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