Deprecated List (biojava 6.1.0 API)

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 #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 #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)