomXMLConverter
 
StructureEvent - Interface in org.biojava.bio.structure.server
 
StructureEventImpl - Class in org.biojava.bio.structure.server
 
StructureEventImpl(Structure) - Constructor for class org.biojava.bio.structure.server.StructureEventImpl
 
StructureException - Exception in org.biojava.bio.structure
An exception during the parsing of a PDB file.
StructureException(String) - Constructor for exception org.biojava.bio.structure.StructureException
Constructs a StructureException object.
StructureException(String, Throwable) - Constructor for exception org.biojava.bio.structure.StructureException
Constructs a StructureException object.
StructureException(Throwable) - Constructor for exception org.biojava.bio.structure.StructureException
Constructs a StructureException object.
StructureFetcherRunnable - Class in org.biojava.bio.structure.server
Deprecated. 
StructureFetcherRunnable(PDBInstallation) - Constructor for class org.biojava.bio.structure.server.StructureFetcherRunnable
Deprecated.
 
StructureGroup - Class in org.biojava3.protmod.structure
Information of a group (residue or ligand) involved in a modification.
StructureGroup() - Constructor for class org.biojava3.protmod.structure.StructureGroup
 
StructureGroup(ResidueNumber, String, boolean) - Constructor for class org.biojava3.protmod.structure.StructureGroup
 
StructureGroupXMLConverter - Class in org.biojava3.protmod.io
 
StructureGroupXMLConverter() - Constructor for class org.biojava3.protmod.io.StructureGroupXMLConverter
 
StructureImpl - Class in org.biojava.bio.structure
Implementation of a PDB Structure.
StructureImpl() - Constructor for class org.biojava.bio.structure.StructureImpl
Constructs a StructureImpl object.
StructureImpl(Group) - Constructor for class org.biojava.bio.structure.StructureImpl
construct a Structure object that only contains a single group
StructureImpl(Chain) - Constructor for class org.biojava.bio.structure.StructureImpl
construct a Structure object that contains a particular chain
StructureIO - Interface in org.biojava.bio.structure.io
Defines the interface how to access Structure (- PDB file) input,output readers, writers.
StructureIOFile - Interface in org.biojava.bio.structure.io
interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.
StructureListener - Interface in org.biojava.bio.structure.server
 
StructureName - Class in org.biojava.bio.structure.align.client
A utility class that makes working with names of structures, domains and ranges easier.
StructureName(String) - Constructor for class org.biojava.bio.structure.align.client.StructureName
 
StructurePairAligner - Class in org.biojava.bio.structure.align
Perform a pairwise protein structure superimposition.
StructurePairAligner() - Constructor for class org.biojava.bio.structure.align.StructurePairAligner
 
StructurePairSelector - Interface in org.biojava.bio.structure.gui.util
To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
StructureProvider - Interface in org.biojava.bio.structure.io
A class that can provide a protein structure object from somewhere.
StructureSequenceMatcher - Class in org.biojava.bio.structure.io
A utility class with methods for matching ProteinSequences with Structures.
StructureSequenceMatcher() - Constructor for class org.biojava.bio.structure.io.StructureSequenceMatcher
 
StructureServer - Interface in org.biojava.bio.structure.server
Deprecated. 
StructureTools - Class in org.biojava.bio.structure
A class that provides some tool methods.
StructureTools() - Constructor for class org.biojava.bio.structure.StructureTools
 
StructureUtil - Class in org.biojava3.protmod.structure
 
StructureViewer - Interface in org.biojava3.structure.gui
 
submit(Callable<T>, String) - Static method in class org.biojava3.core.util.ConcurrencyTools
Queues up a task and adds a log entry.
submit(Callable<T>) - Static method in class org.biojava3.core.util.ConcurrencyTools
Queues up a task and adds a default log entry.
substitutionMatrix - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
SubstitutionMatrix<C extends Compound> - Interface in org.biojava3.alignment.template
Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SubstitutionMatrixHelper - Class in org.biojava3.alignment
Static utility to access substitution matrices that come bundled with BioJava.
substract(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
Deprecated.
use subtract instead.
subtract(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
subtract two atoms ( a - b).
subTree(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
 
SUBTREE_NEIGHBORS - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
suffix(int) - Method in class org.biojava3.genome.parsers.gff.Location
The part of this location after the specified position.
suffix(Location) - Method in class org.biojava3.genome.parsers.gff.Location
The part of this location after the other location (not inclusive).
suggestDomains(Structure) - Static method in class org.biojava.bio.structure.domain.LocalProteinDomainParser
Suggest domains for a protein structure
suggestDomains(Atom[]) - Static method in class org.biojava.bio.structure.domain.LocalProteinDomainParser
Suggest domains for a set of Calpha atoms
sumDeviations() - Method in class org.forester.util.BasicDescriptiveStatistics
 
sumDeviations() - Method in interface org.forester.util.DescriptiveStatistics
 
SUMMARY_POS - Static variable in class org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
Position at which the alignment summary is printed
SUPER_ORTHOLOGOUS - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
SUPPORT - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
support_statistics - Class in org.forester.application
 
support_statistics() - Constructor for class org.forester.application.support_statistics
 
support_transfer - Class in org.forester.application
 
support_transfer() - Constructor for class org.forester.application.support_transfer
 
SupportCount - Class in org.forester.development
 
surf_paup - Class in org.forester.application
 
surf_paup() - Constructor for class org.forester.application.surf_paup
 
surfacing - Class in org.forester.application
 
surfacing() - Constructor for class org.forester.application.surfacing
 
surfacing_old - Class in org.forester.application
 
surfacing_old() - Constructor for class org.forester.application.surfacing_old
 
SurfacingConstants - Class in org.forester.surfacing
 
SurfacingConstants() - Constructor for class org.forester.surfacing.SurfacingConstants
 
SurfacingUtil - Class in org.forester.surfacing
 
svd() - Method in class org.biojava.bio.structure.jama.Matrix
Singular Value Decomposition
SVDSuperimposer - Class in org.biojava.bio.structure
A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...
SVDSuperimposer(Atom[], Atom[]) - Constructor for class org.biojava.bio.structure.SVDSuperimposer
Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
swapChildren(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
Swaps the the two childern of a PhylogenyNode node of this Phylogeny.
SYMBOLS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
SymmetricalDistanceMatrixParser - Class in org.forester.phylogenyinference
 
SymmetricalDistanceMatrixParser.InputMatrixType - Enum in org.forester.phylogenyinference
 
SynchronizedOutFile - Class in org.biojava.bio.structure.align.util
 
SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.bio.structure.align.util.SynchronizedOutFile
Create a thread safe wrapper for writing to this file, the file will be gzip compressed.
SynchronizedOutFile(File) - Constructor for class org.biojava.bio.structure.align.util.SynchronizedOutFile
create a thread safe wrapper for working with this file
SystemInfo - Class in org.biojava.bio.structure.align.gui
 
SystemInfo() - Constructor for class org.biojava.bio.structure.align.gui.SystemInfo
 

T

T - Static variable in class org.biojava3.aaproperties.Constraints
 
ta - Class in org.forester.application
 
ta() - Constructor for class org.forester.application.ta
 
Table - Interface in org.biojava3.core.sequence.transcription
Provides a way of separating us from the specific IUPACTable even though this is the only implementing class for the interface.
table(Integer) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.
table(String) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name
table(Table) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
Table.CaseInsensitiveTriplet - Class in org.biojava3.core.sequence.transcription
Class used to hold three nucleotides together and allow for equality to be assessed in a case insensitive manner.
Table.CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
Table.Codon - Class in org.biojava3.core.sequence.transcription
Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon.
Table.Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava3.core.sequence.transcription.Table.Codon
 
Table.Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava3.core.sequence.transcription.Table.Codon
 
TAX_CODE_TO_SCI_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
TAXLABELS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
TAXOMONY_CODE_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
TAXONOMY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Taxonomy - Class in org.forester.phylogeny.data
 
Taxonomy() - Constructor for class org.forester.phylogeny.data.Taxonomy
 
TAXONOMY_AUTHORITY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
TAXONOMY_CODE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
TAXONOMY_COMMON_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
TAXONOMY_EXTRACTION_DEFAULT - Static variable in class org.forester.io.parsers.nhx.NHXParser
 
TAXONOMY_ID - Static variable in class org.forester.io.parsers.nhx.NHXtags
 
TAXONOMY_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
TAXONOMY_NAME - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
TAXONOMY_RANK - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
TAXONOMY_RANKS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
 
TAXONOMY_SCIENTIFIC_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
TAXONOMY_SYNONYM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
TaxonomyAssigner - Class in org.forester.sdi
 
TaxonomyAssigner(Phylogeny, Phylogeny) - Constructor for class org.forester.sdi.TaxonomyAssigner
 
taxonomyBasedDeletionOfExternalNodes(Phylogeny, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
Removes from Phylogeny to_be_stripped all external Nodes which are associated with a species NOT found in Phylogeny reference.
TaxonomyID - Class in org.biojava3.core.sequence
A sequence can be associated with a species or Taxonomy ID
TaxonomyID(String, DataSource) - Constructor for class org.biojava3.core.sequence.TaxonomyID
 
TaxonomyParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
taylor - Static variable in class org.biojava3.phylo.ResidueProperties
 
TC_STR - Static variable in interface org.forester.go.GoXRef
 
TD - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
TD1 - Static variable in class org.biojava.bio.structure.domain.pdp.PDPParameters
 
terminate() - Method in class org.biojava.bio.structure.align.client.FarmJobRunnable
Send signal to terminate calculations
terminate() - Method in class org.biojava.bio.structure.align.FarmJob
 
TERMINATE - Static variable in class org.forester.development.AminoAcid
 
TERMINATE_CODE - Static variable in class org.forester.development.AminoAcid
 
Test - Class in org.forester.development
 
Test() - Constructor for class org.forester.development.Test
 
test(File) - Static method in class org.forester.go.TestGo
 
test() - Static method in class org.forester.pccx.TestPccx
 
test(File) - Static method in class org.forester.phylogenyinference.TestPhylogenyReconstruction
 
test() - Static method in class org.forester.sdi.TestGSDI
 
test(File) - Static method in class org.forester.surfacing.TestSurfacing
 
Test - Class in org.forester.test
 
Test() - Constructor for class org.forester.test.Test
 
TestGo - Class in org.forester.go
 
TestGo() - Constructor for class org.forester.go.TestGo
 
TestGSDI - Class in org.forester.sdi
 
TestGSDI() - Constructor for class org.forester.sdi.TestGSDI
 
TestPccx - Class in org.forester.pccx
 
TestPccx() - Constructor for class org.forester.pccx.TestPccx
 
TestPhylogenyReconstruction - Class in org.forester.phylogenyinference
 
TestPhylogenyReconstruction() - Constructor for class org.forester.phylogenyinference.TestPhylogenyReconstruction
 
TestSurfacing - Class in org.forester.surfacing
 
TestSurfacing() - Constructor for class org.forester.surfacing.TestSurfacing
 
TEXT_ONLY - Static variable in class org.biojava.bio.structure.align.gui.MenuCreator
 
TEXT_SCALE_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
 
TextFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.features
A implmentation of AbstractFeature
TextFeature(String, String, String, String) - Constructor for class org.biojava3.core.sequence.features.TextFeature
 
Thr - Static variable in class org.biojava3.phylo.ResidueProperties
 
time - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
Timer - Class in org.biojava3.ronn
A simple timer, calculates the time interval between two events.
Timer() - Constructor for class org.biojava3.ronn.Timer
 
Timer(TimeUnit) - Constructor for class org.biojava3.ronn.Timer
 
times(double) - Method in class org.biojava.bio.structure.jama.Matrix
Multiply a matrix by a scalar, C = s*A
times(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
Linear algebraic matrix multiplication, A * B
timesEquals(double) - Method in class org.biojava.bio.structure.jama.Matrix
Multiply a matrix by a scalar in place, A = s*A
tiny - Static variable in class org.biojava3.phylo.ResidueProperties
 
TMP_DIR - Static variable in class org.biojava.bio.structure.align.util.UserConfiguration
 
toAlignedPairs(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
Prints the alignment in the simplest form: a list of aligned residues.
toBinaryDomainCombinations() - Method in class org.forester.surfacing.AdjactantDirectedCombinableDomains
 
toBinaryDomainCombinations() - Method in class org.forester.surfacing.BasicCombinableDomains
 
toBinaryDomainCombinations() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
toBinaryDomainCombinations() - Method in interface org.forester.surfacing.CombinableDomains
 
toBinaryDomainCombinations() - Method in class org.forester.surfacing.DirectedCombinableDomains
 
toBinaryDomainCombinations() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
This should return all binary domain combinations present in the genome.
toCE(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
toCE(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
 
toChar() - Method in enum org.forester.phylogenyinference.CharacterStateMatrix.BinaryStates
 
toCIEXYZ(float[]) - Method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
toDASStructure(XMLWriter) - Method in class org.biojava.bio.structure.io.FileConvert
convert a protein Structure to a DAS Structure XML response .
toDBSearchResult() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
toDBSearchResult(AFPChain) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
 
toDoubleArray(Collection<Number>) - Static method in class org.biojava.bio.structure.align.util.CollectionTools
 
toDssp3State - Static variable in class org.biojava3.phylo.ResidueProperties
 
toFatcat(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.model.AFPChain
 
toFatCat(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
 
toFatCatCore(AFPChain, Atom[], Atom[], boolean, boolean, boolean, boolean) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
Output in FatCatCore format
toggleSelection(AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
toggleSelection(AlignedPosition) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
toggleSelection(AlignedPosition) - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
 
toggleSelection(AlignedPosition) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
 
toGraphDescribingLanguage(BinaryDomainCombination.OutputFormat, String, String) - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
toGraphDescribingLanguage(BinaryDomainCombination.OutputFormat, String, String) - Method in interface org.forester.surfacing.BinaryDomainCombination
 
toIndex(int) - Method in class org.biojava3.core.sequence.views.ReversedSequenceView
 
toIntArray(Collection<Number>) - Static method in class org.biojava.bio.structure.align.util.CollectionTools
 
TOL_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
TOL_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
TOL_TAXONOMY_ID_TYPE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping
 
TOL_WEBSERVER - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
toList(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
For the given Sequence this will return a List filled with the Compounds of that Sequence.
TolParser - Class in org.forester.io.parsers.tol
 
TolParser() - Constructor for class org.forester.io.parsers.tol.TolParser
 
TolXmlHandler - Class in org.forester.io.parsers.tol
 
TolXmlMapping - Class in org.forester.io.parsers.tol
 
toNewHampshire(List<Phylogeny>, boolean, boolean, File, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshire(Phylogeny, boolean, boolean) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshire(Phylogeny, boolean, boolean, File) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshire(Phylogeny[], boolean, boolean, File, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshire(boolean) - Method in class org.forester.phylogeny.Phylogeny
 
toNewHampshire(boolean, boolean) - Method in class org.forester.phylogeny.PhylogenyNode
 
toNewHampshireX(List<Phylogeny>, File, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshireX(Phylogeny) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshireX(Phylogeny, File) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshireX(Phylogeny[], File, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNewHampshireX() - Method in class org.forester.phylogeny.Phylogeny
 
toNewHampshireX() - Method in class org.forester.phylogeny.PhylogenyNode
Converts this PhylogenyNode to a New Hampshire X (NHX) String representation.
toNexus(File, List<Phylogeny>) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNexus(File, Phylogeny) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNexus(Phylogeny) - Method in class org.forester.io.writers.PhylogenyWriter
 
toNexus() - Method in class org.forester.phylogeny.Phylogeny
 
toNHX() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
toNHX() - Method in class org.forester.development.AminoAcidSequence
 
toNHX() - Method in class org.forester.go.BasicGoTerm
 
toNHX() - Method in class org.forester.phylogeny.data.Accession
 
toNHX() - Method in class org.forester.phylogeny.data.Annotation
 
toNHX() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
toNHX() - Method in class org.forester.phylogeny.data.BranchColor
 
toNHX() - Method in class org.forester.phylogeny.data.BranchData
 
toNHX() - Method in class org.forester.phylogeny.data.BranchWidth
 
toNHX() - Method in class org.forester.phylogeny.data.Confidence
 
toNHX() - Method in class org.forester.phylogeny.data.Date
 
toNHX() - Method in class org.forester.phylogeny.data.Distribution
 
toNHX() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
toNHX() - Method in class org.forester.phylogeny.data.Event
 
toNHX() - Method in class org.forester.phylogeny.data.Identifier
 
toNHX() - Method in class org.forester.phylogeny.data.NodeData
 
toNHX() - Method in interface org.forester.phylogeny.data.PhylogenyData
 
toNHX() - Method in class org.forester.phylogeny.data.Point
 
toNHX() - Method in class org.forester.phylogeny.data.PropertiesMap
 
toNHX() - Method in class org.forester.phylogeny.data.Property
 
toNHX() - Method in class org.forester.phylogeny.data.ProteinDomain
 
toNHX() - Method in class org.forester.phylogeny.data.Reference
 
toNHX() - Method in class org.forester.phylogeny.data.Sequence
 
toNHX() - Method in class org.forester.phylogeny.data.SequenceRelation
 
toNHX() - Method in class org.forester.phylogeny.data.Taxonomy
 
toNHX() - Method in class org.forester.phylogeny.data.Uri
 
toPDB(Structure, Structure) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
converts the alignment to a PDB file each of the structures will be represented as a model.
toPDB() - Method in class org.biojava.bio.structure.AtomImpl
 
toPDB(StringBuffer) - Method in class org.biojava.bio.structure.AtomImpl
 
toPDB() - Method in class org.biojava.bio.structure.DBRef
Convert the DBRef object to a DBREF record as it is used in PDB files
toPDB(StringBuffer) - Method in class org.biojava.bio.structure.DBRef
Append the PDB representation of this DBRef to the provided StringBuffer
toPDB() - Method in class org.biojava.bio.structure.io.FileConvert
Convert a structure into a PDB file.
toPDB(Atom) - Static method in class org.biojava.bio.structure.io.FileConvert
Prints the content of an Atom object as a PDB formatted line.
toPDB(Atom, StringBuffer) - Static method in class org.biojava.bio.structure.io.FileConvert
print ATOM record in the following syntax
toPDB() - Method in class org.biojava.bio.structure.PDBHeader
Return a PDB representation of the PDB Header
toPDB(StringBuffer) - Method in class org.biojava.bio.structure.PDBHeader
Appends a PDB representation of the PDB header to the provided StringBuffer
toPDB() - Method in interface org.biojava.bio.structure.PDBRecord
Returns a PDB file like representation of this record.
toPDB(StringBuffer) - Method in interface org.biojava.bio.structure.PDBRecord
Appends a PDB file like representation of this record to the provided StringBuffer.
toPDB() - Method in class org.biojava.bio.structure.ResidueNumber
 
toPDB() - Method in class org.biojava.bio.structure.Site
 
toPDB(StringBuffer) - Method in class org.biojava.bio.structure.Site
 
toPDB() - Method in class org.biojava.bio.structure.SSBond
 
toPDB(StringBuffer) - Method in class org.biojava.bio.structure.SSBond
append the PDB representation of this SSBOND to the provided StringBUffer
toPDB() - Method in interface org.biojava.bio.structure.Structure
create a String that contains the contents of a PDB file .
toPDB() - Method in class org.biojava.bio.structure.StructureImpl
create a String that contains the contents of a PDB file.
toPhyloXML(Writer, int, String) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
 
toPhyloXML(Writer, int, String) - Method in class org.forester.development.AminoAcidSequence
 
toPhyloXML(Writer, int, String) - Method in class org.forester.go.BasicGoTerm
 
toPhyloXML(File, List<Phylogeny>, int, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXML(File, Phylogeny, int) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXML(Phylogeny, int) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXML(Phylogeny[], int, File, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXML(Writer, List<Phylogeny>, int, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXML(Writer, Phylogeny, int) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXML(Writer, Phylogeny[], int, String) - Method in class org.forester.io.writers.PhylogenyWriter
 
toPhyloXml(Writer, PhylogenyNode, int, String) - Static method in class org.forester.io.writers.PhyloXmlNodeWriter
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Accession
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Annotation
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BinaryCharacters
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BranchColor
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BranchData
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BranchWidth
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Confidence
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Date
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Distribution
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.DomainArchitecture
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Event
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Identifier
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.NodeData
 
toPhyloXML(Writer, int, String) - Method in interface org.forester.phylogeny.data.PhylogenyData
Writes a phyloXML representation of this phylogeny data.
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Point
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.PropertiesMap
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Property
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.ProteinDomain
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Reference
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Sequence
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.SequenceRelation
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Taxonomy
 
toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Uri
 
toPhyloXML(int) - Method in class org.forester.phylogeny.Phylogeny
 
toRGB(float[]) - Method in class org.biojava.bio.structure.gui.util.color.HSVColorSpace
 
toRotMat() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
toRotMat(AFPChain) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
 
torsionAngle(Atom, Atom, Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
torsion angle = angle between the normal vectors of the two plains a-b-c and b-c-d.
toScoresList(AFPChain) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
 
toShortString() - Method in class org.forester.go.GoNameSpace
 
toStartIndex(int) - Method in class org.biojava3.core.sequence.views.WindowedSequence
Calculates start index according to the equation start = ( (index-1) - windowSize) +1
toString() - Method in class org.biojava.bio.structure.align.ce.CeParameters
 
toString() - Method in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
 
toString() - Method in class org.biojava.bio.structure.align.ce.StartupParameters
 
toString() - Method in class org.biojava.bio.structure.align.client.CountProgressListener
 
toString() - Method in class org.biojava.bio.structure.align.client.FarmJobParameters
 
toString() - Method in class org.biojava.bio.structure.align.client.PdbPair
 
toString() - Method in class org.biojava.bio.structure.align.client.StructureName
 
toString() - Method in class org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
 
toString() - Method in class org.biojava.bio.structure.align.fatcat.FatCat
 
toString() - Method in class org.biojava.bio.structure.align.gui.jmol.AtomInfo
 
toString() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
 
toString() - Method in class org.biojava.bio.structure.align.helper.IndexPair
 
toString() - Method in class org.biojava.bio.structure.align.helper.JointFragments
 
toString() - Method in class org.biojava.bio.structure.align.model.AFP
 
toString() - Method in class org.biojava.bio.structure.align.model.AFPChain
 
toString() - Method in class org.biojava.bio.structure.align.pairwise.AlignmentResult
 
toString() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
print the idx positions of this alignment
toString() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
 
toString() - Method in class org.biojava.bio.structure.align.StrucAligParameters
 
toString() - Method in class org.biojava.bio.structure.align.xml.PdbPairsMessage
 
toString() - Method in interface org.biojava.bio.structure.AminoAcid
string representation.
toString() - Method in class org.biojava.bio.structure.AminoAcidImpl
string representation.
toString() - Method in class org.biojava.bio.structure.AtomImpl
string representation.
toString() - Method in class org.biojava.bio.structure.Author
 
toString() - Method in class org.biojava.bio.structure.Bond
 
toString() - Method in interface org.biojava.bio.structure.Chain
string representation.
toString() - Method in class org.biojava.bio.structure.ChainImpl
String representation.
toString() - Method in class org.biojava.bio.structure.Compound
 
toString() - Method in class org.biojava.bio.structure.DBRef
String representation of a DBRef.
toString() - Method in class org.biojava.bio.structure.domain.pdp.CutSites
 
toString() - Method in class org.biojava.bio.structure.domain.pdp.CutValues
 
toString() - Method in class org.biojava.bio.structure.domain.pdp.Domain
 
toString() - Method in class org.biojava.bio.structure.domain.pdp.Segment
 
toString() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
 
toString() - Method in class org.biojava.bio.structure.HetatomImpl
 
toString() - Method in class org.biojava.bio.structure.io.mmcif.model.AbstractBean
 
toString() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
 
toString() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor
 
toString() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
 
toString() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
 
toString() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
 
toString() - Method in class org.biojava.bio.structure.io.sifts.SiftsEntity
 
toString() - Method in class org.biojava.bio.structure.io.sifts.SiftsResidue
 
toString() - Method in class org.biojava.bio.structure.io.sifts.SiftsSegment
 
toString() - Method in class org.biojava.bio.structure.jama.Matrix
 
toString() - Method in class org.biojava.bio.structure.JournalArticle
 
toString() - Method in class org.biojava.bio.structure.NucleotideImpl
 
toString() - Method in class org.biojava.bio.structure.PDBHeader
String representation
toString() - Method in class org.biojava.bio.structure.ResidueNumber
 
toString() - Method in enum org.biojava.bio.structure.scop.ScopCategory
 
toString() - Method in class org.biojava.bio.structure.scop.ScopDescription
 
toString() - Method in class org.biojava.bio.structure.scop.ScopDomain
 
toString() - Method in class org.biojava.bio.structure.scop.ScopNode
 
toString() - Method in class org.biojava.bio.structure.secstruc.HBond
 
toString() - Method in class org.biojava.bio.structure.secstruc.SecStruc
 
toString() - Method in class org.biojava.bio.structure.secstruc.SecStrucGroup
 
toString() - Method in class org.biojava.bio.structure.Site
 
toString() - Method in interface org.biojava.bio.structure.Structure
String representation of object.
toString() - Method in class org.biojava.bio.structure.StructureImpl
string representation.
toString() - Method in class org.biojava3.aaproperties.xml.AminoAcidComposition
 
toString() - Method in class org.biojava3.aaproperties.xml.Element
 
toString() - Method in class org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix
Returns in a format similar to the standard NCBI files.
toString() - Method in class org.biojava3.alignment.GuideTree
 
toString() - Method in class org.biojava3.alignment.SimpleAlignedSequence
Provides standard Java language access to results of SimpleAlignedSequence.getSequenceAsString().
toString(int) - Method in class org.biojava3.alignment.SimpleProfile
 
toString(Profile.StringFormat) - Method in class org.biojava3.alignment.SimpleProfile
 
toString() - Method in class org.biojava3.alignment.SimpleProfile
 
toString() - Method in class org.biojava3.alignment.SimpleSubstitutionMatrix
Returns in a format similar to the standard NCBI files.
toString() - Method in interface org.biojava3.alignment.template.Profile
Returns a simple view of the alignment profile.
toString(int) - Method in interface org.biojava3.alignment.template.Profile
Returns a formatted view of the alignment profile.
toString(Profile.StringFormat) - Method in interface org.biojava3.alignment.template.Profile
Returns a formatted view of the alignment profile.
toString() - Method in class org.biojava3.core.sequence.AccessionID
 
toString() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
 
toString() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
 
toString() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
 
toString() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
 
toString() - Method in class org.biojava3.core.sequence.location.SimplePoint
 
toString() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
 
toString(int) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Get a string representation of the MSA with a fixed width
toString(LightweightProfile.StringFormat) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
Support for different MSA formats
toString() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
String representation of the MSA
toString() - Method in class org.biojava3.core.sequence.template.AbstractCompound
 
toString() - Method in class org.biojava3.core.sequence.template.AbstractSequence
 
toString() - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns a simple view of the alignment profile.
toString(int) - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns a formatted view of the alignment profile.
toString(LightweightProfile.StringFormat) - Method in interface org.biojava3.core.sequence.template.LightweightProfile
Returns a formatted view of the alignment profile.
toString(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Shortcut to SequenceMixin.toStringBuilder(org.biojava3.core.sequence.template.Sequence) which calls toString() on the resulting object.
toString() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
 
toString() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
 
toString() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
 
toString() - Method in class org.biojava3.core.util.CRC64Checksum
Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format.
toString() - Method in class org.biojava3.data.sequence.FastaSequence
Same as oneLineFasta
toString() - Method in class org.biojava3.genome.parsers.gff.Feature
 
toString() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
A string representation of the feature.
toString() - Method in class org.biojava3.genome.parsers.gff.FeatureList
Return a string representation of all features in this list.
toString() - Method in class org.biojava3.genome.parsers.gff.Location
Return a string representation of location.
toString() - Method in class org.biojava3.genome.parsers.gff.LocIterator
Get string representation of iterator.
toString() - Method in class org.biojava3.protmod.Component
 
toString() - Method in enum org.biojava3.protmod.ModificationCategory
 
toString() - Method in class org.biojava3.protmod.ModificationConditionImpl
 
toString() - Method in class org.biojava3.protmod.ModificationLinkage
 
toString() - Method in enum org.biojava3.protmod.ModificationOccurrenceType
 
toString() - Method in class org.biojava3.protmod.ProteinModificationImpl
 
toString() - Method in class org.biojava3.protmod.structure.ModifiedCompoundImpl
 
toString() - Method in class org.biojava3.protmod.structure.StructureAtom
 
toString() - Method in class org.biojava3.protmod.structure.StructureAtomLinkage
 
toString() - Method in class org.biojava3.protmod.structure.StructureGroup
 
toString() - Method in class org.biojava3.ronn.Jronn.Range
 
toString() - Method in class org.biojava3.ronn.ModelLoader.Model
 
toString() - Method in class org.biojava3.ws.alignment.qblast.BlastJob
 
toString() - Method in class org.biojava3.ws.hmmer.HmmerDomain
 
toString() - Method in class org.biojava3.ws.hmmer.HmmerResult
 
toString() - Method in class org.forester.development.AminoAcidSequence
 
toString() - Method in class org.forester.go.BasicGoRelationship
 
toString() - Method in class org.forester.go.BasicGoSubset
 
toString() - Method in class org.forester.go.BasicGoTerm
 
toString() - Method in class org.forester.go.BasicGoXRef
 
toString() - Method in class org.forester.go.GoId
 
toString() - Method in class org.forester.go.GoNameSpace
 
toString() - Method in class org.forester.go.PfamToGoMapping
 
toString() - Method in class org.forester.io.parsers.phyloxml.XmlElement
 
toString() - Method in class org.forester.phylogeny.data.Accession
 
toString() - Method in class org.forester.phylogeny.data.Annotation
 
toString() - Method in class org.forester.phylogeny.data.BinaryCharacters
 
toString() - Method in class org.forester.phylogeny.data.BranchColor
 
toString() - Method in class org.forester.phylogeny.data.BranchWidth
 
toString() - Method in class org.forester.phylogeny.data.Confidence
 
toString() - Method in class org.forester.phylogeny.data.Date
 
toString() - Method in class org.forester.phylogeny.data.Distribution
 
toString() - Method in class org.forester.phylogeny.data.DomainArchitecture
 
toString() - Method in class org.forester.phylogeny.data.Event
 
toString() - Method in class org.forester.phylogeny.data.Identifier
 
toString() - Method in class org.forester.phylogeny.data.Point
 
toString() - Method in class org.forester.phylogeny.data.PropertiesMap
 
toString() - Method in class org.forester.phylogeny.data.Property
 
toString() - Method in class org.forester.phylogeny.data.ProteinDomain
 
toString() - Method in class org.forester.phylogeny.data.Reference
 
toString() - Method in class org.forester.phylogeny.data.Sequence
 
toString() - Method in class org.forester.phylogeny.data.Taxonomy
 
toString() - Method in class org.forester.phylogeny.Phylogeny
Converts this Phylogeny to a New Hampshire X (String) representation.
toString() - Method in class org.forester.phylogeny.PhylogenyBranch
 
toString() - Method in class org.forester.phylogeny.PhylogenyNode
 
toString() - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
toString() - Method in enum org.forester.phylogenyinference.CharacterStateMatrix.BinaryStates
 
toString() - Method in enum org.forester.phylogenyinference.CharacterStateMatrix.GainLossStates
 
toString() - Method in class org.forester.phylogenyinference.DiscreteState
 
toString() - Method in class org.forester.sdi.GSDI
 
toString() - Method in class org.forester.sdi.SDI
 
toString() - Method in class org.forester.surfacing.BasicBinaryDomainCombination
 
toString() - Method in class org.forester.surfacing.BasicCombinableDomains
 
toString() - Method in class org.forester.surfacing.BasicDomain
 
toString() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
toString() - Method in class org.forester.surfacing.BasicSpecies
 
toString() - Method in interface org.forester.surfacing.BinaryDomainCombination
This has to return a String representation in the following format: id0 - id1
toString() - Method in class org.forester.surfacing.DomainId
 
toString() - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
toString() - Method in class org.forester.surfacing.ProteinId
 
toString() - Method in class org.forester.tools.TreeSplitMatrix
 
toString() - Method in class org.forester.util.BasicDescriptiveStatistics
 
toString() - Method in class org.forester.util.BasicTable
 
toString() - Method in interface org.forester.util.DescriptiveStatistics
 
toString() - Method in class org.forester.util.GeneralTable
 
toString(NumberFormat) - Method in class org.forester.util.GeneralTable
 
toStringBuffer(DistanceMatrix.Format) - Method in class org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix
 
toStringBuffer(DistanceMatrix.Format) - Method in interface org.forester.phylogenyinference.DistanceMatrix
 
toStringBuffer() - Method in class org.forester.surfacing.BasicDomain
 
toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION) - Method in interface org.forester.surfacing.DomainSimilarity
 
toStringBuffer(PrintableDomainSimilarity.PRINT_OPTION) - Method in class org.forester.surfacing.PrintableDomainSimilarity
 
toStringBuffer(double, double, int, char, int, int) - Method in class org.forester.util.AsciiHistogram
 
toStringBuffer(int, char, int, int) - Method in class org.forester.util.AsciiHistogram
 
toStringBuilder(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString().
toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
 
toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
 
toUnixPath(String) - Static method in class org.biojava.bio.structure.io.util.FileDownloadUtils
Converts path to Unix convention and adds a terminating slash if it was omitted
toWebSiteDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
toWebSiteDisplay(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.bio.structure.align.model.AfpChainWriter
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
toWriter(Writer) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
toWriter(Writer, CharacterStateMatrix.Format) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
toWriter(Writer) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
toWriter(Writer, CharacterStateMatrix.Format) - Method in interface org.forester.phylogenyinference.CharacterStateMatrix
 
toXML(PrintWriter) - Method in class org.biojava.bio.structure.align.util.UserConfiguration
convert Configuration to an XML file so it can be serialized
toXML(XMLWriter) - Method in class org.biojava.bio.structure.align.util.UserConfiguration
convert Configuration to an XML file so it can be serialized add to an already existing xml file.
toXML(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
Convert an afpChain to a simple XML representation
toXML(AFPChain, StringWriter, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
Write the XML representation to a StringWriter
toXML(AFPChain) - Static method in class org.biojava.bio.structure.align.xml.AFPChainXMLConverter
 
toXML(boolean) - Method in class org.biojava.bio.structure.align.xml.HasResultXMLConverter
return flag if the server has a result
toXML(int) - Method in class org.biojava.bio.structure.align.xml.PositionInQueueXMLConverter
 
toXML(SortedSet<String>) - Static method in class org.biojava.bio.structure.align.xml.RepresentativeXMLConverter
 
toXML() - Method in class org.biojava.bio.structure.domain.AssignmentXMLSerializer
 
toXML() - Method in class org.biojava.bio.structure.scop.server.ScopDescriptions
 
toXML() - Method in class org.biojava.bio.structure.scop.server.ScopDomains
 
toXML() - Method in class org.biojava.bio.structure.scop.server.ScopNodes
 
toXML() - Method in class org.biojava.bio.structure.scop.server.TreeSetStringWrapper
 
toXML(Component) - Static method in class org.biojava3.protmod.io.ComponentXMLConverter
 
toXML(Component, PrettyXMLWriter) - Static method in class org.biojava3.protmod.io.ComponentXMLConverter
 
toXML(ModifiedCompound) - Static method in class org.biojava3.protmod.io.ModifiedCompoundXMLConverter
 
toXML(StructureAtom) - Static method in class org.biojava3.protmod.io.StructureAtomXMLConverter
 
toXML(StructureAtom, PrettyXMLWriter) - Static method in class org.biojava3.protmod.io.StructureAtomXMLConverter
 
toXML(StructureGroup, PrettyXMLWriter) - Static method in class org.biojava3.protmod.io.StructureGroupXMLConverter
 
trace() - Method in class org.biojava.bio.structure.jama.Matrix
Matrix trace.
trace1 - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
trace1 - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
trace2 - Variable in class org.biojava.bio.structure.align.ce.CECalculator
 
trace2 - Variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
TranscriptionEngine - Class in org.biojava3.core.sequence.transcription
Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence.
TranscriptionEngine.Builder - Class in org.biojava3.core.sequence.transcription
This class is the way to create a TranslationEngine.
TranscriptionEngine.Builder() - Constructor for class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
TranscriptSequence - Class in org.biojava3.core.sequence
This is the sequence if you want to go from a gene sequence to a protein sequence.
TranscriptSequence(GeneSequence, int, int) - Constructor for class org.biojava3.core.sequence.TranscriptSequence
 
transferInternalNamesToBootstrapSupport(Phylogeny) - Static method in class org.forester.util.ForesterUtil
 
transferInternalNodeNamesToConfidence(Phylogeny) - Static method in class org.forester.util.ForesterUtil
 
transferNodeNameToField(Phylogeny, ForesterUtil.PhylogenyNodeField) - Static method in class org.forester.util.ForesterUtil
 
transferSupportValues(Phylogeny, Phylogeny) - Static method in class org.forester.application.support_transfer
Modifies Phylogeny to with the support values from Phylogeny from.
transform(double) - Method in class org.biojava.bio.structure.gui.util.color.ContinuousColorMapperTransform
An arbitrary transform over reals
transform(double) - Method in class org.biojava.bio.structure.gui.util.color.LogColorMapper
Apply log transform.
transform(double) - Method in class org.biojava.bio.structure.gui.util.color.SqrtColorMapper
Return sqrt(value).
transform(Map<?, ?>) - Method in class org.biojava3.ws.alignment.qblast.MapToStringTransformer
Transforms Map to String, representing every entry as key mappingSequence value , joined by separatorSequence
translate(F) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
translate(F) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
 
translate(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
Quick method to let you go from a CDS to a Peptide quickly.
TRANSLATE - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
translateMany(F) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
translateMany(F) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
 
translateNCodons() - Method in class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
Indicates if we want to force exact translation of compounds or not i.e.
translateNCodons(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
TranslationException - Exception in org.biojava3.core.exceptions
Thrown from AbstractCompundTranslator
TranslationException(String) - Constructor for exception org.biojava3.core.exceptions.TranslationException
 
TranslationException(Exception) - Constructor for exception org.biojava3.core.exceptions.TranslationException
 
TranslationException(String, Exception) - Constructor for exception org.biojava3.core.exceptions.TranslationException
 
transpose() - Method in class org.biojava.bio.structure.jama.Matrix
Matrix transpose.
TREE - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 
TREE_BASE_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
TREE_FAM_INST - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
TREE_FAM_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil
 
TreeConstructionAlgorithm - Enum in org.biojava3.phylo
 
TreeConstructor<C extends AbstractSequence<D>,D extends Compound> - Class in org.biojava3.phylo
Tree constructor uses the forrester tree library to build phylogenetic trees using neighbor joining algorithm.
TreeConstructor(MultipleSequenceAlignment<C, D>, TreeType, TreeConstructionAlgorithm, NJTreeProgressListener) - Constructor for class org.biojava3.phylo.TreeConstructor
 
TreeConstructor(DistanceMatrix, TreeType, TreeConstructionAlgorithm, NJTreeProgressListener) - Constructor for class org.biojava3.phylo.TreeConstructor
 
TreeFontSet - Class in org.forester.archaeopteryx
 
TreePanel - Class in org.forester.archaeopteryx
 
TreeSetStringWrapper - Class in org.biojava.bio.structure.scop.server
 
TreeSetStringWrapper() - Constructor for class org.biojava.bio.structure.scop.server.TreeSetStringWrapper
 
TreeSplitMatrix - Class in org.forester.tools
 
TreeSplitMatrix(Phylogeny, boolean, Phylogeny) - Constructor for class org.forester.tools.TreeSplitMatrix
 
TreeSplitMatrix(Phylogeny, boolean, Set<PhylogenyNode>) - Constructor for class org.forester.tools.TreeSplitMatrix
If strict is true, target nodes (all external nodes of the phylogeny for which support values are to be calculated) is not used for anything during construction.
TreeType - Enum in org.biojava3.phylo
 
triggerDocumentEnd() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerDocumentStart() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerGeneric(String, List<String>, List<String>) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerMouseOverPosition(int, int) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
 
triggerNewChemComp(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewChemCompDescriptor(ChemCompDescriptor) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewEntity(Entity) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewEntityPolySeq(EntityPolySeq) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewRefine(Refine) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewStructAsym(StructAsym) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerNewStructKeywords(StructKeywords) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
 
triggerSelectionLocked(boolean) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
 
trimStop(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
Imperfect code.
trimStop(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
 
Trp - Static variable in class org.biojava3.phylo.ResidueProperties
 
tryAllCPs - Variable in class org.biojava.bio.structure.align.ce.OptimalCECPParameters
If true, ignores OptimalCECPParameters.cpPoint and tries all possible cp points.
TURN - Static variable in class org.biojava.bio.structure.io.PDBFileParser
Turn secondary structure assignment.
turn - Static variable in class org.biojava3.phylo.ResidueProperties
 
turnmax - Static variable in class org.biojava3.phylo.ResidueProperties
 
turnmin - Static variable in class org.biojava3.phylo.ResidueProperties
 
twistOptimized(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.AFPTwister
superimposing according to the optimized alignment
twistPDB(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.AFPTwister
calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B
TwoBitSequenceReader<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.storage
Implementation of the 2bit encoding.
TwoBitSequenceReader(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
 
TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.storage
Extension of the BitArrayWorker which provides the 2bit implementation code.
TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitSequenceReader.TwoBitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
TwoBitSequenceReader.TwoBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
 
type - Static variable in class org.biojava.bio.structure.AminoAcidImpl
this is an Amino acid.
type - Static variable in class org.biojava.bio.structure.HetatomImpl
this is a "hetatm".
type - Static variable in class org.biojava.bio.structure.NucleotideImpl
this is a "nucleotide", a special occurance of a Hetatom.
type() - Method in class org.biojava3.genome.parsers.gff.Feature
Get feature type, such as "exon" or "CDS".
type() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get the feature type, for example, "exon", "CDS", etc.
TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Tyr - Static variable in class org.biojava3.phylo.ResidueProperties
 

U

UM_BBD_ENZYME_ID_STR - Static variable in interface org.forester.go.GoXRef
 
UM_BBD_PATHWAY_ID_STR - Static variable in interface org.forester.go.GoXRef
 
UM_BBD_REACTIONID_STR - Static variable in interface org.forester.go.GoXRef
 
uminus() - Method in class org.biojava.bio.structure.jama.Matrix
Unary minus
UNASSIGNED_STR - Variable in class org.forester.go.GoNameSpace
 
uncompress(String, FileOutputStream) - Static method in class org.biojava3.core.util.UncompressInputStream
 
UncompressInputStream - Class in org.biojava3.core.util
This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UncompressInputStream(InputStream) - Constructor for class org.biojava3.core.util.UncompressInputStream
 
UNDERSCORE - Static variable in class org.biojava.bio.structure.align.util.AtomCache
 
unexpectedFatalError(String, Exception) - Static method in class org.forester.util.ForesterUtil
 
unexpectedFatalError(String, String) - Static method in class org.forester.util.ForesterUtil
 
unexpectedFatalError(String, String, Exception) - Static method in class org.forester.util.ForesterUtil
 
union(Location) - Method in class org.biojava3.genome.parsers.gff.Location
Return the union.
UNIPROT_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
UniprotProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader
Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.
UniprotProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
The uniprot id is used to retrieve the uniprot XML which is then parsed as a DOM object so we know everything about the protein.
UniprotToFasta - Class in org.biojava3.genome.uniprot
 
UniprotToFasta() - Constructor for class org.biojava3.genome.uniprot.UniprotToFasta
 
unitVector(Atom) - Static method in class org.biojava.bio.structure.Calc
return the unit vector of vector a .
UNKNOWN - Static variable in class org.forester.development.AminoAcid
 
UNKNOWN_CODE - Static variable in class org.forester.development.AminoAcid
 
UNKNOWN_GROUP_LABEL - Static variable in class org.biojava.bio.structure.StructureTools
 
unknownGroup - Static variable in class org.biojava3.aaproperties.profeat.convertor.Convertor
 
UnknownPdbAminoAcidException - Exception in org.biojava.bio.structure
An exception for use during translating amino acids in a PDB file.
UnknownPdbAminoAcidException(String) - Constructor for exception org.biojava.bio.structure.UnknownPdbAminoAcidException
Constructs a PDBParseException object.
UnknownPdbAminoAcidException(String, Throwable) - Constructor for exception org.biojava.bio.structure.UnknownPdbAminoAcidException
Constructs a UnknownPdbAminoAcidException object.
UnknownPdbAminoAcidException(Throwable) - Constructor for exception org.biojava.bio.structure.UnknownPdbAminoAcidException
Constructs a UnknownPdbAminoAcidException object.
unregister(ProteinModification) - Static method in class org.biojava3.protmod.ProteinModificationRegistry
Remove a modification from registry.
unRoot() - Method in class org.forester.phylogeny.Phylogeny
Removes the root PhylogenyNode this Phylogeny.
update(int, int[], AlignerHelper.Last[][]) - Method in class org.biojava3.alignment.routines.AlignerHelper.Cut
 
update(int) - Method in class org.biojava3.core.util.CRC64Checksum
 
update(byte[], int, int) - Method in class org.biojava3.core.util.CRC64Checksum
 
update(String) - Method in class org.biojava3.core.util.CRC64Checksum
 
updateDisplay() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
 
updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.bio.structure.align.ce.CECalculator
Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
updateProgress(String, int) - Method in class org.biojava3.phylo.TreeConstructor
 
updateProgress(String, int, int) - Method in class org.biojava3.phylo.TreeConstructor
 
updateScore(FatCatParameters, AFPChain) - Static method in class org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation
upstream(int) - Method in class org.biojava3.genome.parsers.gff.Location
Return the adjacent location of specified length directly upstream of this location.
URI - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
Uri - Class in org.forester.phylogeny.data
 
Uri(String, String, String) - Constructor for class org.forester.phylogeny.data.Uri
 
Uri(URI) - Constructor for class org.forester.phylogeny.data.Uri
 
Uri(URI, String, String) - Constructor for class org.forester.phylogeny.data.Uri
 
URI_DESC_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
UriParser - Class in org.forester.io.parsers.phyloxml.phylogenydata
 
url - Variable in class org.biojava.bio.structure.domain.RemoteDomainProvider
 
urlPropertyNames - Static variable in class org.biojava.bio.structure.align.gui.SystemInfo
 
UrlTreeReader - Class in org.forester.archaeopteryx
 
USERAGENT - Static variable in class org.biojava.bio.structure.align.util.HTTPConnectionTools
 
UserArgumentProcessor - Interface in org.biojava.bio.structure.align.ce
 
UserConfiguration - Class in org.biojava.bio.structure.align.util
A container to persist config to the file system
UserConfiguration() - Constructor for class org.biojava.bio.structure.align.util.UserConfiguration
Default UserConfiguration: split directory autofetch files default download location.
userData() - Method in class org.biojava3.genome.parsers.gff.Feature
Get HashMap of user data.
userData() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get HashMap of user data.
UTF8 - Static variable in class org.forester.util.ForesterConstants
 
Utils - Class in org.biojava3.aaproperties
This is a utility class that contains utility methods which will facilitates the coding of other methods
Utils() - Constructor for class org.biojava3.aaproperties.Utils
 
UTREE - Static variable in class org.forester.io.parsers.nexus.NexusConstants
 

V

V - Static variable in class org.biojava3.aaproperties.Constraints
 
Val - Static variable in class org.biojava3.phylo.ResidueProperties
 
validate(Fastq) - Method in class org.biojava3.sequencing.io.fastq.IlluminaFastqWriter
Validate the specified FASTQ formatted sequence for writing.
validate(Fastq) - Method in class org.biojava3.sequencing.io.fastq.SangerFastqWriter
Validate the specified FASTQ formatted sequence for writing.
validate(Fastq) - Method in class org.biojava3.sequencing.io.fastq.SolexaFastqWriter
Validate the specified FASTQ formatted sequence for writing.
validateAllowedOptions(List<String>) - Method in class org.forester.util.CommandLineArguments
 
validateAllowedOptionsAsString(List<String>) - Method in class org.forester.util.CommandLineArguments
 
validateMandatoryOptions(List<String>) - Method in class org.forester.util.CommandLineArguments
 
validateMandatoryOptionsAsString(List<String>) - Method in class org.forester.util.CommandLineArguments
 
value - Variable in class org.biojava.bio.structure.align.helper.GapArray
 
valueChanged(ListSelectionEvent) - Method in class org.forester.archaeopteryx.FontChooser
 
valueOf(String) - Static method in enum org.biojava.bio.structure.BondType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.Element
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.ElementType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.PDBStatus.Status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.bio.structure.scop.ScopCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.aaproperties.CommandPrompt.PropertyName
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.aaproperties.PeptideProperties.SingleLetterAACode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.GROUPING
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.TRANSITION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.Alignments.PairInProfileScorerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.Alignments.PairwiseSequenceScorerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.Alignments.ProfileProfileAlignerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.Alignments.RefinerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.routines.AlignerHelper.Last
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.template.AlignedSequence.Step
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.template.GapPenalty.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.alignment.template.Profile.StringFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.DataSource
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.DNASequence.DNAType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.Strand
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.transcription.Frame
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.phylo.TreeConstructionAlgorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.phylo.TreeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.protmod.ModificationCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.protmod.ModificationOccurrenceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ronn.RonnConstraint.Threshold
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.structure.gui.RenderStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ws.alignment.qblast.BlastAlignmentParameterEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ws.alignment.qblast.BlastMatrixEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ws.alignment.qblast.BlastOutputFormatEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ws.alignment.qblast.BlastOutputParameterEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.ws.alignment.qblast.BlastProgramEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.go.etc.OntologizerResult.TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.go.GoNameSpace.GoNamespaceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.go.GoRelationship.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.go.GoSubset.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.go.GoXRef.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.go.OBOparser.ReturnType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.FilterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.ReturnType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.io.writers.PhylogenyWriter.FORMAT
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogeny.data.Event.EventType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogeny.data.Property.AppliesTo
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.BinaryStates
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.Format
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.GainLossStates
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.NucleotideStates
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogenyinference.DistanceMatrix.Format
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.phylogenyinference.SymmetricalDistanceMatrixParser.InputMatrixType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.BinaryDomainCombination.DomainCombinationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.BinaryDomainCombination.OutputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.Detailedness
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.tools.PhylogenyDecorator.FIELD
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.forester.util.ForesterUtil.PhylogenyNodeField
Returns the enum constant of this type with the specified name.
valueOfIgnoreCase(String) - Static method in enum org.biojava.bio.structure.Element
Returns the Element that corresponds to the specified element symbol.
values() - Static method in enum org.biojava.bio.structure.BondType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.bio.structure.Element
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.bio.structure.ElementType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
values() - Static method in enum org.biojava.bio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.bio.structure.PDBStatus.Status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.bio.structure.scop.ScopCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.aaproperties.CommandPrompt.PropertyName
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.aaproperties.PeptideProperties.SingleLetterAACode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.GROUPING
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.aaproperties.profeat.IProfeatProperties.TRANSITION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.Alignments.PairInProfileScorerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.Alignments.PairwiseSequenceScorerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.Alignments.ProfileProfileAlignerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.Alignments.RefinerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.routines.AlignerHelper.Last
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.template.AlignedSequence.Step
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.template.GapPenalty.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.alignment.template.Profile.StringFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.DataSource
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.DNASequence.DNAType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.Strand
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.transcription.Frame
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.phylo.TreeConstructionAlgorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.phylo.TreeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.protmod.ModificationCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.protmod.ModificationOccurrenceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ronn.RonnConstraint.Threshold
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.sequencing.io.fastq.FastqVariant
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.structure.gui.RenderStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ws.alignment.qblast.BlastAlignmentParameterEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ws.alignment.qblast.BlastMatrixEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ws.alignment.qblast.BlastOutputFormatEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ws.alignment.qblast.BlastOutputParameterEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.ws.alignment.qblast.BlastProgramEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.go.etc.OntologizerResult.TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.go.GoNameSpace.GoNamespaceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.go.GoRelationship.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.go.GoSubset.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.go.GoXRef.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.go.OBOparser.ReturnType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.FilterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.ReturnType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.io.writers.PhylogenyWriter.FORMAT
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogeny.data.Event.EventType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogeny.data.Property.AppliesTo
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.BinaryStates
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.Format
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.GainLossStates
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogenyinference.CharacterStateMatrix.NucleotideStates
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogenyinference.DistanceMatrix.Format
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.phylogenyinference.SymmetricalDistanceMatrixParser.InputMatrixType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.BinaryDomainCombination.DomainCombinationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.BinaryDomainCombination.OutputFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.Detailedness
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.tools.PhylogenyDecorator.FIELD
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.forester.util.ForesterUtil.PhylogenyNodeField
Returns an array containing the constants of this enum type, in the order they are declared.
vectorProduct(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
Vector product .
verbose - Static variable in class org.biojava.bio.structure.domain.pdp.CutDomain
 
VERBOSE - Static variable in class org.forester.tools.PhylogenyDecorator
 
verifySequence(Sequence<AminoAcidCompound>) - Method in class org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet
 
verifySequence(Sequence<AminoAcidCompound>) - Method in class org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
 
verifySequence(Sequence<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
 
verifySequence(Sequence<C>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
 
verifySequence(Sequence<C>) - Method in interface org.biojava3.core.sequence.template.CompoundSet
 
version - Static variable in class org.biojava.bio.structure.align.ce.CeCPMain
version history: 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment.
version - Static variable in class org.biojava.bio.structure.align.ce.CeMain
 
version - Static variable in class org.biojava.bio.structure.align.ce.OptimalCECPMain
 
VERSION - Static variable in class org.biojava.bio.structure.align.fatcat.FatCat
 
viewer - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
 
viewer - Static variable in class org.biojava3.structure.gui.JmolViewerImpl
 

W

W - Static variable in class org.biojava3.aaproperties.Constraints
 
W3C_XML_SCHEMA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
 
W3C_XML_SCHEMA - Static variable in class org.forester.io.parsers.tol.TolParser
 
WAIT_INCREMENT - Static variable in class org.biojava3.ws.alignment.qblast.NCBIQBlastService
Number of milliseconds by which expected job execution time is incremented if it is not finished yet.
WebservicesManager - Class in org.forester.archaeopteryx.webservices
 
WebservicesManager.WsPhylogenyFormat - Enum in org.forester.archaeopteryx.webservices
 
WebserviceUtil - Class in org.forester.archaeopteryx.webservices
 
WebserviceUtil() - Constructor for class org.forester.archaeopteryx.webservices.WebserviceUtil
 
WebStartDBSearch - Class in org.biojava.bio.structure.align.webstart
A Web Start wrapper for a FarmJobRunnable.
WebStartDBSearch() - Constructor for class org.biojava.bio.structure.align.webstart.WebStartDBSearch
 
WebStartDBSearchResults - Class in org.biojava.bio.structure.align.webstart
 
WebStartDBSearchResults() - Constructor for class org.biojava.bio.structure.align.webstart.WebStartDBSearchResults
 
WebStartMain - Class in org.biojava.bio.structure.align.webstart
 
WebStartMain() - Constructor for class org.biojava.bio.structure.align.webstart.WebStartMain
 
WHITE_BLACK_GRADIENT - Static variable in class org.biojava.bio.structure.gui.util.color.GradientMapper
 
WHITE_SPACE - Static variable in class org.biojava3.data.sequence.SequenceUtil
A whitespace character: [\t\n\x0B\f\r]
WIDTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
 
WIKIPEDIA_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
 
WIKIPEDIA_STR - Static variable in interface org.forester.go.GoXRef
 
window(int, int) - Method in class org.biojava3.genome.parsers.gff.Location
Enable a "sliding window" iteration over a location to use with Java's "for" loop construct.
windowActivated(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowActivated(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowActivated(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
windowClosed(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowClosed(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowClosed(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
windowClosing(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowClosing(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowClosing(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
windowDeactivated(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowDeactivated(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowDeactivated(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
windowDeiconified(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowDeiconified(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowDeiconified(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
WindowedSequence<C extends Compound> - Class in org.biojava3.core.sequence.views
A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works.
WindowedSequence(Sequence<C>, int) - Constructor for class org.biojava3.core.sequence.views.WindowedSequence
 
windowIconified(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowIconified(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowIconified(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
windowOpened(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.AligPanel
 
windowOpened(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay
 
windowOpened(WindowEvent) - Method in class org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
 
WindowsUtils - Class in org.forester.util
 
winSize - Variable in class org.biojava.bio.structure.align.ce.CeParameters
 
withDescription(String) - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified description.
withQuality(String) - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified quality scores.
withSequence(String) - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified sequence.
withVariant(FastqVariant) - Method in class org.biojava3.sequencing.io.fastq.FastqBuilder
Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
wordWrap(String, int) - Static method in class org.forester.util.ForesterUtil
 
workingListToSequences(List<List<T>>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
 
wrap(Sequence<C>) - Method in enum org.biojava3.core.sequence.transcription.Frame
Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.
wrapToRna(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.
write(String) - Method in class org.biojava.bio.structure.align.util.SynchronizedOutFile
 
write(Appendable, Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data out
write(FeatureList, String) - Static method in class org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
Write features in FeatureList to file.
write(OutputStream, LinkedHashMap<String, ChromosomeSequence>) - Method in class org.biojava3.genome.parsers.gff.GFF3Writer
Output gff3 format for a DNA Sequence
write(int) - Method in class org.biojava3.ronn.NullOutputStream
 
write(File, Fastq...) - Method in interface org.biojava3.sequencing.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified file.
write(File, Iterable<Fastq>) - Method in interface org.biojava3.sequencing.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified file.
write(OutputStream, Fastq...) - Method in interface org.biojava3.sequencing.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified output stream.
write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava3.sequencing.io.fastq.FastqWriter
Write the specified FASTQ formatted sequences to the specified output stream.
writeAllDomainsChangedOnAllSubtrees(Phylogeny, boolean, String, String) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeBinaryDomainCombinationsFileForGraphAnalysis(String[][], File, GenomeWideCombinableDomains, int, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, CharacterStateMatrix.GainLossStates, String, String, String, Map<String, String>) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, CharacterStateMatrix.GainLossStates, String, String, String, BinaryDomainCombination.OutputFormat) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeBinaryStatesMatrixToList(Map<DomainId, List<GoId>>, Map<GoId, GoTerm>, GoNameSpace, boolean, CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, CharacterStateMatrix.GainLossStates, String, String, String, String, String, Map<DomainId, Set<String>>[], SortedSet<String>, SortedSet<String>, String) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeDomainCombinationsCountsFile(String[][], File, Writer, GenomeWideCombinableDomains, int, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeDomainSimilaritiesToFile(StringBuilder, StringBuilder, Writer, SortedSet<DomainSimilarity>, boolean, List<Species>, PrintableDomainSimilarity.PRINT_OPTION, DomainSimilarity.DomainSimilaritySortField, DomainSimilarity.DomainSimilarityScoring, boolean) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeFasta(OutputStream, List<FastaSequence>, int) - Static method in class org.biojava3.data.sequence.SequenceUtil
Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line
writeFasta(OutputStream, List<FastaSequence>) - Static method in class org.biojava3.data.sequence.SequenceUtil
Writes FastaSequence in the file, each sequence will take one line only
writeGeneSequence(File, Collection<GeneSequence>, boolean) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
writeGeneSequence(OutputStream, Collection<GeneSequence>, boolean) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
writeIndent() - Method in class org.biojava3.core.util.PrettyXMLWriter
 
writeMatrixToFile(CharacterStateMatrix<?>, String, CharacterStateMatrix.Format) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeMatrixToFile(File, List<DistanceMatrix>) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeNexusBinaryChractersBlock(Writer) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
writeNexusCharstatelabels(Writer) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
writeNexusMatrix(Writer) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
writeNexusTaxaBlock(Writer, Phylogeny) - Static method in class org.forester.io.writers.PhylogenyWriter
 
writeNexusTaxaBlock(Writer) - Method in class org.forester.phylogenyinference.BasicCharacterStateMatrix
 
writeNexusTreesBlock(Writer, List<Phylogeny>) - Static method in class org.forester.io.writers.PhylogenyWriter
 
writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write a collection of NucleotideSequences to a file
writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write a collection of NucleotideSequences to a file
writePhylogenyToFile(Phylogeny, String) - Static method in class org.forester.surfacing.SurfacingUtil
 
writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write collection of protein sequences to a file
writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write collection of protein sequences to a stream
writeSequence(File, Sequence<?>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write a sequence to a file
writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Write a sequence to OutputStream
writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava3.core.sequence.io.FastaWriterHelper
Method which will write your given Sequences to the specified OutputStream.
writeTaxonomyLinks(Writer, String) - Static method in class org.forester.surfacing.SurfacingUtil
 

X

XML_SCHEMA_INSTANCE - Static variable in class org.forester.util.ForesterConstants
 
XmlElement - Class in org.forester.io.parsers.phyloxml
 
XmlElement(String, String, String, Attributes) - Constructor for class org.forester.io.parsers.phyloxml.XmlElement
 
XMLHelper - Class in org.biojava3.core.util
 
XMLHelper() - Constructor for class org.biojava3.core.util.XMLHelper
 
XMLUtil - Class in org.biojava.bio.structure.scop.server
Utility classes for the XML serialization and de-serialization of SCOP.
XMLUtil() - Constructor for class org.biojava.bio.structure.scop.server.XMLUtil
 
XMLWriter - Interface in org.biojava3.core.util
Simple interface for building XML documents.
XX_STR - Static variable in interface org.forester.go.GoXRef
 
xyMax - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 
xyStart - Variable in class org.biojava3.alignment.template.AbstractMatrixAligner
 

Y

Y - Static variable in class org.biojava3.aaproperties.Constraints
 

Z

zappo - Static variable in class org.biojava3.phylo.ResidueProperties
 
ZERO_DIFF - Static variable in class org.forester.util.ForesterUtil
 
zStrAlign(int, int, double, int) - Method in class org.biojava.bio.structure.align.ce.CECalculator
 
zStrAlign(int, int, double, int) - Method in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 
zThr - Static variable in class org.biojava.bio.structure.align.ce.CECalculator
 
zThr - Static variable in class org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
 

_

_fm_small - Variable in class org.forester.archaeopteryx.TreeFontSet
 
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