/*
 *                    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;

/**
 * Holds the results of quaternary symmetry perception.
 *
 * @author Peter Rose
 *
 */
public class QuatSymmetryResults {
        private Subunits subunits = null;
        private RotationGroup rotationGroup = null;
        private HelixLayers helixLayers = null;
        private String method = null;
        private double sequenceIdentityThreshold = 0;
        private boolean local = false;
        private boolean preferredResult = false;

        public QuatSymmetryResults(Subunits subunits, RotationGroup rotationGroup, String method) {
        //      SymmetryDeviation sd = new SymmetryDeviation(subunits, rotationGroup);
        //      rotationGroup.setSymmetryDeviation(sd.getSymmetryDeviation());
                this.subunits = subunits;
                this.rotationGroup = rotationGroup;
                this.method = method;
        }

        public QuatSymmetryResults(Subunits subunits, HelixLayers helixLayers, String method) {
        //      SymmetryDeviation sd = new SymmetryDeviation(subunits, helixLayers);
        //      helixLayers.setSymmetryDeviation(sd.getSymmetryDeviation());
                this.subunits = subunits;
                this.helixLayers = helixLayers;
                this.method = method;
        }

        /**
         * Returns protein subunit information that was used to determine symmetry information
         *
         * @return
         */
        public Subunits getSubunits() {
                return subunits;
        }

        /**
         * Returns rotation group (point group) information representing rotational quaternary symmetry,
         * see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
         *
         * @return rotation group
         */
        public RotationGroup getRotationGroup() {
                return rotationGroup;
        }

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

        /**
         * Returns name of method used for symmetry perception.
         *
         * @return method
         */
        public String getMethod() {
                return method;
        }


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


        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();
        }

        /**
         * Returns the average Calpha trace RMSD for all symmetry operations
         * @return
         * @deprecated use {@link getScores()} instead.
         */
        @Deprecated
        public double getAverageTraceRmsd() {
                if (helixLayers != null && helixLayers.size() > 0) {
                        return helixLayers.getScores().getRmsd();
                } else if (rotationGroup != null && rotationGroup.getOrder() > 0) {
                        return rotationGroup.getScores().getRmsd();
                }
                return 0;
        }

        /**
         * Returns the average Calpha trace Tm for all symmetry operations
         * @return
         * @deprecated use {@link getScores()} instead.
         */
        @Deprecated
        public double getAverageTraceTmScoreMin() {
                if (helixLayers != null && helixLayers.size() > 0) {
                        return helixLayers.getScores().getTm();
                } else if (rotationGroup != null && rotationGroup.getOrder() > 0) {
                        return rotationGroup.getScores().getTm();
                }
                return 0;
        }

        public int getNucleicAcidChainCount() {
                return subunits.getNucleicAcidChainCount();
        }

        public double getSequenceIdentityThreshold() {
                return sequenceIdentityThreshold;
        }

        public void setSequenceIdentityThreshold(double sequenceIdentityThreshold) {
                this.sequenceIdentityThreshold = sequenceIdentityThreshold;
        }

        @Override
        public String toString() {
                StringBuilder sb = new StringBuilder();

                sb.append("Stoichiometry         : ");
                sb.append(getSubunits().getStoichiometry());
                sb.append("\n");
                sb.append("Pseudostoichiometry   : ");
                sb.append(getSubunits().isPseudoStoichiometric());
                sb.append("\n");
                sb.append("Pseudosymmetry        : ");
                sb.append(getSubunits().isPseudoSymmetric());
                sb.append("\n");
                sb.append("Min sequence identity : ");
                sb.append(Math.round(getSubunits().getMinSequenceIdentity()*100));
                sb.append("\n");
                sb.append("Max sequence identity : ");
                sb.append(Math.round(getSubunits().getMaxSequenceIdentity()*100));
                sb.append("\n");
                sb.append("Symmetry              : ");
                sb.append(getSymmetry());
                sb.append("\n");
                sb.append("Symmetry RMSD         : ");
                sb.append((float) getAverageTraceRmsd());
                sb.append("\n");
                sb.append("Symmetry TmScoreMin   : ");
                sb.append((float) getAverageTraceTmScoreMin());
                sb.append("\n");
                sb.append("Prefered result       : ");
                sb.append(isPreferredResult());
                sb.append("\n");

                return sb.toString();
        }

        /**
         * Return true
         * @return
         */
        public boolean isLocal() {
                return local;
        }

        public void setLocal(boolean local) {
                this.local = local;
        }

        public boolean isPreferredResult() {
                return preferredResult;
        }

        public void setPreferredResult(boolean preferredResult) {
                this.preferredResult = preferredResult;
        }
}