/*
 *                    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 14, 2010
 * Author: Mark Chapman
 * @author Paolo Pavan
 */

package org.biojava.nbio.core.alignment;

import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.core.sequence.AccessionID;
import org.biojava.nbio.core.sequence.Strand;
import org.biojava.nbio.core.sequence.location.SimpleLocation;
import org.biojava.nbio.core.sequence.location.template.Location;
import org.biojava.nbio.core.sequence.location.template.Point;
import org.biojava.nbio.core.sequence.template.*;
import org.biojava.nbio.core.util.Equals;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;

/**
 * Implements a data structure for a {@link Sequence} within an alignment.
 *
 * @author Mark Chapman
 * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
 */
public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements Serializable, AlignedSequence<S, C> {


        private static final long serialVersionUID = 1L;

        private static final String gap = "-";

        // always stored
        private AlignedSequence<S, C> prev;
        private S original;
        private int length, numBefore, numAfter;
        private Location location;

        // cached (lazily initialized)
        private int numGaps = -1;
        private int numGapPositions = -1;

        private int[] alignmentFromSequence;
        private int[] sequenceFromAlignment;

        /**
         * Creates an {@link AlignedSequence} for the given {@link Sequence} in a global alignment.
         *
         * @param original the original {@link Sequence} before alignment
         * @param steps lists whether the sequence aligns a {@link Compound} or gap at each index of the alignment
         * @throws IllegalArgumentException if given sequence does not fit in alignment
         */
        public SimpleAlignedSequence(S original, List<Step> steps) {
                this(original, steps, 0, 0);
        }

        /**
         * Creates an {@link AlignedSequence} for the given {@link Sequence} in a local alignment.
         *
         * @param original the original {@link Sequence} before alignment
         * @param steps lists whether the sequence aligns a {@link Compound} or gap at each index of the alignment
         * @param numBefore number of {@link Compound}s before a local alignment
         * @param numAfter number of {@link Compound}s after a local alignment
         * @throws IllegalArgumentException if given sequence does not fit in alignment
         */
        public SimpleAlignedSequence(S original, List<Step> steps, int numBefore, int numAfter) {
                this.original = original;
                this.numBefore = numBefore;
                this.numAfter = numAfter;
                length = steps.size();
                setLocation(steps);
        }

        /**
         * Creates a new {@link AlignedSequence} for the given {@link AlignedSequence} in a global alignment.
         *
         * @param prev the previous {@link AlignedSequence} before this alignment
         * @param steps lists whether the sequence aligns a {@link Compound} or gap at each index of the alignment
         * @throws IllegalArgumentException if given sequence does not fit in alignment
         */
        public SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps) {
                this(prev, steps, 0, 0);
        }

        /**
         * Creates a new {@link AlignedSequence} for the given {@link AlignedSequence} in a local alignment.
         *
         * @param prev the previous {@link AlignedSequence} before this alignment
         * @param steps lists whether the sequence aligns a {@link Compound} or gap at each index of the alignment
         * @param numBefore number of {@link Compound}s before a local alignment
         * @param numAfter number of {@link Compound}s after a local alignment
         * @throws IllegalArgumentException if given sequence does not fit in alignment
         */
        public SimpleAlignedSequence(AlignedSequence<S, C> prev, List<Step> steps, int numBefore, int numAfter) {
                this.prev = prev;
                this.original = prev.getOriginalSequence();
                this.numBefore = numBefore;
                this.numAfter = numAfter;
                if (prev instanceof SimpleAlignedSequence<?, ?>) {
                        SimpleAlignedSequence<?, ?> p = (SimpleAlignedSequence<?, ?>) prev;
                        this.numBefore += p.numBefore;
                        this.numAfter += p.numAfter;
                }
                length = steps.size();
                setLocation(steps);
        }

        // methods for AlignedSequence

        @Override
        public void clearCache() {
                alignmentFromSequence = null;
                sequenceFromAlignment = null;
        }

        private void setAlignmentFromSequence() {
                alignmentFromSequence = new int[original.getLength()];
                int s = 1, a = 1;
                for (int i = 0; i < numBefore; i++, s++) {
                        alignmentFromSequence[s - 1] = a;
                }
                for (; s <= alignmentFromSequence.length && a <= length; s++, a++) {
                        while (a <= length && isGap(a)) {
                                a++;
                        }
                        alignmentFromSequence[s - 1] = a;
                }
                a--;
                for (int i = 0; i < numAfter; i++, s++) {
                        alignmentFromSequence[s - 1] = a;
                }
        }

        @Override
        public int[] getAlignmentFromSequence() {
                if (alignmentFromSequence == null)
                        setAlignmentFromSequence();
                return alignmentFromSequence;
        }

        @Override
        public int getAlignmentIndexAt(int sequenceIndex) {
                if (alignmentFromSequence == null)
                        setAlignmentFromSequence();
                return alignmentFromSequence[sequenceIndex - 1];
        }

        @Override
        public Point getEnd() {
                return location.getEnd();
        }

        @Override
        public Location getLocationInAlignment() {
                return location;
        }

        @Override
        public int getNumGaps() {
                if (numGaps == -1) {
                        numGaps = 0;
                        numGapPositions = 0;
                        C cGap = getCompoundSet().getCompoundForString(gap);
                        boolean inGap = false;
                        for (C compound : getAsList()) {
                                if (compound == null || compound.equalsIgnoreCase(cGap)) {
                                        if (!inGap) {
                                                numGaps++;
                                                inGap = true;
                                        }
                                        numGapPositions++;
                                } else {
                                        inGap = false;
                                }
                        }
                }
                return numGaps;
        }

        @Override
        public S getOriginalSequence() {
                return original;
        }

        @Override
        public int getOverlapCount() {
                // TODO handle circular alignments
                return 1;
        }

        private void setSequenceFromAlignment() {
                sequenceFromAlignment = new int[length];
                int a = 1, s = numBefore + 1;
                for (int i = 0; i < getStart().getPosition(); i++, a++) {
                        sequenceFromAlignment[a - 1] = s;
                }
                for (; a <= length; a++) {
                        if (!isGap(a)) {
                                s++;
                        }
                        sequenceFromAlignment[a - 1] = s;
                }
        }

        @Override
        public int[] getSequenceFromAlignment() {
                if (sequenceFromAlignment == null)
                        setSequenceFromAlignment();
                return sequenceFromAlignment;
        }

        @Override
        public int getSequenceIndexAt(int alignmentIndex) {
                if (sequenceFromAlignment == null)
                        setSequenceFromAlignment();
                return sequenceFromAlignment[alignmentIndex - 1];
        }

        @Override
        public Point getStart() {
                return location.getStart();
        }

        @Override
        public boolean isCircular() {
                return location.isCircular();
        }

        @Override
        public boolean isGap(int alignmentIndex) {
                if (getStart().getPosition() <= alignmentIndex && alignmentIndex <= getEnd().getPosition()) {
                        if (!location.isComplex()) {
                                return false;
                        }
                        for (Location sublocation : location) {
                                if (sublocation.getStart().getPosition() <= alignmentIndex &&
                                                alignmentIndex <= sublocation.getEnd().getPosition()) {
                                        return false;
                                }
                        }
                }
                return true;
        }

        // methods for Sequence

        @Override
        public int countCompounds(C... compounds) {
                int count = 0;
                List<C> search = Arrays.asList(compounds);
                for (C compound : getAsList()) {
                        if (search.contains(compound)) {
                                count++;
                        }
                }
                return count;
        }

        @Override
        public AccessionID getAccession() {
                return original.getAccession();
        }

        @Override
        public List<C> getAsList() {
                List<C> compounds = new ArrayList<C>();
                for (int i = 1; i <= length; i++) {
                        compounds.add(getCompoundAt(i));
                }
                return compounds;
        }

        @Override
        public boolean equals(Object o){

                if(! Equals.classEqual(this, o)) {
                        return false;
                }

                Sequence<C> other = (Sequence<C>)o;
                if ( original.getAsList().size() != other.getAsList().size())
                        return false;

                for ( int i = 0 ; i< original.getAsList().size() ; i++){
                        if ( ! original.getAsList().get(i).equalsIgnoreCase(other.getAsList().get(i)))
                                return false;
                }
                return true;
        }

        @Override
        public int hashCode(){
                String s = getSequenceAsString();
                return s.hashCode();
        }

        @Override
        public C getCompoundAt(int alignmentIndex) {
                return alignmentIndex >= 1 && alignmentIndex <= length && isGap(alignmentIndex) ?
                                getCompoundSet().getCompoundForString(gap) :
                                original.getCompoundAt(getSequenceIndexAt(alignmentIndex));
        }

        @Override
        public CompoundSet<C> getCompoundSet() {
                return original.getCompoundSet();
        }

        @Override
        public int getIndexOf(C compound) {
                for (int i = 1; i <= length; i++) {
                        if (compound.equals(getCompoundAt(i))) {
                                return i;
                        }
                }
                return -1;
        }

        @Override
        public int getLastIndexOf(C compound) {
                for (int i = length; i >= 1; i--) {
                        if (compound.equals(getCompoundAt(i))) {
                                return i;
                        }
                }
                return -1;
        }

        @Override
        public int getLength() {
                return length;
        }

        @Override
        public String getSequenceAsString() {
                return SequenceMixin.toString(this);
        }

        @Override
        public SequenceView<C> getSubSequence(Integer start, Integer end) {
                return SequenceMixin.createSubSequence(this, start, end);
        }

        // method for Iterable

        @Override
        public Iterator<C> iterator() {
                return getAsList().iterator();
        }

        // method from Object

        /**
         * Provides standard Java language access to results of {@link #getSequenceAsString()}.
         */
        @Override
        public String toString() {
                return getSequenceAsString();
        }

        // helper method to initialize the location
        private void setLocation(List<Step> steps) {
                List<Location> sublocations = new ArrayList<Location>();
                int start = 0, step = 0, oStep = numBefore+numAfter, oMax = this.original.getLength(), pStep = 0, pMax =
                                (prev == null) ? 0 : prev.getLength();
                boolean inGap = true;

                // build sublocations: pieces of sequence separated by gaps
                for (; step < length; step++) {
                        boolean isGapStep = (steps.get(step) == Step.GAP),
                                        isGapPrev = (pStep < pMax && prev.isGap(pStep + 1));
                        if (!isGapStep && !isGapPrev) {
                                oStep++;
                                if (inGap) {
                                        inGap = false;
                                        start = step + 1;
                                }
                        } else if (!inGap) {
                                inGap = true;
                                sublocations.add(new SimpleLocation(start, step, Strand.UNDEFINED));
                        }
                        if (prev != null && !isGapStep) {
                                pStep++;
                        }
                }
                if (!inGap) {
                        sublocations.add(new SimpleLocation(start, step, Strand.UNDEFINED));
                }

                // combine sublocations into 1 Location
                if (sublocations.size() == 0) {
                        location = null;
                } else if (sublocations.size() == 1) {
                        location = sublocations.get(0);
                } else {
                        location = new SimpleLocation(sublocations.get(0).getStart(), sublocations.get(sublocations.size() - 1).getEnd(),
                                        Strand.UNDEFINED,
                                        false, sublocations);
                }
                // TODO handle circular alignments

                // check that alignment has correct number of compounds in it to fit original sequence
                if (step != length || oStep != oMax || pStep != pMax) {
                        throw new IllegalArgumentException("Given sequence does not fit in alignment.");
                }
        }

        @Override
        //TODO Needs to implements
        public SequenceView<C> getInverse() {
                throw new UnsupportedOperationException("Not supported yet.");
        }

        @Override
        public int getNumGapPositions() {
                if (numGapPositions == -1)
                        getNumGaps();
                return numGapPositions;
        }

        @Override
        public double getCoverage() {
                
                double coverage = getLength() - getNumGapPositions();
                return coverage / getOriginalSequence().getLength();
        }
}