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     */
022    package org.biojava3.core.sequence.io;
023    
024    import java.io.DataInput;
025    import org.biojava3.core.sequence.io.template.SequenceParserInterface;
026    
027    /**
028     * Used to parse a stream of a fasta file to get the sequence
029     * @author Scooter Willis <willishf at gmail dot com>
030     */
031    public class FastaSequenceParser implements SequenceParserInterface {
032    
033        public String getSequence(DataInput dataInput, int sequenceLength) throws Exception {
034            StringBuilder sb;
035            if (sequenceLength != -1) {
036                sb = new StringBuilder(sequenceLength);
037            } else {
038                sb = new StringBuilder();
039            }
040            boolean keepGoing = true;
041            while (keepGoing) {
042                String line = dataInput.readLine();
043                if (line == null || line.startsWith(">")) {
044                    break;
045                }
046                sb.append(line.trim());
047            }
048            return sb.toString();
049        }
050    }