/*
 *                    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 2013-05-23
 *
 */
package org.biojava.nbio.structure.symmetry.core;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.cluster.Subunit;
import org.biojava.nbio.structure.cluster.SubunitCluster;

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

/**
 * Holds the results of quaternary symmetry perception obtained with
 * {@link QuatSymmetryDetector}.
 *
 * @author Peter Rose
 * @author Aleix Lafita
 *
 */
public class QuatSymmetryResults {

        // Optional: the query Structure, if any
        private Structure structure;

        // Information about the clustering process
        private Stoichiometry stoichiometry;
        private boolean local = false;

        // Cached properties
        private List<SubunitCluster> clusters;
        private List<Subunit> subunits;

        // Information about the symmetry
        private SymmetryPerceptionMethod method;
        private HelixLayers helixLayers;
        private RotationGroup rotationGroup = new RotationGroup();

        // TODO we should unify rotational and roto-translational results

        /**
         * Constructor for rotational symmetries.
         * 
         * @param stoichiometry
         *            Stoichiometry used to calculate symmetry
         * @param rotationGroup
         * @param method
         */
        public QuatSymmetryResults(Stoichiometry stoichiometry,
                        RotationGroup rotationGroup, SymmetryPerceptionMethod method) {

                this.stoichiometry = stoichiometry;
                this.clusters = stoichiometry.getClusters();

                subunits = new ArrayList<Subunit>();
                for (SubunitCluster c : clusters) {
                        subunits.addAll(c.getSubunits());
                }
                        
                this.rotationGroup = rotationGroup;
                this.method = method;
        }

        /**
         * Constructor for roto-translational symmetries.
         * 
         * @param stoichiometry
         *            Stoichiometry used to calculate symmetry
         * @param helixLayers
         * @param method
         */
        public QuatSymmetryResults(Stoichiometry stoichiometry,
                        HelixLayers helixLayers, SymmetryPerceptionMethod method) {

                this.stoichiometry = stoichiometry;
                this.clusters = stoichiometry.getClusters();
                
                subunits = new ArrayList<Subunit>();
                for (SubunitCluster c : clusters) {
                        subunits.addAll(c.getSubunits());
                }

                this.helixLayers = helixLayers;
                this.method = method;
        }

        /**
         * Determine if this symmetry result is a subset of the other Symmetry result.
         * Checks the following conditions:
         * - 'Other' includes all subunits of 'this'.
         * - 'Other' has the same or higher order than 'this'.
         *
         * Special treatment for the helical symmetry:
         * - 'Other' includes all subunits of 'this'.
         * - 'this' may be Cn, as well as H
         *
         *  Note that isSupersededBy establishes a partial order, i.e. for some
         *  symmetries A and B, neither A.isSupersededBy(B) nor B.isSupersededBy(A)
         *  may be true.
         *
         * @param other
         *            QuatSymmetryResults
         *
         * @return true if other supersedes this, false otherwise
         */

        public boolean isSupersededBy(QuatSymmetryResults other) {
                if(other.getSymmetry().startsWith("H")) {
                        if(this.getSymmetry().startsWith("C") || this.getSymmetry().startsWith("H")) {
                                if (other.subunits.containsAll(this.subunits)) {
                                        return true;
                                }
                        }
                        return false;
                }

                if (this.getSymmetry().startsWith("H")) {
                        return false;
                }

                if (this.rotationGroup.getOrder() <= other.rotationGroup.getOrder() &&
                                other.subunits.containsAll(this.subunits)) {
                        return true;
                }
                return false;
        }

        /**
         * Returns the List of SubunitCluster used to calculate symmetry.
         *
         * @return an unmodifiable view of the original List
         */
        public List<SubunitCluster> getSubunitClusters() {
                return Collections.unmodifiableList(clusters);
        }

        /**
         * Returns the List of Subunits used to calculate symmetry.
         *
         * @return an unmodifiable view of the List
         */
        public List<Subunit> getSubunits() {            
                return Collections.unmodifiableList(subunits);          
        }
        
        /**
         * Return the number of Subunits involved in the symmetry.
         * 
         * @return the number of Subunits
         */
        public int getSubunitCount() {
                return subunits.size();
        }
        
        /**
         * @return rotation group (point group) information representing rotational
         *         quaternary symmetry.
         */
        public RotationGroup getRotationGroup() {
                return rotationGroup;
        }

        /**
         * @return helix layers (layer lines) as a list of helices that describe a
         *         helical structure.
         */
        public HelixLayers getHelixLayers() {
                return helixLayers;
        }

        /**
         * @return the method used for symmetry perception.
         */
        public SymmetryPerceptionMethod getMethod() {
                return method;
        }

        /**
         * @return the symmetry group symbol. For point groups returns the point
         *         group symbol and for helical symmetry returns "H".
         */
        public String getSymmetry() {
                if (helixLayers != null && helixLayers.size() > 0) {
                        return "H";
                } else if (rotationGroup != null && rotationGroup.getOrder() > 0) {
                        return rotationGroup.getPointGroup();
                }
                return "";
        }

        /**
         * @return the quaternary scores as an object
         */
        public QuatSymmetryScores getScores() {
                if (helixLayers != null && helixLayers.size() > 0) {
                        return helixLayers.getScores();
                } else if (rotationGroup != null && rotationGroup.getOrder() > 0) {
                        return rotationGroup.getScores();
                }
                return new QuatSymmetryScores();
        }

        public Stoichiometry getStoichiometry() {
                return stoichiometry;
        }

        public boolean isPseudoStoichiometric() {
                return stoichiometry.isPseudoStoichiometric();
        }

        /**
         * A local result means that only a subset of the original Subunits was used
         * for symmetry determination.
         * 
         * @return true if local result, false otherwise
         */
        public boolean isLocal() {
                return local;
        }

        /**
         * A local result means that only a subset of the original Subunits was used
         * for symmetry determination.
         * 
         * @param local
         *            true if local result, false otherwise
         */
        void setLocal(boolean local) {
                this.local = local;
        }

        public Structure getStructure() {
                return structure;
        }

        public void setStructure(Structure structure) {
                this.structure = structure;
        }

        @Override
        public String toString() {
                return "QuatSymmetryResults [stoichiometry: " + getStoichiometry()
                                + ", symmetry: " + getSymmetry() + ", pseudo-stoichiometric: "
                                + isPseudoStoichiometric() + ", local: " + local + ", method: "
                                + method + "]";
        }

}