Uses of Interface
uk.ac.roslin.ensembl.model.core.Gene

Packages that use Gene

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

Uses of Gene in uk.ac.roslin.ensembl.dao.compara

Methods in uk.ac.roslin.ensembl.dao.compara with parameters of type Gene

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	HomologyDAO.getHomologiesForGene(Gene g) Specification of Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.

Method parameters in uk.ac.roslin.ensembl.dao.compara with type arguments of type Gene

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	HomologyDAO.getHomologiesForGenesBySpecies(List<? extends Gene> genes, Species target_sp, String chrName) Specification of Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.

Uses of Gene in uk.ac.roslin.ensembl.dao.coreaccess

Methods in uk.ac.roslin.ensembl.dao.coreaccess that return Gene

Modifier and Type	Method and Description
Gene	GeneDAO.addGeneByIDOnParent(Integer id, DNASequence parent)
Gene	GeneDAO.addGeneByStableIDOnParent(String stableID, DNASequence parent)
Gene	GeneDAO.getGeneByID(Integer id)
Gene	GeneDAO.getGeneByStableID(String stableId)

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

Modifier and Type	Method and Description
List<? extends Gene>	GeneDAO.getGenesByExactName(String name)
List<? extends Gene>	GeneDAO.getGenesByNameBeginning(String name)
List<? extends Gene>	GeneDAO.getGenesForVegaID(String id)

Methods in uk.ac.roslin.ensembl.dao.coreaccess with parameters of type Gene

Modifier and Type	Method and Description
List<? extends Transcript>	TranscriptDAO.getTranscriptsForGene(Gene gene)

Uses of Gene in uk.ac.roslin.ensembl.dao.database.compara

Methods in uk.ac.roslin.ensembl.dao.database.compara with parameters of type Gene

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	DBHomologyDAO.getHomologiesForGene(Gene g) Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.

Method parameters in uk.ac.roslin.ensembl.dao.database.compara with type arguments of type Gene

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	DBHomologyDAO.getHomologiesForGenesBySpecies(List<? extends Gene> genes, Species target_sp, String chrName) Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.

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

Methods in uk.ac.roslin.ensembl.dao.database.coreaccess with parameters of type Gene

Modifier and Type	Method and Description
List<DATranscript>	DBTranscriptDAO.getTranscriptsForGene(Gene gene)

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

Classes in uk.ac.roslin.ensembl.datasourceaware.core that implement Gene

Modifier and Type	Class and Description
class	DAGene

Uses of Gene in uk.ac.roslin.ensembl.mapper.compara

Methods in uk.ac.roslin.ensembl.mapper.compara with parameters of type Gene

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	HomologyPairMapper.getHomologiesForGene(Gene g)

Uses of Gene in uk.ac.roslin.ensembl.model.compara

Classes in uk.ac.roslin.ensembl.model.compara with type parameters of type Gene

Modifier and Type	Interface and Description
interface	HomologyPairRelationship<CLAZZ extends Gene> extends HomologyRelationship for those Relationships that are binary
interface	HomologyRelationship<CLAZZ extends Gene> Ensembl schema and PerlAPI claims that homology relationships are not necessarily only binary, i.e. the could have more than two members.

Uses of Gene in uk.ac.roslin.ensembl.model.core

Methods in uk.ac.roslin.ensembl.model.core that return Gene

Modifier and Type	Method and Description
Gene	Transcript.getGene()
Gene	Species.getGeneByStableID(String stableID)
Gene	Species.getGeneByStableID(String stableID, String dbVersion)

Methods in uk.ac.roslin.ensembl.model.core that return types with arguments of type Gene

Modifier and Type	Method and Description
List<? extends Gene>	Species.getGenesForExactName(String name)
List<? extends Gene>	Species.getGenesForExactName(String name, String dbVersion)
List<? extends Gene>	Species.getGenesForNameBeginning(String name)
List<? extends Gene>	Species.getGenesForNameBeginning(String name, String dbVersion)
List<? extends Gene>	Species.getGenesForVegaID(String vegaID)
List<? extends Gene>	Species.getGenesForVegaID(String vegaID, String dbVersion)
List<? extends Gene>	DNASequence.getGenesOnRegion(Coordinate coord)
List<? extends Gene>	DNASequence.getGenesOnRegion(Integer start, Integer stop)
List<? extends Gene>	DNASequence.getGenesOnRegion(Integer start, Integer stop, Coordinate.Strand strand)