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.model.core; 022 023 import java.util.HashMap; 024 import java.util.List; 025 import org.biojava3.core.sequence.compound.NucleotideCompound; 026 import org.biojava3.core.sequence.template.Sequence; 027 import uk.ac.roslin.ensembl.exception.DAOException; 028 import uk.ac.roslin.ensembl.model.Coordinate; 029 import uk.ac.roslin.ensembl.model.Coordinate.Strand; 030 import uk.ac.roslin.ensembl.model.CoordinateSet; 031 import uk.ac.roslin.ensembl.model.MappableObject; 032 import uk.ac.roslin.ensembl.model.MappingSet; 033 import uk.ac.roslin.ensembl.model.ObjectType; 034 035 /** 036 * 037 * @author paterson 038 */ 039 public interface DNASequence extends CoreObject, MappableObject, Sequence<NucleotideCompound> { 040 041 public Integer getDBSeqLength() ; 042 043 public void setDBSeqLength(Integer seqLength) ; 044 045 public CoordinateSystem getCoordSystem() ; 046 047 public void setCoordSystem(CoordinateSystem coordSystem) ; 048 049 public String getName() ; 050 051 public void setName(String name) ; 052 053 public List<? extends Gene> getGenesOnRegion(Coordinate coord) throws DAOException ; 054 055 public List<? extends Gene> getGenesOnRegion(Integer start, Integer stop) throws DAOException ; 056 057 public List<? extends Gene> getGenesOnRegion(Integer start, Integer stop, Strand strand) throws DAOException ; 058 059 public String getSequenceAsString(Integer begin, Integer end) ; 060 061 public String getReverseComplementSequenceAsString(Integer begin, Integer end) ; 062 063 public String getReverseComplementSequenceAsString() ; 064 065 public HashMap<ObjectType, ? extends MappingSet> getObjectTypeMappings() ; 066 067 public HashMap<ObjectType, CoordinateSet> getMappedRegions() ; 068 069 }