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.DAAnalyzedFeature

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

All Implemented Interfaces:

Serializable, Analyzed, CoreObject, Feature, Gene, VegaFeature, WithDisplayXRef, IdentifiableObject, MappableObject, StableID, XRefed

public class DAGene
extends DAAnalyzedFeature
implements Gene, VegaFeature, XRefed

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

Modifier and Type	Field and Description
protected HashMap<ExternalDBType,Set<DAXRef>>	typedXRefs
protected Set<DAXRef>	xrefs

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

current, description, displayName, displayXRef, initialized, length, mappedObjectTypes, mappings, objectTypeMappings, status, thisSequence

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

comparaFactories, creationDate, modificationDate, species, stableID, version

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

daComparator, daoFactory, dbVersion, id, registry, schemaVersion

Constructor Summary

Constructors

Constructor and Description
DAGene()
DAGene(DAOCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
void	addHomology(EnsemblComparaDivision division, DAHomologyPairRelationship homology)
void	addTranscript(Transcript transcript)
protected void	addTypedXRefs(ExternalDBType type, Collection<? extends XRef> xrefs)
TreeSet<String>	getAllSynonyms()
Set<DAXRef>	getAllXRefs()
String	getBiotype()
DATranscript	getCanonicalTranscript()
Integer	getCanonicalTranscriptID()
DATranslation	getCanonicalTranslation()
EnsemblComparaDivision	getComparaDivision() Note the special case for Bacteria in collections in DB >16
String	getDisplayName()
DAXRef	getDisplayXRef()
Integer	getHomoeologueCount()
List<DAHomologyPairRelationship>	getHomologies() Returns all Homologies (as a List of HomologyPairRelationships) in the default ComparaDivision for this Gene.
List<DAHomologyPairRelationship>	getHomologies(EnsemblComparaDivision comparaDivision) Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.
List<DAHomologyPairRelationship>	getHomologies(EnsemblComparaDivision comparaDivision, Species sp) Returns Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for the specified Species.
List<DAHomologyPairRelationship>	getHomologies(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
Integer	getOrthologueCount()
Integer	getParalogueCount()
String	getStableID()
TreeSet<String>	getSynonyms(XRef xref)
Collection<DATranscript>	getTranscripts()
ObjectType	getType()
String	getVegaID() Returns any curated VegaID for the Gene, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).
Set<DAXRef>	getVegaXRefs()
protected Set<DAXRef>	getXRefs(ExternalDBType type) Returns preloaded XRefs of given type: Note - does not lazy load these
void	setBiotype(String biotype)
void	setCanonicalTranscript(DATranscript transcript)
void	setCanonicalTranscriptID(Integer canonicalTranscriptID)
void	setDisplayXRef(DAXRef xref)
void	setHomoeologueCount(Integer homoeologueCount)
void	setOrthologueCount(Integer orthologueCount)
void	setParalogueCount(Integer paralogueCount)
boolean	setSearchedHomologies(EnsemblComparaDivision comparaDivision)
void	setStableID(String stableID)

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalyzedFeature

getAnalysis, getAnalysisID, setAnalysisID

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature

addMappedObjectType, addMapping, clearAllMappings, convertChromosomePositionToFeature, convertToTargetCoordinate, convertToTargetPosition, getAnnotationLevelMappings, getBuildLevelMappings, getChromosomeMapping, getChromosomeMapping, getChromosomeMappings, getCreationDate, getDescription, getFlankingTargetSequenceAsString, getId, getLength, getLoadedMappings, getLoadedMappings, getModificationDate, getPaddedFlankingTargetSequenceAsString, getRNASequence, getRNASequenceAsString, getRNASequenceAsString, getSequence, getSequenceAsString, getSequenceAsString, getStatus, getTargetSequence, getTopLevelMappings, getTopLevelTargetCoordinates, getTopLevelTargetSequence, getVersion, inititializeTopLevel, isCurrent, isInitialized, isObjectTypeMapped, setCurrent, setDescription, setDisplayName, setInitialized, setLength, setStatus

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

getAssembly, getComparaFactory, getComparaFactory, getDaoFactory, getSpecies, setCreationDate, setDBVersion, setModificationDate, setSpecies, setVersion

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

getDBVersion, getHashID, getRegistry, getSchemaVersion, isLazyloadAllowed, setDaoFactory, setId, setLazyloadAllowed, 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, getChromosomeMapping, getChromosomeMappings, isCurrent, isObjectTypeMapped

Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject

addMapping, clearAllMappings, getLoadedMappings, getLoadedMappings

Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject

getDBVersion, getHashID, getId, getSchemaVersion, setId

Methods inherited from interface uk.ac.roslin.ensembl.model.core.Analyzed

getAnalysis, getAnalysisID, setAnalysisID

Field Detail

xrefs

protected Set<DAXRef> xrefs

typedXRefs

protected HashMap<ExternalDBType,Set<DAXRef>> typedXRefs

Constructor Detail

DAGene

public DAGene()

DAGene

public DAGene(DAOCoreFactory factory)

Method Detail

getType

public ObjectType getType()

Specified by:

getType in interface IdentifiableObject

getBiotype

public String getBiotype()

Specified by:

getBiotype in interface Gene

setBiotype

public void setBiotype(String biotype)

getTranscripts

public Collection<DATranscript> getTranscripts()

Specified by:

getTranscripts in interface Gene

addTranscript

public void addTranscript(Transcript transcript)

getCanonicalTranscript

public DATranscript getCanonicalTranscript()

Specified by:

getCanonicalTranscript in interface Gene

setCanonicalTranscript

public void setCanonicalTranscript(DATranscript transcript)

getStableID

public String getStableID()

Specified by:

getStableID in interface StableID

Overrides:

getStableID in class DACoreObject

setStableID

public void setStableID(String stableID)

Specified by:

setStableID in interface StableID

Overrides:

setStableID in class DACoreObject

getCanonicalTranscriptID

public Integer getCanonicalTranscriptID()

setCanonicalTranscriptID

public void setCanonicalTranscriptID(Integer canonicalTranscriptID)

getCanonicalTranslation

public DATranslation getCanonicalTranslation()

Specified by:

getCanonicalTranslation in interface Gene

getComparaDivision

public EnsemblComparaDivision getComparaDivision()

Note the special case for Bacteria in collections in DB >16

Overrides:

getComparaDivision in class DACoreObject

Returns:

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 Gene

getHomologies

public List<DAHomologyPairRelationship> getHomologies(EnsemblComparaDivision comparaDivision)

Returns all Homologies (as a List of HomologyPairRelationships) in the specified ComparaDivision for this Gene.

Specified by:

getHomologies in interface Gene

Parameters:

comparaDivision -

getHomologies

public List<DAHomologyPairRelationship> getHomologies(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 Gene

Parameters:

sp -

getHomologies

public List<DAHomologyPairRelationship> getHomologies(EnsemblComparaDivision comparaDivision,
                                             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 Gene

Parameters:

comparaDivision -

sp -

addHomology

public void addHomology(EnsemblComparaDivision division,
               DAHomologyPairRelationship homology)

setSearchedHomologies

public boolean setSearchedHomologies(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 Gene

Returns:

List

getXRefs

protected Set<DAXRef> getXRefs(ExternalDBType type)

Returns preloaded XRefs of given type: Note - does not lazy load these

Parameters:

type -

getDisplayXRef

public DAXRef getDisplayXRef()

Specified by:

getDisplayXRef in interface WithDisplayXRef

setDisplayXRef

public void setDisplayXRef(DAXRef xref)

getVegaID

public String getVegaID()

Returns any curated VegaID for the Gene, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).

Specified by:

getVegaID in interface VegaFeature

Returns:

String the VegaID of this Gene

getVegaXRefs

public Set<DAXRef> getVegaXRefs()

Specified by:

getVegaXRefs in interface VegaFeature

getAllXRefs

public Set<DAXRef> getAllXRefs()

Specified by:

getAllXRefs in interface XRefed

getAllSynonyms

public TreeSet<String> getAllSynonyms()

Specified by:

getAllSynonyms in interface XRefed

getSynonyms

public TreeSet<String> getSynonyms(XRef xref)

Specified by:

getSynonyms in interface XRefed

addTypedXRefs

protected void addTypedXRefs(ExternalDBType type,
                 Collection<? extends XRef> xrefs)

getOrthologueCount

public Integer getOrthologueCount()

setOrthologueCount

public void setOrthologueCount(Integer orthologueCount)

getParalogueCount

public Integer getParalogueCount()

setParalogueCount

public void setParalogueCount(Integer paralogueCount)

getHomoeologueCount

public Integer getHomoeologueCount()

setHomoeologueCount

public void setHomoeologueCount(Integer homoeologueCount)