- C_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
-
- C_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
-
- calculateAnalyticalLogLikelihood(IntervalList) - Static method in class jebl.evolution.coalescent.Coalescent
-
Calculates the log likelihood of this set of coalescent intervals,
using an analytical integration over theta.
- calculateLogLikelihood() - Method in class jebl.evolution.coalescent.Coalescent
-
Calculates the log likelihood of this set of coalescent intervals,
given a demographic model.
- calculateLogLikelihood(IntervalList, DemographicFunction) - Static method in class jebl.evolution.coalescent.Coalescent
-
Calculates the log likelihood of this set of coalescent intervals,
given a demographic model.
- CalculateSplitRates - Class in jebl.evolution.trees
-
Created by IntelliJ IDEA.
- CalculateSplitRates(NexusImporter) - Constructor for class jebl.evolution.trees.CalculateSplitRates
-
- cancel() - Method in class jebl.util.BasicProgressListener
-
- Cancelable - Interface in jebl.util
-
Checks whether some operation has been cancelled; This will typically
be used as a callback because it can only query whether a task has
been cancelled, rather than cancel it (there is no cancel() method).
- CannotBuildDistanceMatrixException - Exception in jebl.evolution.distances
-
- CannotBuildDistanceMatrixException(String, String, String) - Constructor for exception jebl.evolution.distances.CannotBuildDistanceMatrixException
-
- CannotBuildDistanceMatrixException(String) - Constructor for exception jebl.evolution.distances.CannotBuildDistanceMatrixException
-
- CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.AminoAcids
-
- CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.Codons
-
- CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.Nucleotides
-
- CANONICAL_STATES - Static variable in class jebl.evolution.sequences.AminoAcids
-
Deprecated.
- CANONICAL_STATES - Static variable in class jebl.evolution.sequences.Codons
-
- CANONICAL_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
-
Deprecated.
- CanonicalSequence - Class in jebl.evolution.sequences
-
A default implementation of the Sequence interface
that converts sequence characters to
States such that calling getString() will always return
uppercase residues with nucleotide U residues converted to T
- CanonicalSequence(SequenceType, Taxon, CharSequence) - Constructor for class jebl.evolution.sequences.CanonicalSequence
-
Creates a sequence with a name corresponding to the taxon name.
- CanonicalSequence(SequenceType, Taxon, State[]) - Constructor for class jebl.evolution.sequences.CanonicalSequence
-
Creates a sequence with a name corresponding to the taxon name
- cardinality() - Method in class jebl.util.FixedBitSet
-
- CataclysmicDemographic - Class in jebl.evolution.coalescent
-
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
- CataclysmicDemographic() - Constructor for class jebl.evolution.coalescent.CataclysmicDemographic
-
Construct demographic model with default settings
- CataclysmicDemographic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.CataclysmicDemographic
-
Construct demographic model with given settings
- Character - Interface in jebl.evolution.characters
-
- CharacterType - Interface in jebl.evolution.characters
-
- charAt(int) - Method in class jebl.evolution.io.ByteBuilder
-
- CHEMICAL_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids
-
- choleskyFactor(double[][]) - Static method in class jebl.math.MatrixCalc
-
Cholesky factorization (aka Cholesky Decomposition)
This factorization can be used when square matrix is symmetric and positive definite.
- choleskySolve(double[][], double[]) - Static method in class jebl.math.MatrixCalc
-
Cholesky solve
Once the matrix is decomposed with the above routine, one can solve the triangular factor with backsubstitution.
- choose(double, double) - Static method in class jebl.math.Binomial
-
Binomial coefficient n choose k
- choose2(int) - Static method in class jebl.math.Binomial
-
get n choose 2
- CILIATE - Static variable in class jebl.evolution.sequences.GeneticCode
-
- CladeHeightMetric - Class in jebl.evolution.treemetrics
-
For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA.
- CladeHeightMetric() - Constructor for class jebl.evolution.treemetrics.CladeHeightMetric
-
- CladeHeightMetric(List<Taxon>) - Constructor for class jebl.evolution.treemetrics.CladeHeightMetric
-
- CladeSystem - Class in jebl.evolution.trees
-
Stores a set of unique clades for a tree
- CladeSystem() - Constructor for class jebl.evolution.trees.CladeSystem
-
- CladeSystem(RootedTree) - Constructor for class jebl.evolution.trees.CladeSystem
-
- cleanSequence(CharSequence, SequenceType) - Static method in class jebl.evolution.sequences.Utils
-
Produce a clean sequence filtered of spaces and digits.
- clear() - Method in class jebl.evolution.align.ProfileCharacter
-
- clear(int) - Method in class jebl.util.FixedBitSet
-
- clearAllProgress() - Method in class jebl.util.CompositeProgressListener
-
Clear all progress, including that of previous subtasks.
- clearLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
-
- closeReader() - Method in class jebl.evolution.io.ImportHelper
-
- CLUSTALW - Static variable in class jebl.evolution.align.scores.NucleotideScores
-
- ClusteringTreeBuilder<T extends Tree> - Class in jebl.evolution.trees
-
An abstract base class for clustering algorithms from pairwise distances
- Coalescent - Class in jebl.evolution.coalescent
-
A likelihood function for the coalescent.
- Coalescent(RootedTree, DemographicFunction) - Constructor for class jebl.evolution.coalescent.Coalescent
-
- Coalescent(IntervalList, DemographicFunction) - Constructor for class jebl.evolution.coalescent.Coalescent
-
- CoalescentIntervalGenerator - Class in jebl.evolution.treesimulation
-
This is a class that draws coalescent intervals under the given demographic function.
- CoalescentIntervalGenerator(DemographicFunction) - Constructor for class jebl.evolution.treesimulation.CoalescentIntervalGenerator
-
- CODON - Static variable in interface jebl.evolution.sequences.SequenceType
-
- Codons - Class in jebl.evolution.sequences
-
- Codons() - Constructor for class jebl.evolution.sequences.Codons
-
- CodonState - Class in jebl.evolution.sequences
-
As of 2007-07-30, instances of this class are only constructed for non-ambigous
nucleotide triplets - see
Codons.
- CompactRootedTree - Class in jebl.evolution.trees
-
A memory efficient rooted tree.
- CompactRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.CompactRootedTree
-
Do all the hard work.
- compareTo(Object) - Method in class jebl.evolution.alignments.ConsensusSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.AminoAcidState
-
- compareTo(Object) - Method in class jebl.evolution.sequences.BasicSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.CanonicalSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.FilteredSequence
-
- compareTo(Object) - Method in class jebl.evolution.sequences.NucleotideState
-
- compareTo(Object) - Method in class jebl.evolution.sequences.State
-
- compareTo(Object) - Method in class jebl.evolution.taxa.Taxon
-
- complement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
-
- complement(FixedBitSet) - Static method in class jebl.util.FixedBitSet
-
- complement() - Method in class jebl.util.FixedBitSet
-
- COMPLEMENTARY_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
-
Deprecated.
- CompositeProgressListener - Class in jebl.util
-
A
ProgressListener that is suitable for a task that consists of several subtasks.
- CompositeProgressListener(ProgressListener, double...) - Constructor for class jebl.util.CompositeProgressListener
-
construct a new composite ProgressListener.
- CompositeProgressListener(ProgressListener, int) - Constructor for class jebl.util.CompositeProgressListener
-
Construct a CompositeProgressListener with a number of evenly weighted subtasks.
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.CompactRootedTree
-
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.MutableRootedTree
-
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedSubtree
-
- conceptuallyUnrooted() - Method in interface jebl.evolution.trees.RootedTree
-
Due to current implementation limitations, trees store "branch" information in nodes.
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- consensus(boolean, boolean) - Static method in enum jebl.util.MaybeBoolean
-
- ConsensusSequence - Class in jebl.evolution.alignments
-
- ConsensusSequence(Taxon, Alignment) - Constructor for class jebl.evolution.alignments.ConsensusSequence
-
Creates a FilteredSequence wrapper to the given source sequence.
- ConsensusTreeBuilder<T extends Tree> - Class in jebl.evolution.trees
-
A
TreeBuilder that builds a consensus tree for a set of trees on identical leaf sets.
- ConsensusTreeBuilder.Method - Enum in jebl.evolution.trees
-
Supported consensus methods.
- ConstantPopulation - Class in jebl.evolution.coalescent
-
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
- ConstantPopulation() - Constructor for class jebl.evolution.coalescent.ConstantPopulation
-
Construct demographic model with default settings
- ConstantPopulation(double) - Constructor for class jebl.evolution.coalescent.ConstantPopulation
-
Construct demographic model with given settings
- ConstExponential - Class in jebl.evolution.coalescent
-
This class models exponential growth from an initial population size.
- ConstExponential() - Constructor for class jebl.evolution.coalescent.ConstExponential
-
Construct demographic model with default settings
- ConstExponential(double, double, double) - Constructor for class jebl.evolution.coalescent.ConstExponential
-
Construct demographic model with given settings
- ConstLogistic - Class in jebl.evolution.coalescent
-
This class models logistic growth from an initial population size.
- ConstLogistic() - Constructor for class jebl.evolution.coalescent.ConstLogistic
-
Construct demographic model with default settings
- ConstLogistic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.ConstLogistic
-
Construct demographic model with given settings
- constructConsensus(Alignment) - Static method in class jebl.evolution.alignments.ConsensusSequence
-
- contains(int) - Method in class jebl.util.FixedBitSet
-
- CONTINUOUS - Static variable in interface jebl.evolution.characters.CharacterType
-
- ContinuousCharacter - Class in jebl.evolution.characters
-
- ContinuousCharacter(String, String) - Constructor for class jebl.evolution.characters.ContinuousCharacter
-
Constructs a basic ContinuousCharacter object with no taxa added yet
- ContinuousCharacter(String, String, Set<Taxon>) - Constructor for class jebl.evolution.characters.ContinuousCharacter
-
Constructs a basic ContinuousCharacter object with taxa added
- copy(double[], double[]) - Static method in class jebl.math.MultivariateMinimum
-
Copy source vector into target vector
- copy(double[][], double[][]) - Static method in class jebl.util.Utils
-
Copies all of source into dest - assumes dest to be large enough
- copyIntervals(Intervals) - Method in class jebl.evolution.coalescent.Intervals
-
- copyMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
-
copy one matrix into another
- copyTree(RootedTree) - Static method in class jebl.evolution.trees.Utils
-
This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
- createExternalNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
-
Creates a new external node with the given taxon.
- createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Creates a new external node with the given taxon.
- createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
-
Creates a new external node with the given taxon.
- createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.MutableRootedTree
-
Once a SimpleRootedTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
- createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Once a SimpleRootedTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
- createInternalNode(List<Node>) - Method in class jebl.evolution.trees.SimpleTree
-
Once a SimpleTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
- createNodeDensityComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
-
- createNodeDensityMinNodeHeightComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
-
- createNodes(RootedTree, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Clones the entire tree structure from the given RootedTree.
- createNodes(Tree, Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Clones the entire tree structure from the given (unrooted) Tree.
- createNullMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that looses all output
- createOrderEnumerator(int) - Method in interface jebl.math.OrderEnumerator.OEFactory
-
For generating an ordering from 0..size-1.
- createSimpleMonitor(PrintWriter) - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a print stream
- createSplitMonitor(MinimiserMonitor, MinimiserMonitor) - Static method in class jebl.math.MinimiserMonitor.Utils
-
creates a monitor such that all information sent to monitor is based on two sub monitors
- createStringMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that Stores output (use toString() to access current results)
- createSystemErrorMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a System.err
- createSystemOuptutMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a System.out
- G_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
-
- G_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
-
- GammaFunction - Class in jebl.math
-
gamma function
- GammaFunction() - Constructor for class jebl.math.GammaFunction
-
- GAP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
-
- GAP_STATE - Static variable in class jebl.evolution.sequences.Codons
-
- GAP_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
-
- gapFraction() - Method in class jebl.evolution.align.ProfileCharacter
-
- GaplessSequence - Class in jebl.evolution.sequences
-
- GaplessSequence(Sequence) - Constructor for class jebl.evolution.sequences.GaplessSequence
-
- generateFactory(boolean) - Static method in class jebl.math.OrthogonalSearch
-
Generate a MultivariateMinimum.Factory for an OrthogonalSearch
- generateNewMinimiser() - Method in interface jebl.math.MultivariateMinimum.Factory
-
Generate a new Multivariate Minimum
- generateScores(String) - Static method in class jebl.evolution.align.scores.ScoresFactory
-
For any matrix.
- generateScores(String, int) - Static method in class jebl.evolution.align.scores.ScoresFactory
-
For Blosum and Pam matrices
- generateScores(String, float) - Static method in class jebl.evolution.align.scores.ScoresFactory
-
For calculated nucleotide matrices.
- GENETIC_CODES - Static variable in class jebl.evolution.sequences.GeneticCode
-
- GeneticCode - Class in jebl.evolution.sequences
-
A set of standard genetic codes.
- get(int, double) - Method in class jebl.evolution.trees.MostProbableTopology
-
Get the most probable tree(s)
- getAdjacencies(Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns a list of nodes connected to this node by an edge
- getAdjacencies(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getAdjacencies(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getAdjacencies(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleTree
-
- getAdjusted(OrderEnumerator, int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getAdjusted(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
-
- getAdjustedFactory(OrderEnumerator.OEFactory, int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getAlignments() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
The indices for these correspond to those for the getScoreMatrix() matrix.
- getAllTaxa() - Static method in class jebl.evolution.taxa.Taxon
-
- getAlphabet() - Method in class jebl.evolution.align.scores.AminoAcidScores
-
- getAlphabet() - Method in class jebl.evolution.align.scores.NucleotideScores
-
- getAlphabet() - Method in interface jebl.evolution.align.scores.ScoreMatrix
-
- getAlphabet() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
-
- getAlphabet(SequenceType) - Static method in class jebl.evolution.sequences.SequenceType.Utils
-
- getAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getArgmax(int[]) - Static method in class jebl.util.Utils
-
Find the maximum "argument".
- getArgmax(double[]) - Static method in class jebl.util.Utils
-
Find the maximum "argument" (of a double array).
- getArgument(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getArgument(int) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getArgument(int) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getArgument(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the value of the nth argument of this function.
- getArgument(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the value of the nth argument of this function.
- getArgument(int) - Method in class jebl.evolution.coalescent.Expansion
-
- getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getArgumentCount() - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getArgumentCount() - Method in class jebl.evolution.coalescent.ConstExponential
-
- getArgumentCount() - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getArgumentCount() - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the number of arguments for this function.
- getArgumentCount() - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the number of arguments for this function.
- getArgumentCount() - Method in class jebl.evolution.coalescent.Expansion
-
- getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getArgumentName(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the name of the nth argument of this function.
- getArgumentName(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the name of the nth argument of this function.
- getArgumentName(int) - Method in class jebl.evolution.coalescent.Expansion
-
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getAttribute(String) - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getAttribute(String) - Method in class jebl.evolution.sequences.BasicSequence
-
- getAttribute(String) - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getAttribute(String) - Method in class jebl.evolution.sequences.FilteredSequence
-
- getAttribute(String) - Method in class jebl.evolution.taxa.Taxon
-
- getAttribute(String) - Method in class jebl.evolution.trees.BaseEdge
-
- getAttribute(String) - Method in class jebl.evolution.trees.BaseNode
-
- getAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getAttribute(String) - Method in class jebl.evolution.trees.RootedSubtree
-
- getAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
-
- getAttribute(String) - Method in interface jebl.util.Attributable
-
- getAttribute(String) - Method in class jebl.util.AttributableHelper
-
- getAttributeMap() - Method in class jebl.evolution.sequences.BasicSequence
-
- getAttributeMap() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getAttributeMap() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getAttributeMap() - Method in class jebl.evolution.taxa.Taxon
-
- getAttributeMap() - Method in class jebl.evolution.trees.BaseEdge
-
- getAttributeMap() - Method in class jebl.evolution.trees.BaseNode
-
- getAttributeMap() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getAttributeMap() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getAttributeMap() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getAttributeMap() - Method in class jebl.evolution.trees.RootedSubtree
-
- getAttributeMap() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getAttributeMap() - Method in class jebl.evolution.trees.SimpleTree
-
- getAttributeMap() - Method in interface jebl.util.Attributable
-
Gets the entire attribute map.
- getAttributeMap() - Method in class jebl.util.AttributableHelper
-
- getAttributeNames() - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getAttributeNames() - Method in class jebl.evolution.sequences.BasicSequence
-
- getAttributeNames() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getAttributeNames() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getAttributeNames() - Method in class jebl.evolution.taxa.Taxon
-
- getAttributeNames() - Method in class jebl.evolution.trees.BaseEdge
-
- getAttributeNames() - Method in class jebl.evolution.trees.BaseNode
-
- getAttributeNames() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getAttributeNames() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getAttributeNames() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getAttributeNames() - Method in class jebl.evolution.trees.RootedSubtree
-
- getAttributeNames() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getAttributeNames() - Method in class jebl.evolution.trees.SimpleTree
-
- getAttributeNames() - Method in interface jebl.util.Attributable
-
- getAttributeNames() - Method in class jebl.util.AttributableHelper
-
- getAvailableAminoAcidScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
-
- getAvailableNucleotideScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
-
- getBiasAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getBiasAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.ClusteringTreeBuilder
-
A factory method to create a ClusteringTreeBuilder
- getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.TreeBuilderFactory
-
- getCanonicalStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
-
- getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Codons
-
- getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
-
- getCanonicalStateCount() - Method in interface jebl.evolution.sequences.SequenceType
-
Get number of canonical states
- getCanonicalStates() - Static method in class jebl.evolution.sequences.AminoAcids
-
- getCanonicalStates() - Static method in class jebl.evolution.sequences.Codons
-
- getCanonicalStates() - Static method in class jebl.evolution.sequences.Nucleotides
-
- getCanonicalStates() - Method in interface jebl.evolution.sequences.SequenceType
-
Get a list of canonical states ordered by their indices.
- getCanonicalStates() - Method in class jebl.evolution.sequences.State
-
- getCataclysmTime() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
- getChildren(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getChildren(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getChildren(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getChildren(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getChildren(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getChildren(Node) - Method in interface jebl.evolution.trees.RootedTree
-
- getChildren(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getChildren(Node) - Method in class jebl.evolution.trees.SortedRootedTree
-
- getClade(int) - Method in class jebl.evolution.trees.CladeSystem
-
- getCladeCount() - Method in class jebl.evolution.trees.CladeSystem
-
get number of unique clades
- getCladeFrequency(int) - Method in class jebl.evolution.trees.CladeSystem
-
get clade frequency
- getCladeString(int) - Method in class jebl.evolution.trees.CladeSystem
-
- getCleanString() - Method in class jebl.evolution.sequences.BasicSequence
-
- getCleanString() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getCoalescentEvents(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Returns the number coalescent events in an interval
- getCoalescentEvents(int) - Method in class jebl.evolution.coalescent.Intervals
-
- getCode() - Method in class jebl.evolution.sequences.State
-
Returns the 1 letter code for this state.
- getCodeLength() - Method in interface jebl.evolution.sequences.SequenceType
-
- getCodeTable() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns a length-64 string that for each nucleotide triplet contains the single-character
amino acid code (see
AminoAcids to which that triplet is translated in this genetic code.
- getCodonsForAminoAcid(AminoAcidState) - Method in class jebl.evolution.sequences.GeneticCode
-
- getColumn(double[][], int) - Static method in class jebl.math.MatrixCalc
-
takes a matrix and gets a column, then returns it as a vector
- getCombined(OrthogonalHints, int, OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
-
- getCommonAncestorNode(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
- getComplementaryState(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
-
- getConstant(int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getConstantFactory(int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getCopy(double[]) - Static method in class jebl.util.Utils
-
Clones an array of doubles
- getCopy(double[], int, int) - Static method in class jebl.util.Utils
-
Clones an array of doubles from index start (inclusive) to index end (exclusive)
- getCopy(double[], int) - Static method in class jebl.util.Utils
-
Clones an array of doubles from index start (inclusive) to end
- getCopy(byte[]) - Static method in class jebl.util.Utils
-
Clones an array of bytes
- getCopy(String[]) - Static method in class jebl.util.Utils
-
Clones an array of Strings
- getCopy(double[][]) - Static method in class jebl.util.Utils
-
Clones an array of doubles
- getCopy(int[][]) - Static method in class jebl.util.Utils
-
Clones a matrix of ints
- getCopy(double[][][]) - Static method in class jebl.util.Utils
-
Clones an array of doubles
- getCopy(byte[][]) - Static method in class jebl.util.Utils
-
Clones an array of bytes
- getCopy(boolean[][]) - Static method in class jebl.util.Utils
-
Clones an array of booleans
- getCopy(int[]) - Static method in class jebl.util.Utils
-
Clones an array of ints
- getCopy(int[], int) - Static method in class jebl.util.Utils
-
Clones an array of ints
- getDecimalPlaces() - Method in class jebl.util.NumberFormatter
-
Get the number of decimal places to display when formatted.
- getDeclineRate() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
returns the positive-valued decline rate
- getDefaultDistanceModel(List<Sequence>) - Static method in class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
-
- getDegree(Graph, Node) - Static method in class jebl.evolution.graphs.Graph.Utils
-
- getDegree() - Method in interface jebl.evolution.graphs.Node
-
Get the number of edges connected to this node.
- getDemographic(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
- getDemographic(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getDemographic(double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getDemographic(double) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getDemographic(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Gets the value of the demographic function N(t) at time t.
- getDemographic(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Gets the value of the demographic function N(t) at time t.
- getDemographic(double) - Method in class jebl.evolution.coalescent.Expansion
-
- getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getDemographic(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
Gets the value of the demographic function N(t) at time t.
- getDesc() - Method in interface jebl.evolution.characters.Character
-
return the description of the character
- getDesc() - Method in class jebl.evolution.characters.ContinuousCharacter
-
- getDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getDescendantTips(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Gets a set of tip nodes descended from the given node.
- getDescription() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the description of the genetic code
- getDimension() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- getDimension() - Method in class jebl.evolution.substmodel.MatrixExponential
-
- getDimension() - Method in interface jebl.evolution.substmodel.RateMatrix
-
- getDistance(int, int) - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets the distance at a particular row and column
- getDistance(Taxon, Taxon) - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets the distance between 2 taxa
- getDistance(int, int) - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets the distance at a particular row and column
- getDistance(Taxon, Taxon) - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets the distance between 2 taxa
- getDistances() - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets a 2-dimensional array containing the distances
- getDistances() - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets a 2-dimensional array containing the distances
- getEdge(Node, Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getEdge(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getEdge(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedSubtree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
-
Returns the Edge that connects these two nodes
- getEdgeLength(Node, Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns the length of the edge that connects these two nodes
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
-
- getEdges(Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns a list of edges connected to this node
- getEdges() - Method in interface jebl.evolution.graphs.Graph
-
- getEdges(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getEdges() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getEdges(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getEdges(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Returns a list of edges connected to this node
- getEdges() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getEdges(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
Returns a list of edges connected to this node
- getEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getEdges(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
Returns a list of edges connected to this node
- getEdges() - Method in class jebl.evolution.trees.RootedSubtree
-
- getEdges(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Returns a list of edges connected to this node
- getEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getEdges(Node) - Method in class jebl.evolution.trees.SimpleTree
-
Returns a list of edges connected to this node
- getEdges() - Method in class jebl.evolution.trees.SimpleTree
-
- getEquilibriumFrequencies() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- getEquilibriumFrequencies() - Method in interface jebl.evolution.substmodel.RateMatrix
-
- getEquilibriumFrequency(int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- getEquilibriumFrequency(int) - Method in interface jebl.evolution.substmodel.RateMatrix
-
- getEstimatedScores() - Method in class jebl.evolution.align.BartonSternberg
-
- getExternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getExternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getExternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.RootedSubtree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.SimpleTree
-
The set of external edges.
- getExternalEdges() - Method in interface jebl.evolution.trees.Tree
-
- getExternalNodeCount(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
Return the number of external nodes under this node.
- getExternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getExternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getExternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getExternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getExternalNodes() - Method in class jebl.evolution.trees.RootedSubtree
-
- getExternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getExternalNodes() - Method in class jebl.evolution.trees.SimpleTree
-
- getExternalNodes() - Method in interface jebl.evolution.trees.Tree
-
- getFormattedValue(double) - Method in class jebl.util.NumberFormatter
-
Returns a string containing the current value for this column with
appropriate formatting.
- getFractionCompleted() - Method in class jebl.util.BasicProgressListener
-
- getFullName() - Method in class jebl.evolution.sequences.State
-
A descriptive name for this state.
- getGaplessLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
-
Gets the site location index for this sequence excluding
any gaps.
- getGappedLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
-
Gets the site location index for this sequence that corresponds
to a location given excluding all gaps.
- getGapState() - Static method in class jebl.evolution.sequences.AminoAcids
-
- getGapState() - Static method in class jebl.evolution.sequences.Codons
-
- getGapState() - Static method in class jebl.evolution.sequences.Nucleotides
-
- getGapState() - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to a gap
- getGeneticCodes() - Static method in class jebl.evolution.sequences.GeneticCode
-
Returns an iterable that allows you to iterate over all the standard genetic codes
- getGeneticCodesArray() - Static method in class jebl.evolution.sequences.GeneticCode
-
- getGrowthRate() - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
returns growth rate.
- getHeight(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getHeight(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getHeight(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getHeight(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getHeight(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getHeight(Node) - Method in interface jebl.evolution.trees.RootedTree
-
- getHeight(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getHeight(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
-
- getImmutableProfileCharacter(char) - Static method in class jebl.evolution.align.ProfileCharacter
-
An immutable ProfileCharacter that uses less memory than a mutable profile character.
- getIndex() - Method in class jebl.evolution.sequences.State
-
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
Calculates the integral 1/N(x) dx between start and finish.
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getIntegral(double, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Calculates the integral 1/N(x) dx between start and finish
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.Expansion
-
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).
- getIntensity(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).
- getIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).
- getInternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getInternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getInternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.RootedSubtree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.SimpleTree
-
The set of internal edges.
- getInternalEdges() - Method in interface jebl.evolution.trees.Tree
-
- getInternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getInternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getInternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getInternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getInternalNodes() - Method in class jebl.evolution.trees.RootedSubtree
-
- getInternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getInternalNodes() - Method in class jebl.evolution.trees.SimpleTree
-
- getInternalNodes() - Method in interface jebl.evolution.trees.Tree
-
- getInternalParameterBoundaries(int, double[]) - Method in interface jebl.math.OrthogonalHints
-
A boundary is a value of a parameter for which values lower than the boundary and values
higher than the boundary are better treated as two separate functions (IE, they
are only piecewise connected), and minimisation should be performed over both ranges
individually (and then the true minimum taken as the minimuma of the ranges)
- getInternalParameterBoundaries(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
-
- getInterval(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Gets an interval.
- getInterval(int) - Method in class jebl.evolution.coalescent.Intervals
-
- getInterval(double, int, double) - Method in class jebl.evolution.treesimulation.CoalescentIntervalGenerator
-
Calculates the waiting time to the next coalescent for a given critical value
(an intensity).
- getInterval(double, int, double) - Method in interface jebl.evolution.treesimulation.IntervalGenerator
-
Calculates the waiting time to the next coalescent for a given critical value
(an intensity).
- getIntervalCount() - Method in interface jebl.evolution.coalescent.IntervalList
-
get number of intervals
- getIntervalCount() - Method in class jebl.evolution.coalescent.Intervals
-
- getIntervalType(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Returns the type of interval observed.
- getIntervalType(int) - Method in class jebl.evolution.coalescent.Intervals
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getInverseIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns value of inverse demographic intensity function
(returns time, needed for simulation of coalescent intervals).
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns value of inverse demographic intensity function
(returns time, needed for simulation of coalescent intervals).
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).
- getLabelCount() - Method in class jebl.evolution.trees.SplitSystem
-
get number of labels
- getLastDelimiter() - Method in class jebl.evolution.io.ImportHelper
-
- getLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
-
- getLength() - Method in class jebl.evolution.alignments.ConsensusSequence
-
Returns the length of the sequence
- getLength() - Method in interface jebl.evolution.alignments.Pattern
-
- getLength() - Method in interface jebl.evolution.graphs.Edge
-
- getLength() - Method in class jebl.evolution.sequences.BasicSequence
-
Returns the length of the sequence
- getLength() - Method in class jebl.evolution.sequences.CanonicalSequence
-
Returns the length of the sequence
- getLength() - Method in class jebl.evolution.sequences.FilteredSequence
-
Returns the length of the sequence
- getLength() - Method in interface jebl.evolution.sequences.Sequence
-
Get the length of the sequence
- getLength(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getLength(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getLength(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getLength(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getLength(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getLength(Node) - Method in interface jebl.evolution.trees.RootedTree
-
- getLength(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getLength(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
-
- getLineageCount(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Returns the number of uncoalesced lineages within this interval.
- getLineageCount(IntervalList, double) - Static method in class jebl.evolution.coalescent.IntervalList.Utils
-
- getLineageCount(int) - Method in class jebl.evolution.coalescent.Intervals
-
- getLineNumber() - Method in class jebl.evolution.io.ImportHelper
-
- getLowerBound(int) - Method in class jebl.evolution.coalescent.Coalescent
-
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getLowerBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the lower bound of the nth argument of this function.
- getLowerBound(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the lower bound of the nth argument of this function.
- getLowerBound(int) - Method in class jebl.evolution.coalescent.Expansion
-
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getLowerBound(int) - Method in interface jebl.math.MultivariateFunction
-
get lower bound of argument n
- getLowerBound() - Method in class jebl.math.OrthogonalLineFunction
-
- getLowerBound() - Method in interface jebl.math.UnivariateFunction
-
get lower bound of argument
- getMatch() - Method in class jebl.evolution.align.Align
-
- getMatch() - Method in class jebl.evolution.align.NeedlemanWunschAffine
-
- getMatch(char[], char[]) - Method in class jebl.evolution.align.NeedlemanWunschAffine
-
- getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
-
- getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
-
- getMatch() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
- getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
-
- getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
-
- getMatchScores(int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
- getMatrixString() - Method in class jebl.evolution.align.scores.Scores
-
- getMax() - Method in class jebl.evolution.align.SequenceShuffler
-
- getMax(double[]) - Static method in class jebl.util.Utils
-
Calculate the max of an array
- getMax(double[], int, int) - Static method in class jebl.util.Utils
-
Calculate the max of an array
- getMaxTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
- getMean() - Method in class jebl.evolution.align.SequenceShuffler
-
- getMean(double[]) - Static method in class jebl.util.Utils
-
Calculate the mean value of an array
- getMemoryRequiredForAlignment(int) - Static method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
-
- getMessage() - Method in class jebl.util.BasicProgressListener
-
- getMetaComments() - Method in class jebl.evolution.io.ImportHelper
-
This method has been introduced because this class previously skipped over consecutive comments and discarded all
but the last.
- getMethodDescription() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
-
Returns a human readable name of this consensus tree building method
- getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.BilleraMetric
-
- getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.CladeHeightMetric
-
- getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.RobinsonsFouldMetric
-
- getMetric(RootedTree, RootedTree) - Method in interface jebl.evolution.treemetrics.RootedTreeMetric
-
calculates the metric between two rooted trees
- getMin() - Method in class jebl.evolution.align.SequenceShuffler
-
- getMin(double[]) - Static method in class jebl.util.Utils
-
Calculate the min of an array
- getMinNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
- getMinTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
- getMostFrequentState() - Method in interface jebl.evolution.alignments.Pattern
-
Returns the most frequent state in this pattern
- getN0() - Method in class jebl.evolution.coalescent.ConstantPopulation
-
returns initial population size.
- getN1() - Method in class jebl.evolution.coalescent.ConstExponential
-
- getN1() - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getN1() - Method in class jebl.evolution.coalescent.Expansion
-
- getName() - Method in class jebl.evolution.align.scores.AminoAcidScores
-
- getName() - Method in class jebl.evolution.align.scores.Blosum45
-
- getName() - Method in class jebl.evolution.align.scores.Blosum50
-
- getName() - Method in class jebl.evolution.align.scores.NucleotideScores
-
- getName() - Method in interface jebl.evolution.align.scores.ScoreMatrix
-
- getName() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
-
- getName() - Method in interface jebl.evolution.characters.Character
-
return the name of the character
- getName() - Method in interface jebl.evolution.characters.CharacterType
-
- getName() - Method in class jebl.evolution.characters.ContinuousCharacter
-
- getName() - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getName() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the name of the genetic code
- getName() - Method in class jebl.evolution.sequences.Nucleotides
-
- getName() - Method in interface jebl.evolution.sequences.SequenceType
-
name of data type
- getName() - Method in class jebl.evolution.sequences.State
-
- getName() - Method in class jebl.evolution.sequences.StateClassification.Default
-
- getName() - Method in interface jebl.evolution.sequences.StateClassification
-
- getName() - Method in class jebl.evolution.taxa.Taxon
-
get the name of the taxon
- getName() - Method in class jebl.evolution.taxa.TaxonomicLevel
-
get the name of the taxonomic level
- getName() - Method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
-
- getName() - Method in enum jebl.evolution.trees.TreeBuilderFactory.Method
-
- getNcbiTranslationTableNumber() - Method in class jebl.evolution.sequences.GeneticCode
-
- getNext() - Method in interface jebl.math.OrderEnumerator
-
The next value in the enumeration
- getNextBlockName() - Method in class jebl.evolution.io.NexusImporter
-
- getNexusDataType() - Method in interface jebl.evolution.sequences.SequenceType
-
- getNode(Taxon) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getNode(Taxon) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getNode(Taxon) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getNode(Taxon) - Method in class jebl.evolution.trees.RootedSubtree
-
- getNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
-
- getNode(Taxon) - Method in interface jebl.evolution.trees.Tree
-
- getNodes(Edge) - Method in interface jebl.evolution.graphs.Graph
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes() - Method in interface jebl.evolution.graphs.Graph
-
- getNodes(int) - Method in interface jebl.evolution.graphs.Graph
-
- getNodes(Edge) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getNodes() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getNodes(int) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getNodes(Edge) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getNodes(int) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getNodes(Edge) - Method in class jebl.evolution.trees.MutableRootedTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getNodes(int) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getNodes(Edge) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getNodes(int) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getNodes(Edge) - Method in class jebl.evolution.trees.RootedSubtree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes() - Method in class jebl.evolution.trees.RootedSubtree
-
- getNodes(int) - Method in class jebl.evolution.trees.RootedSubtree
-
- getNodes(Edge) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getNodes(int) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getNodes(Edge) - Method in class jebl.evolution.trees.SimpleTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes() - Method in class jebl.evolution.trees.SimpleTree
-
- getNodes(int) - Method in class jebl.evolution.trees.SimpleTree
-
- getNodes(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
All nodes in subtree - parents before children (pre - order).
- getNormalized(double[]) - Static method in class jebl.math.Random
-
- getNull() - Static method in class jebl.math.OrthogonalHints.Utils
-
- getNumArguments() - Method in class jebl.evolution.coalescent.Coalescent
-
- getNumArguments() - Method in interface jebl.math.MultivariateFunction
-
get number of arguments
- getNumOfStates() - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getOrdered(int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getOrderedFactory() - Static method in class jebl.math.OrderEnumerator.Utils
-
- getOriginalFrequencies(double[]) - Static method in class jebl.evolution.substmodel.WAG
-
get the frequencies of the original data set that
formed the basis for the estimation of the rate matrix
- getOriginalFrequencies() - Static method in class jebl.evolution.substmodel.WAG
-
- getOrthogonalHints() - Method in class jebl.evolution.coalescent.Coalescent
-
- getOrthogonalHints() - Method in interface jebl.math.MultivariateFunction
-
- getParent(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getParent(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getParent(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getParent(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getParent(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getParent(Node) - Method in interface jebl.evolution.trees.RootedTree
-
- getParent(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getParentEdge(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getParentEdge(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getParentEdge(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getParentEdge(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getPathLength(Tree, Node, Node) - Static method in class jebl.evolution.trees.Utils
-
- getPatternCount() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getPatternCount() - Method in interface jebl.evolution.alignments.Patterns
-
- getPatternCount() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getPatternLength() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getPatternLength() - Method in interface jebl.evolution.alignments.Patterns
-
- getPatternLength() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getPatterns() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getPatterns() - Method in interface jebl.evolution.alignments.Patterns
-
Get a list of all the patterns
- getPatterns() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getProgress() - Method in class jebl.evolution.io.ImportHelper
-
- getR2() - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getRelativeRates() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- getRelativeRates() - Method in interface jebl.evolution.substmodel.RateMatrix
-
- getRestricted(OrderEnumerator, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getRestrictedFactory(OrderEnumerator.OEFactory, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getRootNode() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getRootNode() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getRootNode() - Method in class jebl.evolution.trees.MutableRootedTree
-
The root of the tree has the largest node height of
all nodes in the tree.
- getRootNode() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getRootNode() - Method in class jebl.evolution.trees.RootedSubtree
-
The root of the tree has the largest node height of
all nodes in the tree.
- getRootNode() - Method in interface jebl.evolution.trees.RootedTree
-
The root of the tree has the largest node height of
all nodes in the tree.
- getRootNode() - Method in class jebl.evolution.trees.SimpleRootedTree
-
The root of the tree has the largest node height of
all nodes in the tree.
- getRootProgressListener() - Method in class jebl.util.CompositeProgressListener
-
- getSampleCount() - Method in interface jebl.evolution.coalescent.IntervalList
-
get the total number of sampling events.
- getSampleCount() - Method in class jebl.evolution.coalescent.Intervals
-
- getScore() - Method in class jebl.evolution.align.Align
-
- getScore() - Method in class jebl.evolution.align.BartonSternberg
-
- getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
-
- getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
-
- getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
-
- getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
-
- getScore(Sequence, Sequence) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
-
- getScore() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
- getScore(Sequence, Sequence) - Method in interface jebl.evolution.align.PairwiseAligner
-
- getScore(char, char) - Method in interface jebl.evolution.align.scores.ScoreMatrix
-
- getScore(char, char) - Method in class jebl.evolution.align.scores.Scores
-
- getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
-
- getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
-
- getScore(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
-
- getScore(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
-
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
- getScores() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
The indices for these correspond to those for the getAlignments() matrix.
- getSE(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
-
- getSelectedNodes() - Method in class jebl.evolution.trees.TreeSelectionChangeEvent
-
- getSequence(Taxon) - Method in class jebl.evolution.alignments.BasicAlignment
-
- getSequence(Taxon) - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getSequence(Taxon) - Method in interface jebl.evolution.sequences.Sequences
-
- getSequenceCharacters() - Method in class jebl.evolution.sequences.BasicSequence
-
Get the sequence characters representing the sequence.
- getSequenceList() - Method in interface jebl.evolution.alignments.Alignment
-
- getSequenceList() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getSequenceList() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getSequences() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getSequences() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getSequences() - Method in interface jebl.evolution.sequences.Sequences
-
- getSequenceType() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getSequenceType() - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getSequenceType() - Method in interface jebl.evolution.alignments.Pattern
-
- getSequenceType() - Method in interface jebl.evolution.alignments.Patterns
-
- getSequenceType() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getSequenceType() - Method in class jebl.evolution.sequences.BasicSequence
-
- getSequenceType() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getSequenceType() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getSequenceType() - Method in interface jebl.evolution.sequences.Sequence
-
- getSequenceType() - Method in class jebl.evolution.sequences.TranslatedSequence
-
- getSequenceType() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- getSequenceType() - Method in interface jebl.evolution.substmodel.RateMatrix
-
Get the data type of this rate matrix
- getSetName(State) - Method in class jebl.evolution.sequences.StateClassification.Default
-
- getSetName(State) - Method in interface jebl.evolution.sequences.StateClassification
-
- getSetNames() - Method in class jebl.evolution.sequences.StateClassification.Default
-
- getSetNames() - Method in interface jebl.evolution.sequences.StateClassification
-
- getShape() - Method in class jebl.evolution.coalescent.LogisticGrowth
-
- getShuffled(int) - Static method in class jebl.math.OrderEnumerator.Utils
-
- getShuffledFactory() - Static method in class jebl.math.OrderEnumerator.Utils
-
- getSignificantFigures() - Method in class jebl.util.NumberFormatter
-
Get the number of significant figures to display when formatted.
- getSiteCount() - Method in interface jebl.evolution.alignments.Alignment
-
- getSiteCount() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getSiteCount() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getSiteScores(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
-
Calculates the minimum number of siteScores for the parsimony reconstruction of a
a set of character patterns on a tree.
- getSiteScores(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
-
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
- getSize() - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets the size of the matrix (which is square), i.e., number of rows or columns.
- getSize() - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets the size of the matrix (which is square), i.e., number of rows or columns.
- getSource() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getSplit(int) - Method in class jebl.evolution.trees.SplitSystem
-
get split
- getSplit(List<Taxon>, Tree, Edge, boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
-
get split for branch associated with internal node
- getSplitCount() - Method in class jebl.evolution.trees.SplitSystem
-
get number of splits
- getSplits(Tree) - Static method in class jebl.evolution.trees.SplitUtils
-
creates a split system from a tree
(using tree-induced order of sequences)
- getSplits(List<Taxon>, Tree) - Static method in class jebl.evolution.trees.SplitUtils
-
creates a split system from a tree
(using a pre-specified order of sequences)
- getSplitVector() - Method in class jebl.evolution.trees.SplitSystem
-
get split vector
- getStartCodons() - Method in class jebl.evolution.sequences.GeneticCode
-
- getState(int) - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getState(int) - Method in interface jebl.evolution.alignments.Pattern
-
Get the state for the ith taxon
- getState(char) - Static method in class jebl.evolution.sequences.AminoAcids
-
- getState(String) - Static method in class jebl.evolution.sequences.AminoAcids
-
- getState(int) - Static method in class jebl.evolution.sequences.AminoAcids
-
- getState(int) - Method in class jebl.evolution.sequences.BasicSequence
-
- getState(int) - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getState(NucleotideState, NucleotideState, NucleotideState) - Static method in class jebl.evolution.sequences.Codons
-
- getState(String) - Static method in class jebl.evolution.sequences.Codons
-
Gets the state object for the given code.
- getState(int) - Static method in class jebl.evolution.sequences.Codons
-
- getState(int) - Method in class jebl.evolution.sequences.FilteredSequence
-
- getState(char) - Static method in class jebl.evolution.sequences.Nucleotides
-
- getState(String) - Static method in class jebl.evolution.sequences.Nucleotides
-
- getState(int) - Static method in class jebl.evolution.sequences.Nucleotides
-
- getState(int) - Method in interface jebl.evolution.sequences.Sequence
-
- getState(String) - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to a string code
- getState(char) - Method in interface jebl.evolution.sequences.SequenceType
-
Get state whose code is the one-character string consisting only of code.
- getState(int) - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to a state index
- getStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
-
- getStateCount() - Static method in class jebl.evolution.sequences.Codons
-
- getStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
-
- getStateCount() - Method in interface jebl.evolution.sequences.SequenceType
-
Get number of states including ambiguous states
- getStateDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getStateDesc(int) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getStateFrequency(State) - Method in interface jebl.evolution.alignments.Pattern
-
Returns the frequent of the given state in this pattern
- getStateIndices() - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getStateIndices() - Method in class jebl.evolution.sequences.BasicSequence
-
- getStateIndices() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getStateIndices() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getStateIndices() - Method in interface jebl.evolution.sequences.Sequence
-
- getStateIndices(State[]) - Static method in class jebl.evolution.sequences.Utils
-
- getStates() - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getStates() - Method in interface jebl.evolution.alignments.Pattern
-
- getStates(Tree, Node) - Method in class jebl.evolution.parsimony.FitchParsimony
-
Returns the reconstructed character states for a given node in the tree.
- getStates(Tree, Node) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
-
Returns the reconstructed character states for a given node in the tree.
- getStates() - Static method in class jebl.evolution.sequences.AminoAcids
-
- getStates() - Method in class jebl.evolution.sequences.BasicSequence
-
- getStates() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getStates() - Static method in class jebl.evolution.sequences.Codons
-
- getStates() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getStates() - Static method in class jebl.evolution.sequences.Nucleotides
-
- getStates() - Method in interface jebl.evolution.sequences.Sequence
-
- getStates() - Method in interface jebl.evolution.sequences.SequenceType
-
Get a list of states ordered by their indices.
- getStateSet() - Method in interface jebl.evolution.alignments.Pattern
-
- getStateSet(String) - Method in class jebl.evolution.sequences.StateClassification.Default
-
- getStateSet(String) - Method in interface jebl.evolution.sequences.StateClassification
-
- getStdev() - Method in class jebl.evolution.align.SequenceShuffler
-
- getStopCodonCount() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the number of terminator amino acids.
- getStopCodons() - Method in class jebl.evolution.sequences.GeneticCode
-
- getString() - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getString() - Method in class jebl.evolution.sequences.BasicSequence
-
- getString() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getString() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getString() - Method in interface jebl.evolution.sequences.Sequence
-
- getSubmatrix(Collection<Taxon>) - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets a sub-matrix for only those taxa in the collection (all
of which should be present in this matrix).
- getSubmatrix(Collection<Taxon>) - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets a sub-matrix for only those taxa in the collection (all
of which should be present in this matrix).
- getSuggestedOrdering(OrderEnumerator) - Method in interface jebl.math.OrthogonalHints
-
If there is a "best" ordering to use it can be specified here,
if not should return null
- getSum(double[]) - Static method in class jebl.util.Utils
-
Calculate the total of an array
- getSupportAttributeName() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
-
- getTaxa() - Method in class jebl.evolution.alignments.BasicAlignment
-
- getTaxa() - Method in interface jebl.evolution.alignments.Pattern
-
- getTaxa() - Method in interface jebl.evolution.alignments.Patterns
-
- getTaxa() - Method in class jebl.evolution.alignments.ResampledAlignment
-
- getTaxa() - Method in interface jebl.evolution.characters.Character
-
get a Set of all the taxa for this character
- getTaxa() - Method in class jebl.evolution.characters.ContinuousCharacter
-
- getTaxa() - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getTaxa() - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
- getTaxa() - Method in interface jebl.evolution.distances.DistanceMatrix
-
- getTaxa() - Method in class jebl.evolution.trees.CompactRootedTree
-
- getTaxa() - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getTaxa() - Method in class jebl.evolution.trees.MutableRootedTree
-
- getTaxa() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getTaxa() - Method in class jebl.evolution.trees.RootedSubtree
-
- getTaxa() - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getTaxa() - Method in class jebl.evolution.trees.SimpleTree
-
- getTaxa() - Method in class jebl.evolution.trees.SplitSystem
-
get taxon list
- getTaxa() - Method in interface jebl.evolution.trees.Tree
-
- getTaxon() - Method in class jebl.evolution.alignments.ConsensusSequence
-
- getTaxon() - Method in class jebl.evolution.sequences.BasicSequence
-
- getTaxon() - Method in class jebl.evolution.sequences.CanonicalSequence
-
- getTaxon() - Method in class jebl.evolution.sequences.FilteredSequence
-
- getTaxon() - Method in interface jebl.evolution.sequences.Sequence
-
- getTaxon(String) - Static method in class jebl.evolution.taxa.Taxon
-
A static method that returns a Taxon object with the given name.
- getTaxon(Node) - Method in class jebl.evolution.trees.CompactRootedTree
-
- getTaxon(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- getTaxon(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
- getTaxon(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- getTaxon(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
- getTaxon(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- getTaxon(Node) - Method in class jebl.evolution.trees.SimpleTree
-
- getTaxon(Node) - Method in interface jebl.evolution.trees.Tree
-
- getTaxonomicLevel() - Method in class jebl.evolution.taxa.Taxon
-
get the taxonomic level of the taxon
- getTaxonomicLevel(String) - Static method in class jebl.evolution.taxa.TaxonomicLevel
-
A static method that returns a TaxonomicLevel object with the given name.
- getTaxonomicLevels() - Static method in class jebl.evolution.taxa.TaxonomicLevel
-
Returns a Set containing all the currently created taxonomic levels.
- getTestSequence1() - Static method in class jebl.evolution.sequences.SequenceTester
-
- getTestSequence1(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
-
- getTestSequence2() - Static method in class jebl.evolution.sequences.SequenceTester
-
- getTestSequence2(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
-
- getThreeLetterName() - Method in class jebl.evolution.sequences.AminoAcidState
-
- getTime() - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getTipCount(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Return the number of leaves under this node.
- getTipsForTaxa(RootedTree, Collection<Taxon>) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Gets a set of external nodes that correspond to the given taxa.
- getTotal(double[], int, int) - Static method in class jebl.math.Random
-
- getTotal(double[]) - Static method in class jebl.math.Random
-
- getTotalDuration() - Method in interface jebl.evolution.coalescent.IntervalList
-
get the total duration of these intervals.
- getTotalDuration() - Method in class jebl.evolution.coalescent.Intervals
-
- getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
A utility method for speed, transfers trans prob information quickly
into store
- getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.MatrixExponential
-
A utility method for speed, transfers trans prob information quickly
into store
- getTransitionProbabilities(double[][]) - Method in interface jebl.evolution.substmodel.RateMatrix
-
A utility method for speed, transfers trans prob information quickly
into store.
- getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.MatrixExponential
-
- getTransitionProbability(int, int) - Method in interface jebl.evolution.substmodel.RateMatrix
-
- getTranslation(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the state associated with AminoAcid represented by codonState.
- getTranslation(NucleotideState, NucleotideState, NucleotideState) - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the state associated with AminoAcid represented by the three nucleotides.
- getTranslation(String) - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the state associated with AminoAcid represented by the three nucleotides.
- getTree() - Method in class jebl.evolution.trees.TreeChangeEvent
-
- getTripletCode(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
-
- getType() - Method in interface jebl.evolution.characters.Character
-
return the CharacterType of the character
- getType() - Method in class jebl.evolution.characters.ContinuousCharacter
-
- getType() - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getUniqueName() - Method in interface jebl.evolution.substmodel.RateMatrix
-
- getUniqueName() - Method in class jebl.evolution.substmodel.WAG
-
- getUnknownState() - Static method in class jebl.evolution.sequences.AminoAcids
-
- getUnknownState() - Static method in class jebl.evolution.sequences.Codons
-
- getUnknownState() - Static method in class jebl.evolution.sequences.Nucleotides
-
- getUnknownState() - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to an unknown
- getUpperBound(int) - Method in class jebl.evolution.coalescent.Coalescent
-
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
-
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- getUpperBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the upper bound of the nth argument of this function.
- getUpperBound(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the upper bound of the nth argument of this function.
- getUpperBound(int) - Method in class jebl.evolution.coalescent.Expansion
-
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- getUpperBound(int) - Method in interface jebl.math.MultivariateFunction
-
get upper bound of argument n
- getUpperBound() - Method in class jebl.math.OrthogonalLineFunction
-
- getUpperBound() - Method in interface jebl.math.UnivariateFunction
-
get upper bound of argument
- getV() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
-
- getValue(Taxon) - Method in interface jebl.evolution.characters.Character
-
get a value for a taxon containing the character
- getValue(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
-
- getValue(Taxon) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- getWeight() - Method in interface jebl.evolution.alignments.Pattern
-
Get the weight of this pattern
- getX() - Method in class jebl.evolution.align.Traceback
-
- getY() - Method in class jebl.evolution.align.Traceback
-
- getZero() - Static method in class jebl.math.OrderEnumerator.Utils
-
- getZeroFactory() - Static method in class jebl.math.OrderEnumerator.Utils
-
- gradient(MultivariateFunction, double[]) - Static method in class jebl.math.NumericalDerivative
-
determine gradient
- gradient(MultivariateFunction, double[], double[]) - Static method in class jebl.math.NumericalDerivative
-
determine gradient
- Graph - Interface in jebl.evolution.graphs
-
- Graph.NoEdgeException - Exception in jebl.evolution.graphs
-
This class is thrown by getEdgeLength(node1, node2) if node1 and node2
are not directly connected by an edge.
- Graph.NoEdgeException() - Constructor for exception jebl.evolution.graphs.Graph.NoEdgeException
-
- Graph.Utils - Class in jebl.evolution.graphs
-
- guessSequenceType(CharSequence) - Static method in class jebl.evolution.sequences.Utils
-
Guess type of sequence from contents.
- S_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
-
- S_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
-
- safeNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
- same(double, double) - Static method in class jebl.math.MachineAccuracy
-
- scale(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- score - Variable in class jebl.evolution.align.PairwiseAligner.Result
-
- score(ProfileCharacter, ProfileCharacter, Scores) - Static method in class jebl.evolution.align.ProfileCharacter
-
- score - Variable in class jebl.evolution.align.scores.Scores
-
- ScoreMatrix - Interface in jebl.evolution.align.scores
-
- Scores - Class in jebl.evolution.align.scores
-
Base class for all score matrices in the package.
- Scores() - Constructor for class jebl.evolution.align.scores.Scores
-
- scoreSelf(ProfileCharacter, Scores) - Static method in class jebl.evolution.align.ProfileCharacter
-
- ScoresFactory - Class in jebl.evolution.align.scores
-
- ScoresFactory() - Constructor for class jebl.evolution.align.scores.ScoresFactory
-
- second - Variable in class jebl.util.HashPair
-
- secondDerivative(UnivariateFunction, double) - Static method in class jebl.math.NumericalDerivative
-
determine second derivative
- selectArgument(int) - Method in class jebl.math.OrthogonalLineFunction
-
use only the specified argument in the
constructed univariate function
and keep all others constant
- selectionChanged(TreeSelectionChangeEvent) - Method in class jebl.evolution.trees.TreeChangeListener
-
The selected nodes in the tree have changed.
- Sequence - Interface in jebl.evolution.sequences
-
A biomolecular sequence.
- SequenceAlignmentsDistanceMatrix - Class in jebl.evolution.align
-
Builds a distance matrix by performing a series of pairwise alignments between the
specified sequences (unlike the methods in jebl.evolution.distances, which
extract the pairwise distances from a multiple sequence alignment).
- SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener) - Constructor for class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
-
- SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener, TreeBuilderFactory.DistanceModel) - Constructor for class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
-
- SequenceExporter - Interface in jebl.evolution.io
-
- SequenceImporter - Interface in jebl.evolution.io
-
Interface for importers that do sequences
- Sequences - Interface in jebl.evolution.sequences
-
A set of sequence objects.
- SequenceShuffler - Class in jebl.evolution.align
-
Shuffles a sequence and aligns it again multiple times to give mean and variance of
alignments on random sequences.
- SequenceShuffler() - Constructor for class jebl.evolution.align.SequenceShuffler
-
- SequenceStateException - Exception in jebl.evolution.sequences
-
- SequenceStateException(String) - Constructor for exception jebl.evolution.sequences.SequenceStateException
-
- SequenceTester - Class in jebl.evolution.sequences
-
- SequenceTester() - Constructor for class jebl.evolution.sequences.SequenceTester
-
- SequenceType - Interface in jebl.evolution.sequences
-
Interface for sequences data types.
- SequenceType.Utils - Class in jebl.evolution.sequences
-
- set(int) - Method in class jebl.util.FixedBitSet
-
- setAllArguments(double[]) - Method in class jebl.math.OrthogonalLineFunction
-
set (change) values of all arguments (start values)
- setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
- setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- setArgument(int, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Sets the value of the nth argument of this function.
- setArgument(int, double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Sets the value of the nth argument of this function.
- setArgument(int, double) - Method in class jebl.evolution.coalescent.Expansion
-
- setArgument(int, double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
- setArgument(int, double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- setArgument(double) - Method in class jebl.math.OrthogonalLineFunction
-
set (change) value of a single argument
(the one currently active)
- setAttribute(String, Object) - Method in class jebl.evolution.alignments.ConsensusSequence
-
- setAttribute(String, Object) - Method in class jebl.evolution.sequences.BasicSequence
-
- setAttribute(String, Object) - Method in class jebl.evolution.sequences.CanonicalSequence
-
- setAttribute(String, Object) - Method in class jebl.evolution.sequences.FilteredSequence
-
- setAttribute(String, Object) - Method in class jebl.evolution.taxa.Taxon
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.BaseEdge
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.BaseNode
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.FilteredRootedTree
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.MutableRootedTree
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedSubtree
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleTree
-
- setAttribute(String, Object) - Method in interface jebl.util.Attributable
-
Sets an named attribute for this object.
- setAttribute(String, Object) - Method in class jebl.util.AttributableHelper
-
- setCataclysmTime(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
- setCommentDelimiters(char) - Method in class jebl.evolution.io.ImportHelper
-
- setCommentDelimiters(char, char) - Method in class jebl.evolution.io.ImportHelper
-
- setCommentDelimiters(char, char, char) - Method in class jebl.evolution.io.ImportHelper
-
- setCommentDelimiters(char, char, char, char, char) - Method in class jebl.evolution.io.ImportHelper
-
- setCommentWriter(Writer) - Method in class jebl.evolution.io.ImportHelper
-
- setComplete() - Method in class jebl.util.CompositeProgressListener
-
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.CompactRootedTree
-
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.MutableRootedTree
-
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.RootedSubtree
-
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- setDebug(boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
-
- setDecimalPlaces(int) - Method in class jebl.util.NumberFormatter
-
Set the number of decimal places to display when formatted.
- setDeclineRate(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
sets the decline rate.
- setDesc(String) - Method in interface jebl.evolution.characters.Character
-
set the description of the character
- setDesc(String) - Method in class jebl.evolution.characters.ContinuousCharacter
-
- setDesc(String) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- setDistance(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
Sets the distance (such as time/branch length) used when calculating
the probabilities.
- setDistance(double) - Method in class jebl.evolution.substmodel.MatrixExponential
-
compute transition probabilities for a expected distance
using the prespecified rate matrix
- setDistance(double) - Method in interface jebl.evolution.substmodel.RateMatrix
-
Sets the distance (such as time/branch length) used when calculating
the probabilities.
- setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
Sets the distance (such as time/branch length) used when calculating
the probabilities.
- setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.MatrixExponential
-
compute transition probabilities for a expected distance
using the prespecified rate matrix.
- setDoublingTime(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
An alternative parameterization of this model.
- setEdgeLength(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
-
Set edge distance between two adjacent nodes.
- setEdgeLength(Edge, double) - Method in class jebl.evolution.trees.SimpleTree
-
Change length of an existing edge.
- setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
-
- setGapOpen(float) - Method in class jebl.evolution.align.Align
-
- setGrowthRate(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
sets growth rate.
- setHeight(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
-
- setHeight(Node, double) - Method in class jebl.evolution.trees.RootedSubtree
-
- setHeight(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- setIgnoreNonMinimalUnivariateMinimisations(boolean) - Method in class jebl.math.OrthogonalSearch
-
Should we ignore new minisations that are not as minimal as the current one?
- setIllegalCharacterPolicy(IllegalCharacterPolicy) - Method in class jebl.evolution.io.FastaImporter
-
- setImage(Image) - Method in class jebl.util.ProgressListener
-
Set an image associated with the current progress.
- setInclusion(FixedBitSet) - Method in class jebl.util.FixedBitSet
-
- setIndeterminateProgress() - Method in class jebl.util.ProgressListener
-
Sets indefinite progress (i.e.
- setIsOrdered(boolean) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- setLength(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
-
- setLength(Node, double) - Method in class jebl.evolution.trees.RootedSubtree
-
- setLength(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- setMatrix(RateMatrix) - Method in class jebl.evolution.substmodel.MatrixExponential
-
update rate matrix used in present module
- setMessage(String) - Method in class jebl.util.ProgressListener
-
Set visible user message.
- setMinus(FixedBitSet) - Method in class jebl.util.FixedBitSet
-
- setN0(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
sets initial population size.
- setN1(double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- setN1(double) - Method in class jebl.evolution.coalescent.ConstLogistic
-
- setN1(double) - Method in class jebl.evolution.coalescent.Expansion
-
- setName(String) - Method in interface jebl.evolution.characters.Character
-
set the name of the character
- setName(String) - Method in class jebl.evolution.characters.ContinuousCharacter
-
- setName(String) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- setNumOfStates(int) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- setParametersNoScale(double[]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
- setProgress(double) - Method in class jebl.util.ProgressListener
-
- setProgress(int, int) - Method in class jebl.util.ProgressListener
-
- setProgress(long, long) - Method in class jebl.util.ProgressListener
-
- setProgressMonitor(ProgressMonitor) - Method in class jebl.evolution.align.SequenceShuffler
-
- setProportion(double) - Method in class jebl.evolution.coalescent.ConstExponential
-
- setProportion(double) - Method in class jebl.evolution.coalescent.Expansion
-
- setR2(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- setScores(Scores) - Method in class jebl.evolution.align.Align
-
- setSeed(long) - Static method in class jebl.math.Random
-
Access a default instance of this class, access is synchronized
- setShape(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
- setSignificantFigures(int) - Method in class jebl.util.NumberFormatter
-
Set the number of significant figures to display when formatted.
- setSpikeFactor(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
An alternative parameterization of this model.
- setStateDesc(Map<Integer, String>) - Method in class jebl.evolution.characters.DiscreteCharacter
-
- setTime(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
-
- setTime50(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
An alternative parameterization of this model.
- setTitle(String) - Method in class jebl.util.CompositeProgressListener
-
- setTitle(String) - Method in class jebl.util.ProgressListener
-
Sets a title associated with whatever is being done.
- setTitle(String) - Method in class jebl.util.ProgressListener.Wrapper
-
- setUseCurrentInUnivariateMinimisation(boolean) - Method in class jebl.math.OrthogonalSearch
-
- shuffle(Align, String, String, int) - Method in class jebl.evolution.align.SequenceShuffler
-
- shuffle(int[]) - Static method in class jebl.math.Random
-
Shuffles an array.
- shuffle(int[], int) - Static method in class jebl.math.Random
-
Shuffles an array.
- shuffled(int) - Static method in class jebl.math.Random
-
Returns an array of shuffled indices of length l.
- SimpleListener - Interface in jebl.util
-
- SimpleRootedTree - Class in jebl.evolution.trees
-
A simple, and initially immutable rooted tree implementation.
- SimpleRootedTree() - Constructor for class jebl.evolution.trees.SimpleRootedTree
-
- SimpleRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.SimpleRootedTree
-
Make a copy of the given rooted tree
- SimpleRootedTree(RootedTree, Map<Node, Node>) - Constructor for class jebl.evolution.trees.SimpleRootedTree
-
Make a copy of the given rooted tree
- SimpleRootedTree(Tree, Node, Node, double) - Constructor for class jebl.evolution.trees.SimpleRootedTree
-
Make a copy of the given unrooted tree
- SimpleTree - Class in jebl.evolution.trees
-
A basic implementation on an unrooted tree.
- SimpleTree() - Constructor for class jebl.evolution.trees.SimpleTree
-
Tree (to be constructed by subsequent calls).
- SimpleTree(Tree) - Constructor for class jebl.evolution.trees.SimpleTree
-
Duplicate a tree.
- simulate(IntervalGenerator) - Method in class jebl.evolution.treesimulation.TreeSimulator
-
- simulate(IntervalGenerator, boolean) - Method in class jebl.evolution.treesimulation.TreeSimulator
-
- skipCharacters(String) - Method in class jebl.evolution.io.ImportHelper
-
Skips over any contiguous characters in skip.
- skipSpace() - Method in class jebl.evolution.io.ImportHelper
-
Skips over any space (plus tabs and returns) in the file.
- skipToEndOfLine() - Method in class jebl.evolution.io.ImportHelper
-
Skips to the end of the line.
- skipUntil(String) - Method in class jebl.evolution.io.ImportHelper
-
Skips over the file until a character from delimiters is found.
- skipWhile(String) - Method in class jebl.evolution.io.ImportHelper
-
Skips char any contiguous characters in skip.
- SmithWaterman - Class in jebl.evolution.align
-
- SmithWaterman(Scores, float) - Constructor for class jebl.evolution.align.SmithWaterman
-
- SmithWatermanLinearSpace - Class in jebl.evolution.align
-
- SmithWatermanLinearSpace(Scores, float) - Constructor for class jebl.evolution.align.SmithWatermanLinearSpace
-
- SmithWatermanLinearSpaceAffine - Class in jebl.evolution.align
-
- SmithWatermanLinearSpaceAffine(Scores, float, float) - Constructor for class jebl.evolution.align.SmithWatermanLinearSpaceAffine
-
- SortedRootedTree - Class in jebl.evolution.trees
-
- SortedRootedTree(RootedTree, SortedRootedTree.BranchOrdering) - Constructor for class jebl.evolution.trees.SortedRootedTree
-
- SortedRootedTree(RootedTree, Comparator<Node>) - Constructor for class jebl.evolution.trees.SortedRootedTree
-
- SortedRootedTree.BranchOrdering - Enum in jebl.evolution.trees
-
- SplitSystem - Class in jebl.evolution.trees
-
data structure for a set of splits
- SplitSystem(Collection<Taxon>, int) - Constructor for class jebl.evolution.trees.SplitSystem
-
- SplitUtils - Class in jebl.evolution.trees
-
utilities for split systems
- SQRT_EPSILON - Static variable in class jebl.math.MachineAccuracy
-
- SQRT_SQRT_EPSILON - Static variable in class jebl.math.MachineAccuracy
-
- startReadingTrees() - Method in class jebl.evolution.io.NexusImporter
-
Read nexus blocks until the next TREES block (or the end of the input) is encountered.
- State - Class in jebl.evolution.sequences
-
- STATE_COUNT - Static variable in class jebl.evolution.sequences.AminoAcids
-
- STATE_COUNT - Static variable in class jebl.evolution.sequences.Codons
-
- STATE_COUNT - Static variable in class jebl.evolution.sequences.Nucleotides
-
- StateClassification - Interface in jebl.evolution.sequences
-
- StateClassification.Default - Class in jebl.evolution.sequences
-
- StateClassification.Default(String, String[], State[][]) - Constructor for class jebl.evolution.sequences.StateClassification.Default
-
- STATES - Static variable in class jebl.evolution.sequences.AminoAcids
-
Deprecated.
- STATES - Static variable in class jebl.evolution.sequences.Codons
-
- STATES - Static variable in class jebl.evolution.sequences.Nucleotides
-
Deprecated.
- STOP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
-
- stopCondition(double, double[], double, double, boolean) - Method in class jebl.math.MultivariateMinimum
-
Checks whether optimization should stop
- stripGaps(State[]) - Static method in class jebl.evolution.sequences.Utils
-
- subSequence(int, int) - Method in class jebl.evolution.io.ByteBuilder
-
- SubstScoreMatrix - Class in jebl.evolution.align.scores
-
- SubstScoreMatrix(RateMatrix) - Constructor for class jebl.evolution.align.scores.SubstScoreMatrix
-
- sumVector(double[]) - Static method in class jebl.math.MatrixCalc
-
sum a vector
- swapNodes(Node, int, int) - Method in class jebl.evolution.trees.SimpleRootedTree
-
- V_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
-
- V_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
-
- valueOf(String) - Static method in enum jebl.evolution.coalescent.IntervalList.IntervalType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.io.DistanceMatrixImporter.Triangle
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.io.IllegalCharacterPolicy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.io.NexusImporter.NexusBlock
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in class jebl.evolution.sequences.GeneticCode
-
- valueOf(int) - Static method in class jebl.evolution.sequences.GeneticCode
-
- valueOf(String) - Static method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.ReRootedTree.RootingType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TransformedRootedTree.Transform
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.DistanceModel
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.Method
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.util.MaybeBoolean
-
Returns the enum constant of this type with the specified name.
- valueOf(boolean) - Static method in enum jebl.util.MaybeBoolean
-
- values() - Static method in enum jebl.evolution.coalescent.IntervalList.IntervalType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.io.DistanceMatrixImporter.Triangle
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.io.IllegalCharacterPolicy
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.io.NexusImporter.NexusBlock
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.ReRootedTree.RootingType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TransformedRootedTree.Transform
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.DistanceModel
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.Method
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum jebl.util.MaybeBoolean
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- VERTEBRATE_MT - Static variable in class jebl.evolution.sequences.GeneticCode
-
- VOLUME_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids
-