/*
 *                    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.symmetry.core;

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

/**
 *
 * @author Peter
 */
public class HelixLayers {
        private List<Helix> helices = new ArrayList<Helix>();
        private double symmetryDeviation = 0;

        public int size() {
                return helices.size();
        }

        public void addHelix(Helix helix) {
                helices.add(helix);
        }

        public Helix getHelix(int index) {
                return helices.get(index);
        }

        /*
         * Returns Helix with lowest twist angle
         */
        public Helix getByLowestAngle() {
                double angle = Double.MAX_VALUE;
                Helix lowest = null;
                for (Helix helix: helices) {
                        if (helix.getAngle() < angle) {
                                angle = helix.getAngle();
                                lowest = helix;
                        }
                }
                return lowest;
        }

        /*
         * Returns Helix with largest number of intermolecular contacts
         * between repeat units
         */
        public Helix getByLargestContacts() {
                double contacts = 0;
                Helix largest = null;
                for (Helix helix: helices) {
                        if (helix.getContacts() > contacts) {
                                contacts = helix.getContacts();
                                largest = helix;
                        }
                }
                return largest;
        }

        /*
         * Returns Helix that has the largest number of contacts, besides
         * the Helix with the lowest twist angle
         */
        public Helix getByLargestContactsNotLowestAngle() {
                double contacts = 0;
                Helix lowest = getByLowestAngle();
                // TODO why are there helices with almost identical helix parameters??
                double angle = lowest.getAngle() + 0.05;
                Helix largest = null;
                for (Helix helix: helices) {
                        if (helix == lowest) {
                                continue;
                        }
                        if (helix.getContacts() > contacts && helix.getAngle() > angle) {
                                contacts = helix.getContacts();
                                largest = helix;
                        }
                }
                if (largest == null) {
                        return lowest;
                }
                return largest;
        }

        /**
         * Returns QuatSymmetryScores averaged over all rotations
         * (except the first rotation, which is the unit operation E)
         * @return mean scores average over rotations
         */
        public QuatSymmetryScores getScores() {
                QuatSymmetryScores scores = new QuatSymmetryScores();

                double[] values = new double[helices.size()];

                // minRmsd
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getMinRmsd();
                }
                scores.setMinRmsd(minScores(values));

                // maxRmsd
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getMaxRmsd();
                }
                scores.setMaxRmsd(maxScores(values));

                // Rmsd
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getRmsd();
                }
                scores.setRmsd(averageScores(values));

                // minTm
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getMinTm();
                }
                scores.setMinTm(minScores(values));

                // maxTm
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getMaxTm();
                }
                scores.setMaxTm(maxScores(values));

                // Tm
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getTm();
                }
                scores.setTm(averageScores(values));

                // Rmsd subunit centers
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getRmsdCenters();
                }
                scores.setRmsdCenters(averageScores(values));

                // TmIntra
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getTmIntra();
                }
                scores.setTmIntra(averageScores(values));

                // RmsdIntra
                for (int i = 0; i < helices.size(); i++) {
                        values[i] = helices.get(i).getScores().getRmsdIntra();
                }
                scores.setRmsdIntra(averageScores(values));

                // SymDeviation
                scores.setSymDeviation(symmetryDeviation);

                return scores;
        }

        /**
         * @param symmetryDeviation the symmetryDeviation to set
         */
        public void setSymmetryDeviation(double symmetryDeviation) {
                this.symmetryDeviation = symmetryDeviation;
        }

        private double averageScores(double[] scores) {
                double sum = 0;
                for (double s: scores) {
                        sum += s;
                }
                return sum/scores.length;
        }

        private double minScores(double[] scores) {
                double score = Double.MAX_VALUE;
                for (double s: scores) {
                        score = Math.min(score, s);
                }
                return score;
        }

        private double maxScores(double[] scores) {
                double score = Double.MIN_VALUE;
                for (double s: scores) {
                        score = Math.max(score, s);
                }
                return score;
        }

        public void clear() {
                helices.clear();
        }

        @Override
        public String toString() {
                StringBuilder sb = new StringBuilder();
                sb.append("Helices: ").append(size()).append("\n");
                for (Helix s: helices) {
                        sb.append(s.toString()).append("\n");
                }
                return sb.toString();
        }



}