Deprecated API


Contents
Deprecated Interfaces
org.biojava.bio.structure.server.PDBInstallation
            
org.biojava.bio.structure.server.StructureServer
            
 

Deprecated Classes
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 Fields
org.forester.io.parsers.nhx.NHXtags.BINARY_DOMAIN_COMBINATIONS
           
org.forester.io.parsers.nhx.NHXtags.DOMAINS
           
org.forester.io.parsers.nhx.NHXtags.DOMAINS_SEPARATOR
           
org.forester.io.parsers.nhx.NHXtags.EC_NUMBER
           
 

Deprecated Methods
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.LocIterator.main(String[])
            
org.biojava3.genome.parsers.gff.Feature.main(String[])
            
org.biojava3.genome.parsers.gff.Location.main(String[])
            
org.biojava3.genome.parsers.gff.FeatureList.main(String[])
            
org.biojava.bio.structure.Structure.setHeader(Map)
            
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.