Uses of Interface
org.biojava.bio.program.homologene.Orthologue

Packages that use Orthologue
org.biojava.bio.program.homologene Support classes for Homologene data. 
 

Uses of Orthologue in org.biojava.bio.program.homologene
 

Classes in org.biojava.bio.program.homologene that implement Orthologue
 class SimpleOrthologue
          this entry contains data about the orthologue.
 

Methods in org.biojava.bio.program.homologene that return Orthologue
 Orthologue SimpleHomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)
           
 Orthologue HomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)
          Create an orthologue.
 Orthologue SimpleHomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
           
 Orthologue HomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
          Create an orthologue.
 Orthologue OrthoPair.getFirstOrthologue()
          gets the first orthologue in the orthology relationship.
 Orthologue SimpleOrthoPair.getFirstOrthologue()
           
 Orthologue SimpleHomologeneDB.getOrthologue(String homologeneID)
           
 Orthologue SimpleOrthologueSet.getOrthologue(String homologeneID)
           
 Orthologue HomologeneDB.getOrthologue(String homologeneID)
          Returns an orthologue of specified ID.
 Orthologue OrthologueSet.getOrthologue(String homologeneID)
           
 Orthologue OrthoPair.getSecondOrthologue()
          gets the first orthologue in the orthology relationship.
 Orthologue SimpleOrthoPair.getSecondOrthologue()
           
 Orthologue SimpleOrthologueSet.Iterator.nextOrthologue()
           
 Orthologue OrthologueSet.Iterator.nextOrthologue()
           
 

Methods in org.biojava.bio.program.homologene with parameters of type Orthologue
 boolean OrthologueFilter.accept(Orthologue ortho)
           
 boolean OrthologueFilter.AcceptAll.accept(Orthologue ortho)
           
 boolean OrthologueFilter.Not.accept(Orthologue ortho)
           
 boolean OrthologueFilter.Or.accept(Orthologue ortho)
           
 boolean OrthologueFilter.And.accept(Orthologue ortho)
           
 boolean OrthologueFilter.Xor.accept(Orthologue ortho)
           
 boolean OrthologueFilter.ByTaxonID.accept(Orthologue ortho)
           
 boolean OrthologueFilter.ByTaxon.accept(Orthologue ortho)
           
 boolean OrthologueFilter.ByLocusID.accept(Orthologue ortho)
           
 boolean OrthologueFilter.ByHomologeneID.accept(Orthologue ortho)
           
 boolean OrthologueFilter.ByAccession.accept(Orthologue ortho)
           
 boolean OrthologueFilter.ByTitle.accept(Orthologue ortho)
           
 void SimpleOrthologueSet.addOrthologue(Orthologue ortho)
           
 void OrthologueSet.addOrthologue(Orthologue ortho)
          Add an orthologue to the set.
 OrthoPair SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
           
 OrthoPair HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
          Create a computed orthology entry.
 OrthoPair SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)
           
 OrthoPair HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)
          Create a curated orthology entry.
 void SimpleOrthologueSet.removeOrthologue(Orthologue ortho)
           
 void OrthologueSet.removeOrthologue(Orthologue ortho)
          Remove an orthologue from the set.
 

Constructors in org.biojava.bio.program.homologene with parameters of type Orthologue
SimpleOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
          constructor for the computed form of an orthology relationship.
SimpleOrthoPair(Orthologue first, Orthologue second, String ref)
          constructor for the curated form of an orthology relationship