uk.ac.roslin.ensembl.dao.compara

Interface HomologyDAO

All Known Implementing Classes:

DBHomologyDAO

public interface HomologyDAO

Method Summary

Methods

Modifier and Type	Method and Description
List<? extends HomologyPairRelationship>	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.
List<? extends HomologyPairRelationship>	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.
HashMap<? extends DNASequence,? extends MappingSet>	getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) Specification of Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.
HashMap<? extends DNASequence,? extends MappingSet>	getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) Specification of Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

Method Detail

getHomologiesForGene

List<? extends HomologyPairRelationship> getHomologiesForGene(Gene g)
                                                              throws DAOException

Specification of Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.

Parameters:

g - The query Gene

Returns:

List of HomologyPairRelationships

Throws:

DAOException

getHomologiesForGenesBySpecies

List<? extends HomologyPairRelationship> getHomologiesForGenesBySpecies(List<? extends Gene> genes,
                                                                      Species target_sp,
                                                                      String chrName)
                                                                        throws DAOException

Specification of Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs. The query may be restricted by specifying a target chromosome Name (In effect a filter on the full query, for efficiency where the target chromosome is already known.

Parameters:

genes - theList of query genes

target_sp - The target Species

chrName - The target chromosome name

Returns:

List of HomologyPairRelationships

Throws:

DAOException

getRegionsOfConservedSynteny

HashMap<? extends DNASequence,? extends MappingSet> getRegionsOfConservedSynteny(DNASequence source,
                                                                               Coordinate range,
                                                                               Species target)
                                                                                 throws DAOException

Specification of Data Access method to retrieve all of the regions on DNASequences for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence.

Parameters:

source - DNASequence to be queried

range - Coordinate range of query sequence to be queried

target - the target species

Returns:

HashMap of Syntenic regions against the set of Mappings holding homologous genes

Throws:

DAOException

getRegionsOfConservedSynteny

HashMap<? extends DNASequence,? extends MappingSet> getRegionsOfConservedSynteny(DNASequence source,
                                                                               Coordinate range,
                                                                               Species target,
                                                                               String chrName)
                                                                                 throws DAOException

Specification of Data Access method to retrieve any potential region of conserved synteny on a given Chromosome/fragment for the specified target species, holding genes with homologies to genes found in the given region of the source query sequence. In effect a filter on the full query, for efficiency where the target chromosome is already known.

Parameters:

source - DNASequence to be queried

range - Coordinate range of query sequence to be queried

target - the target species

chrName - the target chromosome name

Returns:

HashMap of Syntenic regions against the set of Mappings holding homologous genes

Throws:

DAOException