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.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

  invalid reference

  #setPDBCode(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

  invalid reference

  #setPDBCode(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)