001/**
002 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003 *
004 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006 * Veterinary Studies, University of Edinburgh.
007 *
008 * Project hosted at: http://jensembl.sourceforge.net
009 *
010 * This is free software: you can redistribute it and/or modify
011 * it under the terms of the GNU General Public License (version 3) as published by
012 * the Free Software Foundation.
013 *
014 * This software is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
021 */
022package uk.ac.roslin.ensembl.mapper.core;
023
024import java.util.HashMap;
025import java.util.List;
026import uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence;
027import uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome;
028
029
030public interface ChromosomeMapper {
031    public DAChromosome getChromosomeByName_CoordSysID(HashMap parameter);
032    public DAAssembledDNASequence getTopLevelFragmentByName_CoordSysID(HashMap parameter);
033    public List<DAChromosome> getChromosomesByCoordSysID(HashMap parameter);
034    public List<DAAssembledDNASequence> getTopLevelFragmentsByCoordSysID(HashMap parameter);
035    public String getSexLinkedChromosomeName(HashMap parameter);
036    public List<HashMap> getAssemblyExceptions(HashMap parameters);
037}