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.biojava3; 022 023 import java.io.Serializable; 024 import org.biojava3.core.sequence.compound.NucleotideCompound; 025 import org.biojava3.core.sequence.template.ProxySequenceReader; 026 027 /** 028 * 029 * @author paterson 030 */ 031 public interface EnsemblDNASequenceReader extends ProxySequenceReader<NucleotideCompound>, Serializable { 032 033 public String getName() ; 034 035 public void setName(String name) ; 036 037 public Integer getCoordSystemID() ; 038 039 public void setCoordSystemID(Integer coordSystemID) ; 040 041 public Integer getLengthInteger(); 042 043 public void setLength(Integer length) ; 044 045 public Integer getSeqRegionID() ; 046 047 public void setSeqRegionID(Integer seqRegionID); 048 049 public String getReverseComplementSequenceAsString(Integer start, Integer end) ; 050 }