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Variant annotation and effect prediction package.
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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.snpeff.fastq;

/**
 * FASTQ formatted sequence.
 */
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 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 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 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;
	}
}