Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.datasourceaware.core
Class DAGene
java.lang.Object
uk.ac.roslin.ensembl.datasourceaware.DAObject
uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
uk.ac.roslin.ensembl.datasourceaware.core.DAFeature
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
Constructor Summary |
DAGene()
|
DAGene(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
|
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 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 |
DAGene
public DAGene()
DAGene
public DAGene(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
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
© Roslin Institute 2010. GNU General Public License, version3