Deprecated API

Contents

• Deprecated Classes
• Deprecated Methods
• Deprecated Constructors

Deprecated Classes

Class and Description
org.biojava.nbio.structure.Identifier Use StructureName instead. Deprecated in v. 4.2.0
org.biojava.nbio.structure.gui.RasmolCommandListener use org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener instead

Deprecated Methods

Method and Description
org.biojava.nbio.alignment.io.StockholmStructure.addSequence(String, String) Use StockholmStructure.appendToSequence(String,String) instead
org.biojava.nbio.structure.align.ce.CECalculator.calc_rmsd(Atom[], Atom[], int, boolean, boolean) Use CECalculator.calc_rmsd(Atom[],Atom[],int,boolean) instead
org.biojava.nbio.structure.StructureTools.cloneCAArray(Atom[]) Use the better-named StructureTools.cloneAtomArray(Atom[]) instead
org.biojava.nbio.structure.StructureTools.convert_3code_1code(String) Use StructureTools.get1LetterCodeAmino(String) instead
org.biojava.nbio.structure.io.PDBFileReader.downloadPDB(String)
org.biojava.nbio.structure.align.util.UserConfiguration.getAutoFetch() Use UserConfiguration.getFetchBehavior()
org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.getAverageTraceRmsd() use QuatSymmetryResults.getScores() instead.
org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.getAverageTraceTmScoreMin() use QuatSymmetryResults.getScores() instead.
org.biojava.nbio.structure.align.util.AtomCache.getBiologicalUnit(String) Renamed to AtomCache.getBiologicalAssembly(String) in 4.2
org.biojava.nbio.structure.align.gui.DisplayAFP.getBlockNrForAlignPos(AFPChain, int) use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
org.biojava.nbio.structure.io.CAConverter.getCAOnly(Chain) Use the more generic CAConverter.getRepresentativeAtomsOnly(Chain) instead
org.biojava.nbio.structure.io.CAConverter.getCAOnly(List<Chain>) Use the more generic CAConverter.getRepresentativeAtomsOnly(List) instead
org.biojava.nbio.structure.Structure.getConnections() use Atom.getBonds() instead
org.biojava.nbio.core.sequence.compound.NucleotideCompound.getConsituents() replaced with NucleotideCompound.getConstituents() due to typographical error
org.biojava.nbio.structure.ChainImpl.getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)
org.biojava.nbio.structure.align.client.StructureName.getName() use StructureName.getIdentifier()
org.biojava.nbio.protmod.structure.ModifiedCompoundImpl.getOriginalModificationId() use getModification().getId()
org.biojava.nbio.structure.align.util.RotationAxis.getOtherTranslation()
org.biojava.nbio.structure.Chain.getParent() use getStructure(Structure) instead.
org.biojava.nbio.structure.ChainImpl.getParent() use getStructure instead.
org.biojava.nbio.structure.StructureImpl.getPdbId()
org.biojava.nbio.structure.Structure.getPdbId() From BioJava 4.2, use Structure.getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
org.biojava.nbio.structure.cath.CathDomain.getPdbId() This method is poorly named; use CathDomain.getThePdbId() or CathDomain.getPdbIdAndChain() instead
org.biojava.nbio.structure.StructureImpl.getRanges()
org.biojava.nbio.structure.Structure.getRanges() From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
org.biojava.nbio.structure.quaternary.BioAssemblyTools.getReducedCAStructure(Structure) Use the more generic BioAssemblyTools.getReducedStructure(Structure)
org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, int) Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String) Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
org.biojava.nbio.structure.StructureImpl.getResidueRanges()
org.biojava.nbio.structure.Structure.getResidueRanges() From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry.getRotationGroup()
org.biojava.nbio.structure.gui.JMatrixPanel.getSaturation()
org.biojava.nbio.structure.gui.JMatrixPanel.getScalevalue()
org.biojava.nbio.structure.scop.ScopInstallation.getScopDownloadURL()
org.biojava.nbio.structure.align.model.AFPChain.getSimilarity1() use getCoverage1() instead
org.biojava.nbio.structure.align.model.AFPChain.getSimilarity2() use getCoverage2() instead
org.biojava.nbio.structure.StructureTools.getSubRanges(Structure, String) Use StructureIdentifier instead (4.2.0)
org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.getSymmetryAxes() because it does not work as expected for open symmetry
org.biojava.nbio.structure.PDBCrystallographicInfo.getZ() As of 4.0, use SpaceGroup.getMultiplicity() and Structure.size()
org.biojava.nbio.structure.align.util.AtomCache.isAutoFetch() Use AtomCache.getFetchBehavior()
org.biojava.nbio.structure.io.LocalPDBDirectory.isAutoFetch() Use LocalPDBDirectory.getFetchBehavior()
org.biojava.nbio.structure.align.StructurePairAligner.isDebug()
org.biojava.nbio.structure.align.util.AtomCache.isFetchCurrent() Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.isFetchCurrent() Use FileParsingParameters#getObsoleteBehavior()
org.biojava.nbio.structure.align.util.AtomCache.isFetchFileEvenIfObsolete() Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.isFetchFileEvenIfObsolete() Use FileParsingParameters#getObsoleteBehavior()
org.biojava.nbio.structure.align.ce.StartupParameters.isPdbDirSplit() Always returns true (4.0.0)
org.biojava.nbio.structure.align.util.AtomCache.isStrictSCOP() since 4.2
org.biojava.nbio.structure.io.FileParsingParameters.isUpdateRemediatedFiles() Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)
org.biojava.nbio.structure.Identifier.loadIdentifier(String, AtomCache) Create a new StructureName instead.
org.biojava.nbio.genome.parsers.gff.Feature.main(String[])
org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[])
org.biojava.nbio.genome.parsers.gff.Location.main(String[])
org.biojava.nbio.genome.parsers.gff.FeatureList.main(String[])
org.biojava.nbio.structure.align.util.AtomCache.setAutoFetch(boolean) Use AtomCache.getFetchBehavior()
org.biojava.nbio.structure.align.util.UserConfiguration.setAutoFetch(boolean) Use UserConfiguration.getFetchBehavior()
org.biojava.nbio.structure.io.LocalPDBDirectory.setAutoFetch(boolean) Use #setFetchBehavior()
org.biojava.nbio.structure.Structure.setConnections(List<Map<String, Integer>>) use Atom.addBond(Bond) instead
org.biojava.nbio.structure.align.StructurePairAligner.setDebug(boolean)
org.biojava.nbio.structure.align.util.AtomCache.setFetchCurrent(boolean) Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.setFetchCurrent(boolean) Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
org.biojava.nbio.structure.align.util.AtomCache.setFetchFileEvenIfObsolete(boolean) Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.setFetchFileEvenIfObsolete(boolean) Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
org.biojava.nbio.structure.StructureImpl.setNmr(boolean)
org.biojava.nbio.structure.Structure.setNmr(boolean)
org.biojava.nbio.structure.Chain.setParent(Structure) use setStructure instead
org.biojava.nbio.structure.ChainImpl.setParent(Structure)
org.biojava.nbio.structure.align.ce.StartupParameters.setPdbDirSplit(boolean) Ignored (4.0.0)
org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)
org.biojava.nbio.structure.gui.JMatrixPanel.setSaturation(float)
org.biojava.nbio.structure.gui.JMatrixPanel.setScalevalue(float)
org.biojava.nbio.structure.scop.ScopInstallation.setScopDownloadURL(String) Use ScopInstallation.addMirror(java.lang.String) instead
org.biojava.nbio.structure.align.util.AtomCache.setStrictSCOP(boolean) Removed in 4.2.0
org.biojava.nbio.structure.io.FileParsingParameters.setUpdateRemediatedFiles(boolean) Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)

Deprecated Constructors

Constructor and Description
org.biojava.nbio.structure.align.model.AFPChain()
org.biojava.nbio.structure.align.util.AtomCache(String, boolean) isSplit parameter is ignored (4.0.0)
org.biojava.nbio.structure.align.util.AtomCache(String, String, boolean) isSplit parameter is ignored (4.0.0)
org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean) Retained for backwards compatability, setting RNAToAminoAcidTranslator.stopAtStopCodons to false
org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean)