Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Datasource Aware Module
v1.09

uk.ac.roslin.ensembl.datasourceaware.core
Class DAGene

java.lang.Object
  extended by uk.ac.roslin.ensembl.datasourceaware.DAObject
      extended by uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
          extended by uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
              extended by uk.ac.roslin.ensembl.datasourceaware.core.DAGene
All Implemented Interfaces:
Serializable, uk.ac.roslin.ensembl.model.core.CoreObject, uk.ac.roslin.ensembl.model.core.Feature, uk.ac.roslin.ensembl.model.core.Gene, uk.ac.roslin.ensembl.model.IdentifiableObject, uk.ac.roslin.ensembl.model.MappableObject

public class DAGene
extends DAFeature
implements uk.ac.roslin.ensembl.model.core.Gene

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
DAFeature.Status
 
Nested classes/interfaces inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
DAObject.DAComparator
 
Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
creationDate, current, description, displayName, displayXRef, mappedObjectTypes, mappings, modificationDate, objectTypeMappings, xrefs
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
comparaFactories, species
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
daComparator, daoFactory, dbVersion, id, registry, schemaVersion
 
Constructor Summary
DAGene()
           
DAGene(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
 
Method Summary
 void addHomology(uk.ac.roslin.ensembl.config.EnsemblComparaDivision division, DAHomologyPairRelationship homology)
           
 void addTranscript(uk.ac.roslin.ensembl.model.core.Transcript transcript)
           
 DAAnalysis getAnalysis()
           
 String getBiotype()
           
 DATranscript getCanonicalTranscript()
           
 Integer getCanonicalTranscriptID()
           
 DATranslation getCanonicalTranslation()
           
 String getDisplayName()
           
 List<DAHomologyPairRelationship> getHomologies()
          Returns all Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene.
 List<DAHomologyPairRelationship> getHomologies(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision)
          Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.
 List<DAHomologyPairRelationship> getHomologies(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision, uk.ac.roslin.ensembl.model.core.Species sp)
          Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species.
 List<DAHomologyPairRelationship> getHomologies(uk.ac.roslin.ensembl.model.core.Species sp)
          Returns Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene for the specified Species.
 List<DAHomologyPairRelationship> getHomologiesWithoutLazyLoad()
          Utility method to get all of the current DAHomologyPairRelationships for this Gene
 String getStableID()
           
 Collection<DATranscript> getTranscripts()
           
 uk.ac.roslin.ensembl.model.ObjectType getType()
           
 void setAnalysis(uk.ac.roslin.ensembl.model.core.Analysis analysis)
           
 void setBiotype(String biotype)
           
 void setCanonicalTranscriptID(Integer canonicalTranscriptID)
           
 boolean setSearchedHomologies(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision)
           
 void setStableID(String stableID)
           
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
addMappedObjectType, addMapping, addXRefs, clearAllMappings, getAnnotationLevelMappings, getBuildLevelMappings, getChromosomeMapping, getCreationDate, getDescription, getDisplayXRef, getMappings, getMappings, getModificationDate, getStatus, getTopLevelMappings, getXRefs, isCurrent, isObjectTypeMapped, setCreationDate, setCurrent, setDescription, setDisplayName, setDisplayXRef, setModificationDate, setStatus
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
getAssembly, getComparaDivision, getComparaFactory, getComparaFactory, getDaoFactory, getSpecies, setDBVersion, setSpecies
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
getDBVersion, getHashID, getId, getRegistry, getSchemaVersion, setDaoFactory, setId, setRegistry
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface uk.ac.roslin.ensembl.model.core.Gene
getDescription
 
Methods inherited from interface uk.ac.roslin.ensembl.model.core.Feature
addMappedObjectType, getChromosomeMapping, isCurrent, isObjectTypeMapped
 
Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject
addMapping, clearAllMappings, getMappings, getMappings
 
Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBVersion, getHashID, getId, getSchemaVersion, setId
 

Constructor Detail

DAGene

public DAGene()

DAGene

public DAGene(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail

getType

public uk.ac.roslin.ensembl.model.ObjectType getType()
Specified by:
getType in interface uk.ac.roslin.ensembl.model.IdentifiableObject

getAnalysis

public DAAnalysis getAnalysis()
Specified by:
getAnalysis in interface uk.ac.roslin.ensembl.model.core.Gene

setAnalysis

public void setAnalysis(uk.ac.roslin.ensembl.model.core.Analysis analysis)

getBiotype

public String getBiotype()
Specified by:
getBiotype in interface uk.ac.roslin.ensembl.model.core.Gene

setBiotype

public void setBiotype(String biotype)

getTranscripts

public Collection<DATranscript> getTranscripts()
Specified by:
getTranscripts in interface uk.ac.roslin.ensembl.model.core.Gene

addTranscript

public void addTranscript(uk.ac.roslin.ensembl.model.core.Transcript transcript)

getCanonicalTranscript

public DATranscript getCanonicalTranscript()
Specified by:
getCanonicalTranscript in interface uk.ac.roslin.ensembl.model.core.Gene

getStableID

public String getStableID()

setStableID

public void setStableID(String stableID)

getCanonicalTranscriptID

public Integer getCanonicalTranscriptID()

setCanonicalTranscriptID

public void setCanonicalTranscriptID(Integer canonicalTranscriptID)

getCanonicalTranslation

public DATranslation getCanonicalTranslation()
Specified by:
getCanonicalTranslation in interface uk.ac.roslin.ensembl.model.core.Gene

getHomologies

public List<DAHomologyPairRelationship> getHomologies()
Returns all Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene. Implemented by calling getHomologies(EnsemblComparaDivision comparaDivision) with the default ComparaDivision for this Gene.

Specified by:
getHomologies in interface uk.ac.roslin.ensembl.model.core.Gene
Returns:

getHomologies

public List<DAHomologyPairRelationship> getHomologies(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision)
Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.

Specified by:
getHomologies in interface uk.ac.roslin.ensembl.model.core.Gene
Parameters:
comparaDivision -
Returns:

getHomologies

public List<DAHomologyPairRelationship> getHomologies(uk.ac.roslin.ensembl.model.core.Species sp)
Returns Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene for the specified Species. Implemented by calling getHomologies(EnsemblComparaDivision comparaDivision, Species sp) with the default ComparaDivision for this Gene.

Specified by:
getHomologies in interface uk.ac.roslin.ensembl.model.core.Gene
Parameters:
sp -
Returns:

getHomologies

public List<DAHomologyPairRelationship> getHomologies(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision,
                                                      uk.ac.roslin.ensembl.model.core.Species sp)
Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species. Cos of the lack of indices it is much faster to implement using the query to get all homologues than restrict to a single gdb.name in the sql [unless you do it by a specific subselect]. So to get homologues for a single species do the whole query and do the filterring in the Java. This allows us to store all homologies at once too.

Specified by:
getHomologies in interface uk.ac.roslin.ensembl.model.core.Gene
Parameters:
comparaDivision -
sp -
Returns:

addHomology

public void addHomology(uk.ac.roslin.ensembl.config.EnsemblComparaDivision division,
                        DAHomologyPairRelationship homology)

setSearchedHomologies

public boolean setSearchedHomologies(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision)

getDisplayName

public String getDisplayName()
Overrides:
getDisplayName in class DAFeature

getHomologiesWithoutLazyLoad

public List<DAHomologyPairRelationship> getHomologiesWithoutLazyLoad()
Utility method to get all of the current DAHomologyPairRelationships for this Gene

Specified by:
getHomologiesWithoutLazyLoad in interface uk.ac.roslin.ensembl.model.core.Gene
Returns:
List

Ensembl Datasource Aware Module
v1.09

Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3