Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Methods

Deprecated Interfaces

Interface and Description
org.biojava.bio.structure.server.PDBInstallation
org.biojava.bio.structure.server.StructureServer

Deprecated Classes

Class and Description
org.biojava.bio.structure.server.FlatFileInstallation
org.biojava.bio.structure.server.MMCIFFileInstallation
org.biojava.bio.structure.gui.RasmolCommandListener use org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener instead
org.biojava.bio.structure.server.SimpleStructureServer
org.biojava.bio.structure.server.StructureFetcherRunnable

Deprecated Methods

Method and Description
org.biojava.bio.structure.align.util.AtomCache.getAtoms(String, boolean) does the same as AtomCache.getAtoms(String) ;
org.biojava.bio.structure.align.gui.DisplayAFP.getBlockNrForAlignPos(AFPChain, int) use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
org.biojava.bio.structure.Chain.getGroup(int) use getAtomGroup or getSeqResGroup instead
org.biojava.bio.structure.ChainImpl.getGroup(int) use getAtomGroup or getSeqResGroup instead
org.biojava.bio.structure.Chain.getGroupByPDB(String) replaced by Chain.getGroupByPDB(ResidueNumber)
org.biojava.bio.structure.Chain.getGroups() use getAtomGroups or getSeqResGroups instead
org.biojava.bio.structure.ChainImpl.getGroups() use getAtomGroups instead
org.biojava.bio.structure.Chain.getGroups(String) use getAtomGroups or getSeqResGroups instead
org.biojava.bio.structure.ChainImpl.getGroups(String) use getAtomGroups instead
org.biojava.bio.structure.Chain.getGroupsByPDB(String, String) replaced by Chain.getGroupsByPDB(ResidueNumber, ResidueNumber)
org.biojava.bio.structure.Chain.getGroupsByPDB(String, String, boolean) replaced by #Chain.getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)
org.biojava.bio.structure.Structure.getHeader() use getPDBHeader instead
org.biojava.bio.structure.Chain.getLength() please use getAtomLength or getLengthSeqRes instead
org.biojava.bio.structure.ChainImpl.getLength() use getAtomLength instead
org.biojava.bio.structure.Chain.getLengthAminos() use getAtomGroups("amino").size() instead.
org.biojava.bio.structure.Chain.getName() replaced by Chain.getChainID()
org.biojava3.protmod.structure.ModifiedCompoundImpl.getOriginalModificationId() use getModification().getId()
org.biojava.bio.structure.Atom.getParent() replaced by Atom.getGroup()
org.biojava.bio.structure.Group.getParent() replaced by Group.getChain()
org.biojava.bio.structure.HetatomImpl.getPDBCode() replaced by #getSeqNum
org.biojava.bio.structure.Group.getPDBCode() replaced by Group.getResidueNumber()
org.biojava.bio.structure.Atom.getPDBline() @deprecated replaced by PDBRecord.toPDB()
org.biojava.bio.structure.AtomImpl.getPDBline()
org.biojava.bio.structure.StructureTools.getPDBResidueNumber(Group) replaced by Group.getResidueNumber()
org.biojava.bio.structure.gui.JMatrixPanel.getSaturation()
org.biojava.bio.structure.gui.JMatrixPanel.getScalevalue()
org.biojava.bio.structure.Chain.getSequence() use getAtomSequence instead
org.biojava.bio.structure.ChainImpl.getSequence() use getAtomSequence instead
org.biojava.bio.structure.align.model.AFPChain.getSimilarity1() use getCoverage1() instead
org.biojava.bio.structure.align.model.AFPChain.getSimilarity2() use getCoverage2() instead
org.biojava3.genome.parsers.gff.FeatureList.main(String[])
org.biojava3.genome.parsers.gff.Feature.main(String[])
org.biojava3.genome.parsers.gff.LocIterator.main(String[])
org.biojava3.genome.parsers.gff.Location.main(String[])
org.biojava.bio.structure.Chain.setName(String) replaced by Chain.setChainID(String)
org.biojava.bio.structure.Group.setParent(Chain)
org.biojava.bio.structure.Atom.setParent(Group) replaced by Atom.setGroup(Group)
org.biojava.bio.structure.HetatomImpl.setPDBCode(String) replaced by HetatomImpl.setResidueNumber(ResidueNumber)
org.biojava.bio.structure.Group.setPDBCode(String) replaced by Group.setResidueNumber(ResidueNumber)
org.biojava.bio.structure.Atom.setPDBline(String) replaced by PDBRecord.toPDB()
org.biojava.bio.structure.AtomImpl.setPDBline(String)
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.