org.snpeff.fastq.FastqVariant Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation
Variant annotation and effect prediction package.
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.snpeff.fastq;

import java.util.HashMap;
import java.util.Map;

/**
 * FASTQ sequence format variant.
 */
public enum FastqVariant {
	/** Sanger FASTQ sequence format variant. */
	FASTQ_SANGER("Original or Sanger format"),

	/** Solexa FASTQ sequence format variant. */
	FASTQ_SOLEXA("Solexa and early Illumina format"),

	/** Illumina FASTQ sequence format variant. */
	FASTQ_ILLUMINA("Illumina 1.3+ format");

	/** Map of FASTQ sequence format variants keyed by name and lowercase-with-dashes name. */
	private static final Map FASTQ_VARIANTS = new HashMap(6);

	static {
		for( FastqVariant fastqVariant : values() ) {
			FASTQ_VARIANTS.put(fastqVariant.name(), fastqVariant);
			FASTQ_VARIANTS.put(fastqVariant.lowercaseName(), fastqVariant);
		}
	}

	/** Description of this FASTQ sequence format variant. */
	private final String description;

	/**
	 * Return the FASTQ sequence format variant with the specified name, if any.  The name may
	 * be specified in either UPPERCASE_WITH_UNDERSCORES
	 * or lowercase-with-dashes style.
	 *
	 * @param name name
	 * @return the FASTQ sequence format variant with the specified name, or null
	 *    if no such FASTQ sequence format variant exists
	 */
	public static FastqVariant parseFastqVariant(final String name) {
		return FASTQ_VARIANTS.get(name);
	}

	/**
	 * Create a new FASTQ sequence format variant with the specified description.
	 *
	 * @param description description of this FASTQ sequence format variant, must not be null
	 */
	private FastqVariant(final String description) {
		if( description == null ) { throw new IllegalArgumentException("description must not be null"); }
		this.description = description;
	}

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

	/**
	 * Return true if this FASTQ sequence format variant is {@link #FASTQ_ILLUMINA}.
	 *
	 * @return true if this FASTQ sequence format variant is {@link #FASTQ_ILLUMINA}
	 */
	public boolean isIllumina() {
		return (this == FASTQ_ILLUMINA);
	}

	/**
	 * Return true if this FASTQ sequence format variant is {@link #FASTQ_SANGER}.
	 *
	 * @return true if this FASTQ sequence format variant is {@link #FASTQ_SANGER}
	 */
	public boolean isSanger() {
		return (this == FASTQ_SANGER);
	}

	/**
	 * Return true if this FASTQ sequence format variant is {@link #FASTQ_SOLEXA}.
	 *
	 * @return true if this FASTQ sequence format variant is {@link #FASTQ_SOLEXA}
	 */
	public boolean isSolexa() {
		return (this == FASTQ_SOLEXA);
	}

	/**
	 * Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
	 *
	 * @return the name of this FASTQ sequence format variant in lowercase-with-dashes style
	 */
	public String lowercaseName() {
		return name().toLowerCase().replace('_', '-');
	}
}