001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on 01-21-2010
021 */
022package org.biojava.nbio.core.sequence.io;
023
024import org.biojava.nbio.core.sequence.io.template.SequenceParserInterface;
025
026import java.io.BufferedReader;
027import java.io.IOException;
028
029/**
030 * Used to parse a stream of a fasta file to get the sequence
031 * @author Scooter Willis <willishf at gmail dot com>
032 */
033public class FastaSequenceParser implements SequenceParserInterface {
034
035        @Override
036        public String getSequence(BufferedReader bufferedReader, int sequenceLength) throws IOException {
037                StringBuilder sb;
038                if (sequenceLength != -1) {
039                        sb = new StringBuilder(sequenceLength);
040                } else {
041                        sb = new StringBuilder();
042                }
043                boolean keepGoing = true;
044                while (keepGoing) {
045                        String line = bufferedReader.readLine();
046                        if (line == null || line.startsWith(">")) {
047                                break;
048                        }
049                        sb.append(line.trim());
050                }
051                return sb.toString();
052        }
053}