/*
 *                    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.biojava.nbio.structure.align.multiple;

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

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;

/**
 * A general implementation of a {@link MultipleAlignment}.
 *
 * @author Aleix Lafita
 * @since 4.1.0
 *
 */
public class MultipleAlignmentImpl extends AbstractScoresCache implements
                Serializable, MultipleAlignment, Cloneable {

        private static final long serialVersionUID = 3432043794125805139L;

        private MultipleAlignmentEnsemble parent;
        private List<BlockSet> blockSets;

        // Cache variables (can be updated)
        private int length;
        private int coreLength;
        private List<Integer> alignResCounts;
        private List<Double> coverages;

        /**
         * Default Constructor. Empty alignment. No structures assigned.
         *
         * @return MultipleAlignment an empty MultipleAlignment instance.
         */
        public MultipleAlignmentImpl() {
                this(new MultipleAlignmentEnsembleImpl()); // assign an empty ensemble.
        }

        /**
         * Constructor linking to an existing ensemble. Automatically adds this
         * alignment to the parent ensemble.
         *
         * @param ensemble
         *            parent MultipleAlignmentEnsemble.
         * @return MultipleAlignment an alignment instance part of an ensemble.
         */
        public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) {

                super();
                parent = ensemble;
                if (parent != null)
                        parent.getMultipleAlignments().add(this);

                blockSets = null;

                length = -1; // Value -1 reserved to indicate that has to be calculated
                coreLength = -1;
                alignResCounts = null; // Value null means not set
                coverages = null;
        }

        /**
         * Copy constructor. Recursively copies member BlockSets.
         *
         * @param ma
         *            MultipleAlignmentImpl to copy.
         * @return MultipleAlignmentImpl identical copy of the alignment.
         */
        public MultipleAlignmentImpl(MultipleAlignmentImpl ma) {

                super(ma); // Copy the scores
                parent = ma.parent;

                length = ma.length;
                coreLength = ma.coreLength;

                blockSets = null;
                if (ma.blockSets != null) {
                        // Make a deep copy of everything
                        this.blockSets = new ArrayList<BlockSet>();
                        for (BlockSet bs : ma.blockSets) {
                                BlockSet newBS = bs.clone();
                                newBS.setMultipleAlignment(this);
                                this.blockSets.add(newBS);
                        }
                }
        }

        @Override
        public void clear() {
                super.clear();
                length = -1;
                coreLength = -1;
                alignResCounts = null;
                for (BlockSet a : getBlockSets()) {
                        a.clear();
                }
        }

        @Override
        public MultipleAlignmentImpl clone() {
                return new MultipleAlignmentImpl(this);
        }

        @Override
        public String toString() {
                List<String> ids = new ArrayList<String>(parent
                                .getStructureIdentifiers().size());
                for (StructureIdentifier i : parent.getStructureIdentifiers()) {
                        ids.add(i.getIdentifier());
                }
                String resume = "Structures:" + ids + " \nAlgorithm:"
                                + parent.getAlgorithmName() + "_" + parent.getVersion()
                                + " \nBlockSets: " + getBlockSets().size() + " \nBlocks: "
                                + getBlocks().size() + " \nLength: " + length()
                                + " \nCore Length: " + getCoreLength();
                for (String score : getScores()) {
                        resume += " \n" + score + ": ";
                        resume += String.format("%.2f", getScore(score));
                }
                return resume;
        }

        @Override
        public List<BlockSet> getBlockSets() {
                if (blockSets == null)
                        blockSets = new ArrayList<BlockSet>();
                return blockSets;
        }

        @Override
        public List<Block> getBlocks() {
                List<Block> blocks = new ArrayList<Block>();
                for (BlockSet bs : getBlockSets()) {
                        blocks.addAll(bs.getBlocks());
                }
                return blocks;
        }

        @Override
        public void setBlockSets(List<BlockSet> blockSets) {
                this.blockSets = blockSets;
        }

        @Override
        public BlockSet getBlockSet(int index) {
                return blockSets.get(index);
        }

        @Override
        public Block getBlock(int index) {
                List<Block> blocks = getBlocks();
                return blocks.get(index);
        }

        @Override
        public List<Atom[]> getAtomArrays() {
                return parent.getAtomArrays();
        }

        @Override
        public StructureIdentifier getStructureIdentifier(int index) {
                return parent.getStructureIdentifiers().get(index);
        }

        @Override
        public int size() {
                return parent.size();
        }

        @Override
        public int length() {
                if (length < 0)
                        updateLength();
                return length;
        }

        @Override
        public int getCoreLength() {
                if (coreLength < 0)
                        updateCoreLength();
                return coreLength;
        }

        /**
         * Force recalculation of the length (aligned columns) based on the BlockSet
         * lengths.
         */
        protected void updateLength() {
                if (getBlockSets().size() == 0) {
                        throw new IndexOutOfBoundsException(
                                        "Empty MultipleAlignment: blockSets size == 0.");
                } // Otherwise try to calculate it from the BlockSet information
                else {
                        length = 0;
                        for (BlockSet blockSet : blockSets)
                                length += blockSet.length();
                }
        }

        /**
         * Force recalculation of the core length (ungapped columns) based on the
         * BlockSet core lengths.
         */
        protected void updateCoreLength() {
                if (getBlockSets().size() == 0) {
                        throw new IndexOutOfBoundsException(
                                        "Empty MultipleAlignment: blockSets size == 0.");
                } // Otherwise try to calculate it from the BlockSet information
                else {
                        coreLength = 0;
                        for (BlockSet blockSet : blockSets)
                                coreLength += blockSet.getCoreLength();
                }
        }

        /**
         * Updates all cached properties
         *
         * @throws StructureException
         */
        protected void updateCache() {
                updateCoreLength();
                updateLength();
        }

        @Override
        public MultipleAlignmentEnsemble getEnsemble() {
                return parent;
        }

        @Override
        public void setEnsemble(MultipleAlignmentEnsemble parent) {
                this.parent = parent;
        }

        @Override
        public List<Integer> getAlignResCounts() {

                if (alignResCounts != null)
                        return alignResCounts;

                alignResCounts = new ArrayList<Integer>(size());
                for (int s = 0; s < size(); s++)
                        alignResCounts.add(0);

                for (BlockSet bs : blockSets) {
                        List<Integer> bscounts = bs.getAlignResCounts();
                        for (int s = 0; s < size(); s++)
                                alignResCounts.set(s, alignResCounts.get(s) + bscounts.get(s));
                }
                return alignResCounts;
        }

        @Override
        public List<Double> getCoverages() {
                
                if (coverages != null)
                        return coverages;
                
                List<Integer> counts = getAlignResCounts();
                coverages = new ArrayList<Double>(size());
                for (int s = 0; s < size(); s++)
                        coverages.add(counts.get(s)
                                        / (double) getAtomArrays().get(s).length);
                return coverages;
        }

}