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    • org.biojava.nbio.genome.io.fastq.FastqParser Maven / Gradle / Ivy

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    /*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.genome.io.fastq;

import com.google.common.io.CharStreams;
import com.google.common.io.LineProcessor;

import java.io.IOException;

/**
 * Low-level event based parser for FASTQ formatted sequences.
 *
 * @since 3.0.3
 */
final class FastqParser
{

	/**
	 * Parse the specified readable.
	 *
	 * @param readable readable, must not be null
	 * @param listener low-level event based parser callback, must not be null
	 * @throws IOException if an I/O error occurs
	 */
	static void parse(final Readable readable, final ParseListener listener)
		throws IOException
	{
		if (readable == null)
		{
			throw new IllegalArgumentException("readable must not be null");
		}
		FastqParserLineProcessor lineProcessor = new FastqParserLineProcessor(listener);
		CharStreams.readLines(readable, lineProcessor);
		if (lineProcessor.getState() == State.COMPLETE)
		{
			listener.complete();
			lineProcessor.setState(State.DESCRIPTION);
		}
		if (lineProcessor.getState() != State.DESCRIPTION)
		{
			throw new IOException("truncated sequence"); // at line " + lineNumber);
		}
	}

	/**
	 * FASTQ formatted sequence parser line processor.
	 */
	private static final class FastqParserLineProcessor implements LineProcessor
	{
		/** Parser state. */
		private State state = State.DESCRIPTION;

		/** Sequence length. */
		private int sequenceLength = 0;

		/** Quality length. */
		private int qualityLength = 0;

		/** Parse listener. */
		private final ParseListener listener;


		/**
		 * Create a new FASTQ formatted sequence parser line processor with the specified parse listener.
		 *
		 * @param listener parse listener, must not be null
		 */
		private FastqParserLineProcessor(final ParseListener listener)
		{
			if (listener == null)
			{
				throw new IllegalArgumentException("listener must not be null");
			}
			this.listener = listener;
		}


		/**
		 * Return the parser state.
		 *
		 * @return the parser state
		 */
		private State getState()
		{
			return state;
		}

		/**
		 * Set the parser state to state.
		 *
		 * @param state parser state
		 */
		private void setState(final State state)
		{
			this.state = state;
		}

		@Override
		public Object getResult()
		{
			return null;
		}

		@Override
		public boolean processLine(final String line) throws IOException
		{
			String sequence = null;
			String quality = null;
			switch (state)
			{
			case DESCRIPTION:
				if (line.startsWith("@"))
				{
					listener.description(line.substring(1).trim());
					state = State.SEQUENCE;
				}
				else
				{
					throw new IOException("description must begin with a '@' character");
				}
				break;
			case SEQUENCE:
				sequence = line.trim();
				listener.sequence(sequence);
				sequenceLength = sequence.length();
				state = State.REPEAT_DESCRIPTION;
				break;
			case REPEAT_DESCRIPTION:
				if (line.startsWith("+"))
				{
					listener.repeatDescription(line.substring(1).trim());
					state = State.QUALITY;
				}
				else
				{
					sequence = line.trim();
					listener.appendSequence(sequence);
					sequenceLength += sequence.length();
				}
				break;
			case QUALITY:
				quality = line.trim();
				listener.quality(quality);
				qualityLength = quality.length();
				state = State.COMPLETE;
				break;
			case COMPLETE:
				if (sequenceLength == qualityLength)
				{
					listener.complete();

					if (line.startsWith("@"))
					{
						listener.description(line.substring(1).trim());
						state = State.SEQUENCE;
					}
					else
					{
						throw new IOException("description must begin with a '@' character");
					}
				}
				else
				{
					quality = line.trim();
					listener.appendQuality(quality);
					qualityLength += quality.length();
				}
				break;
			default:
				break;
			}
			return true;
		}
	}

	/** Parser state. */
	private static enum State
	{
		/** Description parser state. */
		DESCRIPTION,

		/** Sequence parser state. */
		SEQUENCE,

		/** Repeat description parser state. */
		REPEAT_DESCRIPTION,

		/** Quality score parser state. */
		QUALITY,

		/** Complete parser state. */
		COMPLETE;
	};
}
    
    
    
    

    




    
    
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