org.biojava.nbio.genome.io.fastq.Fastq Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of biojava-genome Show documentation
The newest version!
/*
 *                    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;

/**
 * FASTQ formatted sequence.
 *
 * @since 3.0.3
 */
public final class Fastq
{
	/** Description of this FASTQ formatted sequence. */
	private final String description;

	/** Sequence for this FASTQ formatted sequence. */
	private final String sequence;

	/** Quality scores for this FASTQ formatted sequence. */
	private final String quality;

	/** FASTQ sequence format variant for this FASTQ formatted sequence. */
	private final FastqVariant variant;


	/**
	 * Create a new FASTQ formatted sequence from the specified description, sequence, quality scores,
	 * and sequence format variant.
	 *
	 * @param description description of this FASTQ formatted sequence, must not be null
	 * @param sequence sequence for this FASTQ formatted sequence, must not be null
	 * @param quality quality scores for this FASTQ formatted sequence, must not be null
	 * @param variant FASTQ sequence format variant for this FASTQ formatted sequence, must not be null
	 */
	Fastq(final String description,
		  final String sequence,
		  final String quality,
		  final FastqVariant variant)
	{
		if (description == null)
		{
			throw new IllegalArgumentException("description must not be null");
		}
		if (sequence == null)
		{
			throw new IllegalArgumentException("sequence must not be null");
		}
		if (quality == null)
		{
			throw new IllegalArgumentException("quality must not be null");
		}
		if (variant == null)
		{
			throw new IllegalArgumentException("variant must not be null");
		}
		this.description = description;
		this.sequence = sequence;
		this.quality = quality;
		this.variant = variant;
	}


	/**
	 * Return the description of this FASTQ formatted sequence.
	 * The description will not be null.
	 *
	 * @return the description of this FASTQ formatted sequence
	 */
	public String getDescription()
	{
		return description;
	}

	/**
	 * Return the sequence for this FASTQ formatted sequence.
	 * The sequence will not be null.
	 *
	 * @return the sequence for this FASTQ formatted sequence
	 */
	public String getSequence()
	{
		return sequence;
	}

	/**
	 * Return the quality scores for this FASTQ formatted sequence.
	 * The quality scores will not be null.
	 *
	 * @return the quality scores for this FASTQ formatted sequence
	 */
	public String getQuality()
	{
		return quality;
	}

	/**
	 * Return the FASTQ sequence format variant for this FASTQ formatted sequence.
	 * The FASTQ sequence format variant will not be null.
	 *
	 * @return the FASTQ sequence format variant for this FASTQ formatted sequence
	 */
	public FastqVariant getVariant()
	{
		return variant;
	}

	/**
	 * Create and return a new FASTQ formatted sequence from this converted to the
	 * specified FASTQ sequence format variant.
	 *
	 * @since 4.2
	 * @param variant FASTQ sequence format variant, must not be null
	 * @return a new FASTQ formatted sequence from this converted to the
	 *    specified FASTQ sequence format variant
	 */
	public Fastq convertTo(final FastqVariant variant)
	{
		return FastqTools.convert(this, variant);
	}

	/**
	 * Create and return a new FastqBuilder.
	 * The FastqBuilder will not be null.
	 *
	 * @return a new FastqBuilder
	 */
	public static final FastqBuilder builder()
	{
		return new FastqBuilder();
	}

	/**
	 * Create and return a new FastqBuilder configured from the
	 * specified FASTQ formatted sequence.
	 * The FastqBuilder will not be null.
	 *
	 * @since 6.0.0
	 * @param fastq FASTQ formatted sequence, must not be null
	 * @return a new FastqBuilder configured from the specified FASTQ
	 *    formatted sequence
	 */
	public static final FastqBuilder builder(final Fastq fastq)
	{
		return new FastqBuilder(fastq);
	}
}