Class SimpleHomologeneDB
java.lang.Object
org.biojava.bio.program.homologene.AbstractOrthoPairCollection
org.biojava.bio.program.homologene.SimpleOrthoPairCollection
org.biojava.bio.program.homologene.SimpleHomologeneDB
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HomologeneDB,OrthoPairCollection
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
SimpleOrthoPairCollection.Iterator -
Field Summary
Fields inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
groups -
Constructor Summary
Constructors -
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.getOrthologue(String homologeneID) Returns an orthologue of specified ID.Get the HomologeneGroups in this database.Methods inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
add, contains, isEmpty, iteratorMethods inherited from class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
filterMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface org.biojava.bio.program.homologene.HomologeneDB
filter
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Constructor Details
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SimpleHomologeneDB
public SimpleHomologeneDB()
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Method Details
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createOrthologue
public Orthologue createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession) throws ChangeVetoException Description copied from interface:HomologeneDBCreate an orthologue.- Specified by:
createOrthologuein interfaceHomologeneDB- Throws:
ChangeVetoException
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createOrthologue
public Orthologue createOrthologue(int taxonID, String locusID, String homologeneID, String accession) throws IllegalArgumentException, ChangeVetoException Description copied from interface:HomologeneDBCreate an orthologue.- Specified by:
createOrthologuein interfaceHomologeneDB- Throws:
IllegalArgumentExceptionChangeVetoException
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getOrthologue
Description copied from interface:HomologeneDBReturns an orthologue of specified ID.- Specified by:
getOrthologuein interfaceHomologeneDB
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createOrthoPair
public OrthoPair createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) Description copied from interface:HomologeneDBCreate a computed orthology entry.- Specified by:
createOrthoPairin interfaceHomologeneDB
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createOrthoPair
Description copied from interface:HomologeneDBCreate a curated orthology entry.- Specified by:
createOrthoPairin interfaceHomologeneDB
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createOrthoPairSet
Description copied from interface:HomologeneDBCreate a Homologene Group.- Specified by:
createOrthoPairSetin interfaceHomologeneDB
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getOrthoPairSets
Description copied from interface:HomologeneDBGet the HomologeneGroups in this database.- Specified by:
getOrthoPairSetsin interfaceHomologeneDB
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