uk.ac.roslin.ensembl.dao.database.compara

Class DBHomologyDAO

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBBaseDAO

uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO

All Implemented Interfaces:

HomologyDAO

public class DBHomologyDAO
extends DBBaseDAO
implements HomologyDAO

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

configuration, daoFactory

Constructor Summary

Constructors

Constructor and Description
DBHomologyDAO(DAOComparaFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
List<DAHomologyPairRelationship>	getHomologiesForGene(Gene g) Data Access method to retrieve all of the homologies (i.e. to all species) for a given gene with a stableID.
List<DAHomologyPairRelationship>	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.
HashMap<DADNASequence,MappingSet>	getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target) 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<DADNASequence,MappingSet>	getRegionsOfConservedSynteny(DNASequence source, Coordinate range, Species target, String chrName) 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.

Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBBaseDAO

getFactory, setConfiguration, setFactory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DBHomologyDAO

public DBHomologyDAO(DAOComparaFactory factory)
              throws DAOException

Throws:

DAOException

Method Detail

getHomologiesForGene

public List<DAHomologyPairRelationship> getHomologiesForGene(Gene g)
                                                      throws DAOException

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

Specified by:

getHomologiesForGene in interface HomologyDAO

Parameters:

g - The query Gene

Returns:

List of HomologyPairRelationships

Throws:

DAOException

getHomologiesForGenesBySpecies

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

Data Access method to retrieve all of the homologies in the specified target species for a List of genes with stableIDs.

Specified by:

getHomologiesForGenesBySpecies in interface HomologyDAO

Parameters:

genes - theList of query genes

target_sp - The target Species

chrName - The target chromosome name

Returns:

List of HomologyPairRelationships

Throws:

DAOException

getRegionsOfConservedSynteny

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

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.

Specified by:

getRegionsOfConservedSynteny in interface HomologyDAO

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

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

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.

Specified by:

getRegionsOfConservedSynteny in interface HomologyDAO

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