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 */ 020 021 022 package uk.ac.roslin.ensembl.model.database; 023 024 import java.util.HashMap; 025 import java.util.List; 026 import java.util.Set; 027 import uk.ac.roslin.ensembl.exception.DAOException; 028 import uk.ac.roslin.ensembl.model.ObjectType; 029 import uk.ac.roslin.ensembl.model.core.Chromosome; 030 import uk.ac.roslin.ensembl.model.core.CoordinateSystem; 031 import uk.ac.roslin.ensembl.model.core.Species; 032 033 /** 034 * 035 * @author tpaterso 036 */ 037 public interface CollectionCoreDatabase extends CollectionDatabase, CoreDatabase { 038 039 public Object getCoreFactory(Species species) ; 040 041 //note these methods mirror the ones in SingleSpeciesCoreDatabase 042 //but takes the required Species parameter 043 044 public CoordinateSystem getChromosomeLevelCS(Species species) throws DAOException; 045 046 public CoordinateSystem getSequenceLevelCS(Species species) throws DAOException; 047 048 public CoordinateSystem getTopLevelCS(Species species) throws DAOException; 049 050 public CoordinateSystem getCSByID(Species species, Integer id) throws DAOException ; 051 052 public CoordinateSystem getBuildCoordSystem(Species species, String featureType) throws DAOException; 053 054 public Set<? extends CoordinateSystem> getCSForFeature(Species sp, ObjectType feature) throws DAOException ; 055 056 public void setBuildLevels(Species species, HashMap<String,String> keyedValues); 057 058 public String getBuildLevel(Species species, String featureKey) throws DAOException ; 059 060 public List<? extends ObjectType> getFeaturesForCS(Species sp, CoordinateSystem coordSys) throws DAOException; 061 062 public Integer getMaxLengthForFeature(Species sp, ObjectType feature, CoordinateSystem cs) throws DAOException ; 063 064 public void addFeatureCS(String featureType, Integer csID, Integer maxLength, Species sp) ; 065 066 public Chromosome getChromosomeByName(Species species, String name) throws DAOException ; 067 068 public List<? extends Chromosome> getChromosomes(Species species) throws DAOException ; 069 070 }