Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Data Access Module
v1.09

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

java.lang.Object
  extended by uk.ac.roslin.ensembl.dao.database.DBBaseDAO
      extended by uk.ac.roslin.ensembl.dao.database.compara.DBHomologyDAO
All Implemented Interfaces:
uk.ac.roslin.ensembl.dao.compara.HomologyDAO

public class DBHomologyDAO
extends DBBaseDAO
implements uk.ac.roslin.ensembl.dao.compara.HomologyDAO


Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBBaseDAO
configuration, daoFactory
 
Constructor Summary
DBHomologyDAO(uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory factory)
           
 
Method Summary
 List<uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship> getHomologiesForGene(uk.ac.roslin.ensembl.model.core.Gene g)
           
 HashMap<uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence,uk.ac.roslin.ensembl.model.MappingSet> getRegionsOfConservedSynteny(uk.ac.roslin.ensembl.model.core.Chromosome source, uk.ac.roslin.ensembl.model.Coordinate range, uk.ac.roslin.ensembl.model.core.Species target)
           
 
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(uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory factory)
              throws uk.ac.roslin.ensembl.exception.DAOException
Throws:
uk.ac.roslin.ensembl.exception.DAOException
Method Detail

getHomologiesForGene

public List<uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship> getHomologiesForGene(uk.ac.roslin.ensembl.model.core.Gene g)
                                                                                                   throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getHomologiesForGene in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getRegionsOfConservedSynteny

public HashMap<uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence,uk.ac.roslin.ensembl.model.MappingSet> getRegionsOfConservedSynteny(uk.ac.roslin.ensembl.model.core.Chromosome source,
                                                                                                                                           uk.ac.roslin.ensembl.model.Coordinate range,
                                                                                                                                           uk.ac.roslin.ensembl.model.core.Species target)
                                                                                                                                    throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getRegionsOfConservedSynteny in interface uk.ac.roslin.ensembl.dao.compara.HomologyDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

Ensembl Data Access Module
v1.09

Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3