/*
 *                    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/
 *
 * Created on June 21, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

/**
 * Implements an algorithm which computes a score for a sequence alignment pair.  The reported score is the number of
 * alignment columns which have identical {@link Compound}s.
 *
 * @author Mark Chapman
 * @param <S> each {@link Sequence} of the alignment pair is of type S
 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
 */
public class FractionalIdentityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer
		implements PairwiseSequenceScorer<S, C> {

	// always stored
	private S query, target;
	private int max, score;

	// optional cached input field
	private PairwiseSequenceAligner<S, C> aligner;

	/**
	 * Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
	 *
	 * @param aligner a pairwise sequence aligner
	 */
	public FractionalIdentityScorer(PairwiseSequenceAligner<S, C> aligner) {
		query = aligner.getQuery();
		target = aligner.getTarget();
		this.aligner = aligner;
	}

	/**
	 * Creates a fractional identity scorer for an aligned pair of sequences.
	 *
	 * @param pair an aligned pair of sequences
	 */
	public FractionalIdentityScorer(SequencePair<S, C> pair) {
		query = pair.getQuery().getOriginalSequence();
		target = pair.getTarget().getOriginalSequence();
		max = pair.getLength();
		score = pair.getNumIdenticals();
	}

	// methods for PairwiseSequenceScorer

	@Override
	public S getQuery() {
		return query;
	}

	@Override
	public S getTarget() {
		return target;
	}

	// methods for Scorer

	@Override
	public double getMaxScore() {
		if (aligner != null) {
			align();
		}
		return max;
	}

	@Override
	public double getMinScore() {
		return 0;
	}

	@Override
	public double getScore() {
		if (aligner != null) {
			align();
		}
		return score;
	}

	// helper method for initialization from an aligner
	private void align() {
		max = aligner.getPair().getLength();
		score = aligner.getPair().getNumIdenticals();
		aligner = null;
	}

}
