Deprecated API

Contents

• Methods
• Constructors

Deprecated Methods

Method	Description
org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[])
org.biojava.nbio.structure.align.client.PdbPair.getPDBCode1()	use PdbPair.getPDBCode1() instead
org.biojava.nbio.structure.align.client.PdbPair.getPDBCode2()	use PdbPair.getPDBCode2() instead
org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(MultipleAlignment, AbstractAlignmentJmol)	Replace with
org.biojava.nbio.structure.contact.Grid.getContacts()	use Grid.getAtomContacts() instead
org.biojava.nbio.structure.PDBHeader.getDescription()	will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.
org.biojava.nbio.structure.PDBHeader.getIdCode()	use PDBHeader.getPdbId()
org.biojava.nbio.structure.PDBHeader.setDescription(String)	will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.
org.biojava.nbio.structure.PDBHeader.setIdCode(String)	use PDBHeader.setPdbId(PdbId)
org.biojava.nbio.structure.scop.ScopDomain.setPdbId(String)	use ScopDomain.setPdbId(PdbId)
org.biojava.nbio.structure.Structure.getPDBCode()	use Structure.getPdbId() to get a PdbId object or getPdbId().getId() to get a String
org.biojava.nbio.structure.Structure.setPDBCode(String)	use Structure.setPdbId(PdbId)
org.biojava.nbio.structure.StructureImpl.getPDBCode()	use StructureImpl.getPdbId() to get a PdbId object or getPdbId().getId() to get a String
org.biojava.nbio.structure.StructureImpl.setPDBCode(String)	use StructureImpl.setPdbId(PdbId)
org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)

Deprecated Constructors

Constructor	Description
org.biojava.nbio.core.sequence.GeneSequence(ChromosomeSequence, int, int, Strand)
org.biojava.nbio.core.sequence.TranscriptSequence(GeneSequence, int, int)