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

Packages that use DAGene

Package	Description
uk.ac.roslin.ensembl.dao.database
uk.ac.roslin.ensembl.dao.database.coreaccess
uk.ac.roslin.ensembl.datasourceaware.compara
uk.ac.roslin.ensembl.datasourceaware.core
uk.ac.roslin.ensembl.mapper.core

Uses of DAGene in uk.ac.roslin.ensembl.dao.database

Methods in uk.ac.roslin.ensembl.dao.database that return DAGene

Modifier and Type	Method and Description
DAGene	DBSpecies.getGeneByStableID(String stableID)
DAGene	DBSpecies.getGeneByStableID(String stableID, String dbVersion)
DAGene	DBCollectionSpecies.getGeneByStableID(String stableID, String dbVersion)

Methods in uk.ac.roslin.ensembl.dao.database that return types with arguments of type DAGene

Modifier and Type	Method and Description
List<DAGene>	DBSpecies.getGenesForExactName(String name)
List<DAGene>	DBSpecies.getGenesForExactName(String name, String dbVersion)
List<DAGene>	DBCollectionSpecies.getGenesForExactName(String name, String dbVersion)
List<DAGene>	DBSpecies.getGenesForNameBeginning(String name)
List<DAGene>	DBSpecies.getGenesForNameBeginning(String name, String dbVersion)
List<DAGene>	DBSpecies.getGenesForVegaID(String vegaID) Method returns a List of Genes that have been mapped to the given Vega Identifier.
List<DAGene>	DBSpecies.getGenesForVegaID(String vegaID, String dbVersion) Method returns a List of Genes that have been mapped to the given Vega Identifier.
List<DAGene>	DBCollectionSpecies.getGenesForVegaID(String vegaID, String dbVersion) Method returns a List of Genes that have been mapped to the given Vega Identifier.

Uses of DAGene in uk.ac.roslin.ensembl.dao.database.coreaccess

Methods in uk.ac.roslin.ensembl.dao.database.coreaccess that return DAGene

Modifier and Type	Method and Description
DAGene	DBGeneDAO.addGeneByIDOnParent(Integer id, DNASequence parent)
DAGene	DBGeneDAO.addGeneByStableIDOnParent(String stableID, DNASequence parent) The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to
DAGene	DBGeneDAO.getGeneByID(Integer id)
DAGene	DBGeneDAO.getGeneByStableID(String stableID)
DAGene	DBGeneDAO.GeneMappingRowHandler.getObjectResult()
DAGene	DBChromosomeDAO.AssemblyExceptionRowHandler.getObjectResult()

Methods in uk.ac.roslin.ensembl.dao.database.coreaccess that return types with arguments of type DAGene

Modifier and Type	Method and Description
List<DAGene>	DBGeneDAO.getGenesByExactName(String name)
List<DAGene>	DBGeneDAO.getGenesByNameBeginning(String name)
List<DAGene>	DBGeneDAO.getGenesForVegaID(String id) Returns a list of Ensembl Genes matching the query VegaID string.
List<DAGene>	DBGeneDAO.GeneMappingRowHandler.getListResult()
List<DAGene>	DBChromosomeDAO.AssemblyExceptionRowHandler.getListResult()

Constructors in uk.ac.roslin.ensembl.dao.database.coreaccess with parameters of type DAGene

Constructor and Description
DBTranscriptDAO.TranscriptRowHandler(List<HashMap> results, DAGene g)

Uses of DAGene in uk.ac.roslin.ensembl.datasourceaware.compara

Methods in uk.ac.roslin.ensembl.datasourceaware.compara that return DAGene

Modifier and Type	Method and Description
DAGene	InverseHomologyPairRelationshipView.getSource()
DAGene	DAHomologyPairRelationship.getSource()
DAGene	InverseHomologyPairRelationshipView.getTarget()
DAGene	DAHomologyPairRelationship.getTarget()

Methods in uk.ac.roslin.ensembl.datasourceaware.compara that return types with arguments of type DAGene

Modifier and Type	Method and Description
TreeSet<DAGene>	InverseHomologyPairRelationshipView.getMembers()
TreeSet<DAGene>	DAHomologyRelationship.getMembers()
TreeSet<DAGene>	DAHomologyPairRelationship.getMembers()

Methods in uk.ac.roslin.ensembl.datasourceaware.compara with parameters of type DAGene

Modifier and Type	Method and Description
void	DAHomologyPairRelationship.setSource(DAGene source)
void	DAHomologyPairRelationship.setTarget(DAGene target)

Uses of DAGene in uk.ac.roslin.ensembl.datasourceaware.core

Methods in uk.ac.roslin.ensembl.datasourceaware.core that return DAGene

Modifier and Type	Method and Description
DAGene	DATranslation.getGene() Gets the Gene associated with this Translation via the associated Transcript.
DAGene	DATranscript.getGene() Gets the Gene associated with this transcript, using the stableID for the gene set on Transcript initialization.

Methods in uk.ac.roslin.ensembl.datasourceaware.core that return types with arguments of type DAGene

Modifier and Type	Method and Description
List<DAGene>	DADNASequence.getGenesOnRegion(Coordinate coord) Returns a List of Genes on the specified Coordinate region.
List<DAGene>	DADNASequence.getGenesOnRegion(Integer start, Integer stop) Returns a List of Genes on the specified Region.
List<DAGene>	DADNASequence.getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand) Returns a List of Genes on the specified Region.

Methods in uk.ac.roslin.ensembl.datasourceaware.core with parameters of type DAGene

Modifier and Type	Method and Description
void	DATranscript.setGene(DAGene gene)

Uses of DAGene in uk.ac.roslin.ensembl.mapper.core

Methods in uk.ac.roslin.ensembl.mapper.core that return types with arguments of type DAGene

Modifier and Type	Method and Description
List<DAGene>	GeneMapper.getGenesByName(FeatureQuery query)