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.dao.coreaccess; 022 023 import java.util.List; 024 import uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader; 025 import uk.ac.roslin.ensembl.exception.DAOException; 026 import uk.ac.roslin.ensembl.model.core.DNASequence; 027 028 /** 029 * 030 * @author paterson 031 */ 032 public interface DNASequenceDAO { 033 034 public String getSequenceByStartStop(EnsemblDNASequenceReader reader, Integer start, Integer stop) throws DAOException; 035 036 public String getFullSequence(EnsemblDNASequenceReader reader) throws DAOException; 037 038 public DNASequence getSequenceByID(Integer id) throws DAOException ; 039 040 public DNASequence getValidatedSequence(DNASequence seq) throws DAOException ; 041 042 public List<? extends DNASequence> getValidatedSequences(List<? extends DNASequence> sequences) throws DAOException ; 043 044 }