Interface HomologeneDB
- All Known Implementing Classes:
SimpleHomologeneDB
public interface HomologeneDB
Homologene is a NCBI dataset that curates sets
of orthologues from the reference model organisms.
This class is a Collection of methods for handling data from the Homologene dataset.
- Author:
- David Huen, Matthew Pocock
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Method Summary
Modifier and TypeMethodDescriptioncreateOrthologue
(int taxonID, String locusID, String homologeneID, String accession) Create an orthologue.createOrthologue
(Taxon taxon, String locusID, String homologeneID, String accession) Create an orthologue.createOrthoPair
(Orthologue first, Orthologue second, String ref) Create a curated orthology entry.createOrthoPair
(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) Create a computed orthology entry.Create a Homologene Group.filter
(OrthoPairSetFilter filters) Filter the database for a specified group.getOrthologue
(String homologeneID) Returns an orthologue of specified ID.Get the HomologeneGroups in this database.
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Method Details
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createOrthologue
Orthologue createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession) throws ChangeVetoException Create an orthologue.- Throws:
ChangeVetoException
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createOrthologue
Orthologue createOrthologue(int taxonID, String locusID, String homologeneID, String accession) throws ChangeVetoException Create an orthologue.- Throws:
ChangeVetoException
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getOrthologue
Returns an orthologue of specified ID. -
createOrthoPair
OrthoPair createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) Create a computed orthology entry. -
createOrthoPair
Create a curated orthology entry. -
createOrthoPairSet
Create a Homologene Group. -
getOrthoPairSets
Get the HomologeneGroups in this database. -
filter
Filter the database for a specified group.
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