Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Methods

Deprecated Interfaces

org.biojava.bio.structure.server.PDBInstallation

org.biojava.bio.structure.io.StructureIO
Do no use any longer, StructureIO is now a static utility calss on the org.biojava3.structure level..

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 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.biojava3.core.sequence.compound.NucleotideCompound.getConsituents()
replaced with NucleotideCompound.getConstituents() due to typographical error

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.Group.getPDBCode()
replaced by Group.getResidueNumber()

org.biojava.bio.structure.HetatomImpl.getPDBCode()
replaced by #getSeqNum

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.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.Group.setPDBCode(String)
replaced by Group.setResidueNumber(ResidueNumber)

org.biojava.bio.structure.HetatomImpl.setPDBCode(String)
replaced by HetatomImpl.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.