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.model.database;
023
024import java.util.List;
025import java.util.Set;
026import uk.ac.roslin.ensembl.exception.DAOException;
027import uk.ac.roslin.ensembl.model.ObjectType;
028import uk.ac.roslin.ensembl.model.core.AssembledDNASequence;
029import uk.ac.roslin.ensembl.model.core.Chromosome;
030import uk.ac.roslin.ensembl.model.core.CoordinateSystem;
031
032/**
033 *
034 * @author tpaterso
035 */
036public interface SingleSpeciesCoreDatabase extends SingleSpeciesDatabase, CoreDatabase {
037
038   public Object getCoreFactory() ;
039
040    //note these methods are mirrored in CollectionCoreDatabase
041    //where they take the required Species parameter
042
043   public CoordinateSystem getTopLevelCoordSystem() throws DAOException;
044
045   public CoordinateSystem getChromosomeLevelCoordSystem()throws DAOException;
046
047   public CoordinateSystem getSequenceLevelCoordSystem() throws DAOException;
048   
049   public CoordinateSystem getCSByID(Integer id) throws DAOException;
050
051   public CoordinateSystem getBuildCoordSystem(String featureType) throws DAOException ;
052
053   public Set<? extends CoordinateSystem> getCSForFeature(ObjectType featureType) throws DAOException;
054
055   public Chromosome getChromosomeByName(String name) throws DAOException ;
056
057   public List<? extends Chromosome> getChromosomes() throws DAOException ;
058
059   public AssembledDNASequence getFragmentByName(String name) throws DAOException ;
060
061   public List<? extends AssembledDNASequence> getFragments() throws DAOException ;
062
063   public void setBuildLevel(String featureKey, String level) ;
064
065   public String getBuildLevel(String featureType) throws DAOException ;
066
067   public List<? extends ObjectType> getFeaturesForCS(CoordinateSystem coordSys) throws DAOException ;
068
069   public Integer getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs) throws DAOException ;
070
071   public void addFeatureCS(String featureType, Integer csID, Integer maxLength) ;
072   
073   public String getAssemblyName() ;
074
075   public String getComparaName() ;
076   
077   public String getAssemblyAccession() ;
078
079   public void setAssemblyName(String value);
080   
081   public void setAssemblyAccession(String value);
082
083   public void setComparaName(String comparaName);
084    
085}