001 /** 002 * Copyright (C) 2010 The Roslin Institute <contact andy.law@roslin.ed.ac.uk> 003 * 004 * This file is part of the Ensembl Java API demonstration project developed by the 005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of 006 * Veterinary Studies, University of Edinburgh. 007 * 008 * This is free software: you can redistribute it and/or modify 009 * it under the terms of the GNU General Public License (version 3) as published by 010 * the Free Software Foundation. 011 * 012 * This software is distributed in the hope that it will be useful, 013 * but WITHOUT ANY WARRANTY; without even the implied warranty of 014 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 015 * GNU General Public License for more details. 016 * 017 * You should have received a copy of the GNU General Public License 018 * in this software distribution. If not, see <http://www.gnu.org/licenses/gpl-3.0.html/>. 019 */ 020 021 package uk.ac.roslin.ensembl.datasourceaware.core; 022 023 import java.util.HashMap; 024 import java.util.List; 025 import uk.ac.roslin.ensembl.dao.compara.HomologyDAO; 026 import uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory; 027 import uk.ac.roslin.ensembl.exception.DAOException; 028 import uk.ac.roslin.ensembl.model.Coordinate; 029 import uk.ac.roslin.ensembl.model.MappingSet; 030 import uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship; 031 import uk.ac.roslin.ensembl.model.core.Chromosome; 032 import uk.ac.roslin.ensembl.model.core.Species; 033 034 /** 035 * 036 * @author paterson 037 */ 038 public class DAChromosome extends DAAssembledDNASequence implements Chromosome{ 039 040 public DAChromosome() { 041 super(); 042 } 043 044 public DAChromosome(DAOCoreFactory factory) { 045 super(factory); 046 } 047 048 public String getChromosomeName() { 049 return this.getName(); 050 } 051 052 public void setChromosomeName(String name) { 053 this.setName(name); 054 } 055 056 @Override 057 public String toString() { 058 return this.getChromosomeName(); 059 } 060 061 @Override 062 public HashMap<DADNASequence, MappingSet> getRegionsOfConservedSynteny(Coordinate range, 063 Species target) throws DAOException { 064 065 if (target==null) { 066 throw new DAOException("No Sspecies specified for getRegionsOfConservedSynteny"); 067 } 068 069 070 try { 071 HashMap<DADNASequence, MappingSet> syntenies = null; 072 073 HomologyDAO dao = 074 this.getComparaFactory().getHomologyDAO(); 075 076 syntenies = (HashMap<DADNASequence, MappingSet>) dao.getRegionsOfConservedSynteny(this, range, target); 077 078 return syntenies; 079 } catch (DAOException dex) { 080 throw dex; 081 } catch (Exception e) { 082 throw new DAOException("Failed to Access Compara to get Regions of Conserved Synteny", e); 083 } 084 } 085 }