/*
 *                    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 17, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment.template;

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

import java.util.ArrayList;
import java.util.List;

/**
 * Implements common code for an {@link Aligner} for a pair of {@link Sequence}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 abstract class AbstractPairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
                extends AbstractMatrixAligner<S, C> implements PairwiseSequenceAligner<S, C> {

        // additional input fields
        private S query, target;

        // additional output field
        protected SequencePair<S, C> pair;

        /**
         * Before running a pairwise global sequence alignment, data must be sent in via calls to
         * {@link #setQuery(Sequence)}, {@link #setTarget(Sequence)}, {@link #setGapPenalty(GapPenalty)}, and
         * {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
         */
        protected AbstractPairwiseSequenceAligner() {
        }

        /**
         * Prepares for a pairwise global sequence alignment.
         *
         * @param query the first {@link Sequence} of the pair to align
         * @param target the second {@link Sequence} of the pair to align
         * @param gapPenalty the gap penalties used during alignment
         * @param subMatrix the set of substitution scores used during alignment
         */
        protected AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
                        SubstitutionMatrix<C> subMatrix) {
                this(query, target, gapPenalty, subMatrix, false);
        }

        /**
         * Prepares for a pairwise sequence alignment.
         *
         * @param query the first {@link Sequence} of the pair to align
         * @param target the second {@link Sequence} of the pair to align
         * @param gapPenalty the gap penalties used during alignment
         * @param subMatrix the set of substitution scores used during alignment
         * @param local if true, find a region of similarity rather than aligning every compound
         */
        protected AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
                        SubstitutionMatrix<C> subMatrix, boolean local) {
                super(gapPenalty, subMatrix, local);
                this.query = query;
                this.target = target;
                reset();
        }

        /**
         * Sets the query {@link Sequence}.
         *
         * @param query the first {@link Sequence} of the pair to align
         */
        public void setQuery(S query) {
                this.query = query;
                reset();
        }

        /**
         * Sets the target {@link Sequence}.
         *
         * @param target the second {@link Sequence} of the pair to align
         */
        public void setTarget(S target) {
                this.target = target;
                reset();
        }

        // method for PairwiseSequenceAligner

        @Override
        public SequencePair<S, C> getPair() {
                if (pair == null) {
                        align();
                }
                return pair;
        }

        // methods for PairwiseSequenceScorer

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

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

        // methods for AbstractMatrixAligner

        @Override
        protected CompoundSet<C> getCompoundSet() {
                return (query == null) ? null : query.getCompoundSet();
        }

        @Override
        protected List<C> getCompoundsOfQuery() {
                return (query == null) ? new ArrayList<C>() : query.getAsList();
        }

        @Override
        protected List<C> getCompoundsOfTarget() {
                return (target == null) ? new ArrayList<C>() : target.getAsList();
        }

        @Override
        protected int[] getScoreMatrixDimensions() {
                return new int[] { (query == null) ? 1 : query.getLength() + 1, (target == null) ? 1 : target.getLength() + 1,
                                (getGapPenalty() == null || getGapPenalty().getType() == GapPenalty.Type.LINEAR) ? 1 : 3 };
        }

        @Override
        protected int getSubstitutionScore(int queryColumn, int targetColumn) {
                return getSubstitutionMatrix().getValue(query.getCompoundAt(queryColumn), target.getCompoundAt(targetColumn));
        }

        @Override
        protected boolean isReady() {
                return query != null && target != null && getGapPenalty() != null && getSubstitutionMatrix() != null &&
                                query.getCompoundSet().equals(target.getCompoundSet());
        }

        @Override
        protected void reset() {
                super.reset();
                pair = null;
                if (query != null && target != null && getGapPenalty() != null && getSubstitutionMatrix() != null &&
                                query.getCompoundSet().equals(target.getCompoundSet())) {
                        int maxq = 0, maxt = 0;
                        for (C c : query) {
                                maxq += getSubstitutionMatrix().getValue(c, c);
                        }
                        for (C c : target) {
                                maxt += getSubstitutionMatrix().getValue(c, c);
                        }
                        max = Math.max(maxq, maxt);
                        score = min = isLocal() ? 0 : (int) (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
                                        target.getLength()) * getGapPenalty().getExtensionPenalty());
                }
        }

}