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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.
Method Summary | |
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Orthologue |
createOrthologue(int taxonID,
java.lang.String locusID,
java.lang.String homologeneID,
java.lang.String accession)
Create an orthologue. |
Orthologue |
createOrthologue(Taxon taxon,
java.lang.String locusID,
java.lang.String homologeneID,
java.lang.String accession)
Create an orthologue. |
OrthoPair |
createOrthoPair(Orthologue first,
Orthologue second,
SimilarityType type,
double percentIdentity)
Create a computed orthology entry. |
OrthoPair |
createOrthoPair(Orthologue first,
Orthologue second,
java.lang.String ref)
Create a curated orthology entry. |
OrthoPairSet |
createOrthoPairSet()
Create a Homologene Group. |
OrthoPairCollection |
filter(OrthoPairSetFilter filters)
Filter the database for a specified group. |
Orthologue |
getOrthologue(java.lang.String homologeneID)
Returns an orthologue of specified ID. |
OrthoPairCollection |
getOrthoPairSets()
Get the HomologeneGroups in this database. |
Method Detail |
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Orthologue createOrthologue(Taxon taxon, java.lang.String locusID, java.lang.String homologeneID, java.lang.String accession) throws ChangeVetoException
ChangeVetoException
Orthologue createOrthologue(int taxonID, java.lang.String locusID, java.lang.String homologeneID, java.lang.String accession) throws ChangeVetoException
ChangeVetoException
Orthologue getOrthologue(java.lang.String homologeneID)
OrthoPair createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
OrthoPair createOrthoPair(Orthologue first, Orthologue second, java.lang.String ref)
OrthoPairSet createOrthoPairSet()
OrthoPairCollection getOrthoPairSets()
OrthoPairCollection filter(OrthoPairSetFilter filters)
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