org.biojava.bio.program.homologene
Class SimpleHomologeneDB
java.lang.Object
org.biojava.bio.program.homologene.AbstractOrthoPairCollection
org.biojava.bio.program.homologene.SimpleOrthoPairCollection
org.biojava.bio.program.homologene.SimpleHomologeneDB
- All Implemented Interfaces:
- HomologeneDB, OrthoPairCollection
public class SimpleHomologeneDB
- extends SimpleOrthoPairCollection
- implements HomologeneDB
Method Summary |
Orthologue |
createOrthologue(int taxonID,
String locusID,
String homologeneID,
String accession)
Create an orthologue. |
Orthologue |
createOrthologue(Taxon taxon,
String locusID,
String homologeneID,
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,
String ref)
Create a curated orthology entry. |
OrthoPairSet |
createOrthoPairSet()
Create a Homologene Group. |
Orthologue |
getOrthologue(String homologeneID)
Returns an orthologue of specified ID. |
OrthoPairCollection |
getOrthoPairSets()
Get the HomologeneGroups in this database. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SimpleHomologeneDB
public SimpleHomologeneDB()
createOrthologue
public Orthologue createOrthologue(Taxon taxon,
String locusID,
String homologeneID,
String accession)
throws ChangeVetoException
- Description copied from interface:
HomologeneDB
- Create an orthologue.
- Specified by:
createOrthologue
in interface HomologeneDB
- Throws:
ChangeVetoException
createOrthologue
public Orthologue createOrthologue(int taxonID,
String locusID,
String homologeneID,
String accession)
throws IllegalArgumentException,
ChangeVetoException
- Description copied from interface:
HomologeneDB
- Create an orthologue.
- Specified by:
createOrthologue
in interface HomologeneDB
- Throws:
IllegalArgumentException
ChangeVetoException
getOrthologue
public Orthologue getOrthologue(String homologeneID)
- Description copied from interface:
HomologeneDB
- Returns an orthologue of specified ID.
- Specified by:
getOrthologue
in interface HomologeneDB
createOrthoPair
public OrthoPair createOrthoPair(Orthologue first,
Orthologue second,
SimilarityType type,
double percentIdentity)
- Description copied from interface:
HomologeneDB
- Create a computed orthology entry.
- Specified by:
createOrthoPair
in interface HomologeneDB
createOrthoPair
public OrthoPair createOrthoPair(Orthologue first,
Orthologue second,
String ref)
- Description copied from interface:
HomologeneDB
- Create a curated orthology entry.
- Specified by:
createOrthoPair
in interface HomologeneDB
createOrthoPairSet
public OrthoPairSet createOrthoPairSet()
- Description copied from interface:
HomologeneDB
- Create a Homologene Group.
- Specified by:
createOrthoPairSet
in interface HomologeneDB
getOrthoPairSets
public OrthoPairCollection getOrthoPairSets()
- Description copied from interface:
HomologeneDB
- Get the HomologeneGroups in this database.
- Specified by:
getOrthoPairSets
in interface HomologeneDB