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
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
SimpleOrthoPairCollection.Iterator
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Field Summary
Fields inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
groups
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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, iterator
Methods inherited from class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
filter
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods 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:HomologeneDB
Create an orthologue.- Specified by:
createOrthologue
in 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:HomologeneDB
Create an orthologue.- Specified by:
createOrthologue
in interfaceHomologeneDB
- Throws:
IllegalArgumentException
ChangeVetoException
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getOrthologue
Description copied from interface:HomologeneDB
Returns an orthologue of specified ID.- Specified by:
getOrthologue
in interfaceHomologeneDB
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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 interfaceHomologeneDB
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createOrthoPair
Description copied from interface:HomologeneDB
Create a curated orthology entry.- Specified by:
createOrthoPair
in interfaceHomologeneDB
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createOrthoPairSet
Description copied from interface:HomologeneDB
Create a Homologene Group.- Specified by:
createOrthoPairSet
in interfaceHomologeneDB
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getOrthoPairSets
Description copied from interface:HomologeneDB
Get the HomologeneGroups in this database.- Specified by:
getOrthoPairSets
in interfaceHomologeneDB
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