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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;

/**
 * Fluent builder API for creating FASTQ formatted sequences.
 */
public final class FastqBuilder {

	/** Description for this FASTQ formatted sequence builder. */
	private String description;

	/** Sequence for this FASTQ formatted sequence builder. */
	private StringBuilder sequence;

	/** Quality scores for this FASTQ formatted sequence builder. */
	private StringBuilder quality;

	/** FASTQ sequence format variant for this FASTQ formatted sequence builder. */
	private FastqVariant variant = DEFAULT_VARIANT;

	/** Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER. */
	public static final FastqVariant DEFAULT_VARIANT = FastqVariant.FASTQ_SANGER;

	/**
	 * Create a new FASTQ formatted sequence builder.
	 */
	public FastqBuilder() {
		// empty
	}

	/**
	 * Return this FASTQ formatted sequence builder configured with the specified quality scores
	 * appended to its current quality scores.
	 *
	 * @param quality quality scores to append to the quality scores for this FASTQ formatted sequence
	 *    builder, must not be null
	 * @return this FASTQ formatted sequence builder configured with the specified quality scores
	 *    appended to its current quality scores
	 */
	public FastqBuilder appendQuality(final String quality) {
		if( quality == null ) { throw new IllegalArgumentException("quality must not be null"); }
		if( this.quality == null ) {
			this.quality = new StringBuilder(quality.length());
		}
		this.quality.append(quality);
		return this;
	}

	/**
	 * Return this FASTQ formatted sequence builder configured with the specified sequence
	 * appended to its current sequence.
	 *
	 * @param sequence sequence to append to the sequence for this FASTQ formatted sequence builder, must not be null
	 * @return this FASTQ formatted sequence builder configured with the specified sequence
	 *    appended to its current sequence
	 */
	public FastqBuilder appendSequence(final String sequence) {
		if( sequence == null ) { throw new IllegalArgumentException("sequence must not be null"); }
		if( this.sequence == null ) {
			this.sequence = new StringBuilder(sequence.length());
		}
		this.sequence.append(sequence);
		return this;
	}

	/**
	 * Build and return a new FASTQ formatted sequence configured from the properties of this builder.
	 *
	 * @return a new FASTQ formatted sequence configured from the properties of this builder
	 * @throws IllegalStateException if the configuration of this builder results in an illegal state
	 */
	public Fastq build() {
		if( description == null ) { throw new IllegalStateException("description must not be null"); }
		if( sequence == null ) { throw new IllegalStateException("sequence must not be null"); }
		if( quality == null ) { throw new IllegalStateException("quality must not be null"); }
		if( variant == null ) { throw new IllegalStateException("variant must not be null"); }
		if( !sequenceAndQualityLengthsMatch() ) { throw new IllegalStateException("sequence and quality scores must be the same length"); }
		Fastq fastq = new Fastq(description, sequence.toString(), quality.toString(), variant);
		return fastq;
	}

	/**
	 * Return the description for this FASTQ formatted sequence builder.
	 *
	 * @return the description for this FASTQ formatted sequence builder
	 */
	public String getDescription() {
		return description;
	}

	/**
	 * Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
	 *
	 * @return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length
	 */
	public boolean sequenceAndQualityLengthsMatch() {
		// todo: null check?
		return sequence.length() == quality.length();
	}

	/**
	 * Return this FASTQ formatted sequence builder configured with the specified description.
	 *
	 * @param description description for this FASTQ formatted sequence builder, must not be null
	 * @return this FASTQ formatted sequence builder configured with the specified description
	 */
	public FastqBuilder withDescription(final String description) {
		if( description == null ) { throw new IllegalArgumentException("description must not be null"); }
		this.description = description;
		return this;
	}

	/**
	 * Return this FASTQ formatted sequence builder configured with the specified quality scores.
	 *
	 * @param quality quality scores for this FASTQ formatted sequence builder, must not be null
	 * @return this FASTQ formatted sequence builder configured with the specified quality scores
	 */
	public FastqBuilder withQuality(final String quality) {
		if( quality == null ) { throw new IllegalArgumentException("quality must not be null"); }
		if( this.quality == null ) {
			this.quality = new StringBuilder(quality.length());
		}
		this.quality.replace(0, this.quality.length(), quality);
		return this;
	}

	/**
	 * Return this FASTQ formatted sequence builder configured with the specified sequence.
	 *
	 * @param sequence sequence for this FASTQ formatted sequence builder, must not be null
	 * @return this FASTQ formatted sequence builder configured with the specified sequence
	 */
	public FastqBuilder withSequence(final String sequence) {
		if( sequence == null ) { throw new IllegalArgumentException("sequence must not be null"); }
		if( this.sequence == null ) {
			this.sequence = new StringBuilder(sequence.length());
		}
		this.sequence.replace(0, this.sequence.length(), sequence);
		return this;
	}

	/**
	 * Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
	 *
	 * @param variant FASTQ sequence format variant for this FASTQ formatted sequence builder, must not be null
	 * @return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant
	 */
	public FastqBuilder withVariant(final FastqVariant variant) {
		if( variant == null ) { throw new IllegalArgumentException("variant must not be null"); }
		this.variant = variant;
		return this;
	}
}