Uses of Interface
org.biojava.bio.program.homologene.Orthologue
Packages that use Orthologue
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Uses of Orthologue in org.biojava.bio.program.homologene
Classes in org.biojava.bio.program.homologene that implement OrthologueModifier and TypeClassDescriptionclass
this entry contains data about the orthologue.Methods in org.biojava.bio.program.homologene that return OrthologueModifier and TypeMethodDescriptionHomologeneDB.createOrthologue
(int taxonID, String locusID, String homologeneID, String accession) Create an orthologue.HomologeneDB.createOrthologue
(Taxon taxon, String locusID, String homologeneID, String accession) Create an orthologue.SimpleHomologeneDB.createOrthologue
(int taxonID, String locusID, String homologeneID, String accession) SimpleHomologeneDB.createOrthologue
(Taxon taxon, String locusID, String homologeneID, String accession) OrthoPair.getFirstOrthologue()
gets the first orthologue in the orthology relationship.SimpleOrthoPair.getFirstOrthologue()
HomologeneDB.getOrthologue
(String homologeneID) Returns an orthologue of specified ID.OrthologueSet.getOrthologue
(String homologeneID) SimpleHomologeneDB.getOrthologue
(String homologeneID) SimpleOrthologueSet.getOrthologue
(String homologeneID) OrthoPair.getSecondOrthologue()
gets the first orthologue in the orthology relationship.SimpleOrthoPair.getSecondOrthologue()
OrthologueSet.Iterator.nextOrthologue()
SimpleOrthologueSet.Iterator.nextOrthologue()
Methods in org.biojava.bio.program.homologene with parameters of type OrthologueModifier and TypeMethodDescriptionboolean
OrthologueFilter.accept
(Orthologue ortho) boolean
OrthologueFilter.AcceptAll.accept
(Orthologue ortho) boolean
OrthologueFilter.And.accept
(Orthologue ortho) boolean
OrthologueFilter.ByAccession.accept
(Orthologue ortho) boolean
OrthologueFilter.ByHomologeneID.accept
(Orthologue ortho) boolean
OrthologueFilter.ByLocusID.accept
(Orthologue ortho) boolean
OrthologueFilter.ByTaxon.accept
(Orthologue ortho) boolean
OrthologueFilter.ByTaxonID.accept
(Orthologue ortho) boolean
OrthologueFilter.ByTitle.accept
(Orthologue ortho) boolean
OrthologueFilter.Not.accept
(Orthologue ortho) boolean
OrthologueFilter.Or.accept
(Orthologue ortho) boolean
OrthologueFilter.Xor.accept
(Orthologue ortho) void
OrthologueSet.addOrthologue
(Orthologue ortho) Add an orthologue to the set.void
SimpleOrthologueSet.addOrthologue
(Orthologue ortho) HomologeneDB.createOrthoPair
(Orthologue first, Orthologue second, String ref) Create a curated orthology entry.HomologeneDB.createOrthoPair
(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) Create a computed orthology entry.SimpleHomologeneDB.createOrthoPair
(Orthologue first, Orthologue second, String ref) SimpleHomologeneDB.createOrthoPair
(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) void
OrthologueSet.removeOrthologue
(Orthologue ortho) Remove an orthologue from the set.void
SimpleOrthologueSet.removeOrthologue
(Orthologue ortho) Constructors in org.biojava.bio.program.homologene with parameters of type OrthologueModifierConstructorDescriptionSimpleOrthoPair
(Orthologue first, Orthologue second, String ref) constructor for the curated form of an orthology relationshipSimpleOrthoPair
(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) constructor for the computed form of an orthology relationship.