org.biojava.bio.structure.align.util.AtomCache.getAtoms(String, boolean)
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org.biojava.bio.structure.align.gui.DisplayAFP.getBlockNrForAlignPos(AFPChain, int)
use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
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org.biojava.bio.structure.Chain.getGroup(int)
use getAtomGroup or getSeqResGroup instead
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org.biojava.bio.structure.ChainImpl.getGroup(int)
use getAtomGroup or getSeqResGroup instead
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org.biojava.bio.structure.Chain.getGroupByPDB(String)
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org.biojava.bio.structure.Chain.getGroups()
use getAtomGroups or getSeqResGroups instead
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org.biojava.bio.structure.ChainImpl.getGroups()
use getAtomGroups instead
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org.biojava.bio.structure.Chain.getGroups(String)
use getAtomGroups or getSeqResGroups instead
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org.biojava.bio.structure.ChainImpl.getGroups(String)
use getAtomGroups instead
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org.biojava.bio.structure.Chain.getGroupsByPDB(String, String)
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org.biojava.bio.structure.Chain.getGroupsByPDB(String, String, boolean)
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org.biojava.bio.structure.Structure.getHeader()
use getPDBHeader instead
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org.biojava.bio.structure.Chain.getLength()
please use getAtomLength or getLengthSeqRes instead
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org.biojava.bio.structure.ChainImpl.getLength()
use getAtomLength instead
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org.biojava.bio.structure.Chain.getLengthAminos()
use getAtomGroups("amino").size() instead.
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org.biojava.bio.structure.Chain.getName()
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org.biojava3.protmod.structure.ModifiedCompoundImpl.getOriginalModificationId()
use getModification().getId()
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org.biojava.bio.structure.Atom.getParent()
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org.biojava.bio.structure.Group.getParent()
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org.biojava.bio.structure.Group.getPDBCode()
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org.biojava.bio.structure.HetatomImpl.getPDBCode()
replaced by #getSeqNum
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org.biojava.bio.structure.AtomImpl.getPDBline() |
org.biojava.bio.structure.Atom.getPDBline()
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org.biojava.bio.structure.StructureTools.getPDBResidueNumber(Group)
replaced by Group.getResidueNumber()
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org.biojava.bio.structure.gui.JMatrixPanel.getSaturation() |
org.biojava.bio.structure.gui.JMatrixPanel.getScalevalue() |
org.biojava.bio.structure.Chain.getSequence()
use getAtomSequence instead
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org.biojava.bio.structure.ChainImpl.getSequence()
use getAtomSequence instead
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org.biojava.bio.structure.align.model.AFPChain.getSimilarity1()
use getCoverage1() instead
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org.biojava.bio.structure.align.model.AFPChain.getSimilarity2()
use getCoverage2() instead
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org.biojava3.genome.parsers.gff.Location.main(String[]) |
org.biojava3.genome.parsers.gff.Feature.main(String[]) |
org.biojava3.genome.parsers.gff.FeatureList.main(String[]) |
org.biojava3.genome.parsers.gff.LocIterator.main(String[]) |
org.biojava.bio.structure.Structure.setHeader(Map) |
org.biojava.bio.structure.Chain.setName(String)
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org.biojava.bio.structure.Group.setParent(Chain) |
org.biojava.bio.structure.Atom.setParent(Group)
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org.biojava.bio.structure.Group.setPDBCode(String)
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org.biojava.bio.structure.HetatomImpl.setPDBCode(String)
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org.biojava.bio.structure.AtomImpl.setPDBline(String) |
org.biojava.bio.structure.Atom.setPDBline(String)
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org.biojava.bio.structure.gui.JMatrixPanel.setSaturation(float) |
org.biojava.bio.structure.gui.JMatrixPanel.setScalevalue(float) |
org.biojava.bio.structure.Calc.substract(Atom, Atom)
use subtract instead.
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