/*
 *                    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 javax.vecmath.AxisAngle4d;
import javax.vecmath.Matrix4d;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

/**
 *
 * @author Peter
 */
public class Helix {
        private QuatSymmetryScores scores = new QuatSymmetryScores();
        private List<Integer> permutation;
        private List<List<Integer>> repeatUnits;
        private Matrix4d transformation;
        private double rise;
        private int nStart;
        private int fold;
        private int contacts;

        /**
         * @return the scores
         */
        public QuatSymmetryScores getScores() {
                return scores;
        }

        /**
         * @param scores the scores to set
         */
        public void setScores(QuatSymmetryScores scores) {
                this.scores = scores;
        }

        /**
         * @return the permutation
         */
        public List<Integer> getPermutation() {
                return permutation;
        }

        /**
         * @param permutation the permutation to set
         */
        public void setPermutation(List<Integer> permutation) {
                this.permutation = permutation;
        }

        public List<List<Integer>> getRepeatUnits() {
                return repeatUnits;
        }

        public void setRepeatUnits(List<List<Integer>> repeatUnits) {
                this.repeatUnits = repeatUnits;
        }

        /**
         * @return the transformation
         */
        public Matrix4d getTransformation() {
                return transformation;
        }

        /**
         * @param transformation the transformation to set
         */
        public void setTransformation(Matrix4d transformation) {
                this.transformation = transformation;
        }

        public double getRise() {
                return rise;
        }

        public void setRise(double rise) {
                this.rise = rise;
        }

        /**
         * Returns the pitch angle of the helix
         * @param transformation helix transformation
         * @return
         */
        public double getAngle() {
                return getAxisAngle().angle;
        }

        /**
         * Returns the AxisAngle of the helix transformation
         * @param transformation helix transformation
         * @return
         */
        public AxisAngle4d getAxisAngle() {
                AxisAngle4d axis = new AxisAngle4d();
                axis.set(this.transformation);
                return axis;
        }

        public int getnStart() {
                return nStart;
        }

        public void setnStart(int nStart) {
                this.nStart = nStart;
        }

        /**
         * @return the fold
         */
        public int getFold() {
                return fold;
        }

        /**
         * @param fold the fold to set
         */
        public void setFold(int fold) {
                this.fold = fold;
        }

        public int getContacts() {
                return contacts;
        }

        public void setContacts(int contacts) {
                this.contacts = contacts;
        }

        @Override
        public String toString() {
                StringBuilder sb = new StringBuilder();
                sb.append("Permutation   : " + getPermutation() + "\n");
                sb.append("Repeat units  : " + getRepeatUnits() + "\n");
                sb.append("Rise          : " + getRise() + "\n");
                sb.append("Angle         : " + Math.toDegrees(getAngle()) +"\n");
                sb.append("Fold          : " + getFold() + "\n");
                return sb.toString();
        }

        public List<List<Integer>> getLayerLines() {
                List<List<Integer>> layerLines = new ArrayList<List<Integer>>();

                createLineSegments(permutation, layerLines);

//              System.out.println("Line segments: " + layerLines.size());
//              for (List<Integer> lineSegment: layerLines) {
//                      System.out.println(lineSegment);
//              }

                int count = layerLines.size();

                // iteratively join line segments
                do {
                        count = layerLines.size();
                        joinLineSegments(layerLines);
                        // after joining line segments, get rid of the empty line segments left behind
                        trimEmptyLineSegments(layerLines);

//                      System.out.println("Line segments: " + count);
//                      for (List<Integer> lineSegment: layerLines) {
//                              System.out.println(lineSegment);
//                      }
                } while (layerLines.size() < count);

                return layerLines;
        }

        private static void createLineSegments(List<Integer> permutation,
                        List<List<Integer>> layerLines) {
                for (int i = 0; i < permutation.size(); i++) {
                        if (permutation.get(i) != -1 ) {
                                List<Integer> lineSegment = new ArrayList<Integer>();
                                lineSegment.add(i);
                                lineSegment.add(permutation.get(i));
                                layerLines.add(lineSegment);
                        }
                }
        }

        private static void joinLineSegments(List<List<Integer>> layerLines) {
                for (int i = 0; i < layerLines.size()-1; i++) {
                        List<Integer> lineSegmentI = layerLines.get(i);
                        if (! lineSegmentI.isEmpty()) {
                                for (int j = i + 1; j < layerLines.size(); j++) {
                                        List<Integer> lineSegmentJ = layerLines.get(j);
                                        if (! lineSegmentJ.isEmpty()) {
                                                if (lineSegmentI.get(lineSegmentI.size()-1).equals(lineSegmentJ.get(0))) {
//                                                      System.out.println("join right: " + lineSegmentI + " - " + lineSegmentJ);
                                                        lineSegmentI.addAll(lineSegmentJ.subList(1,  lineSegmentJ.size()));
//                                                      System.out.println("joned segment: " + lineSegmentI);
                                                        lineSegmentJ.clear();
                                                } else if ((lineSegmentI.get(0).equals(lineSegmentJ.get(lineSegmentJ.size()-1)))) {
                                                        lineSegmentI.addAll(0, lineSegmentJ.subList(0,  lineSegmentJ.size()-1));
//                                                      System.out.println("join left: " + lineSegmentJ + " - " + lineSegmentI);
//                                                      System.out.println("joned segment: " + lineSegmentI);
                                                        lineSegmentJ.clear();
                                                }
                                        }
                                }
                        }
                }
        }

        private static void trimEmptyLineSegments(List<List<Integer>> layerLines) {
                for (Iterator<List<Integer>> iter = layerLines.iterator(); iter.hasNext();) {
                        if (iter.next().isEmpty()) {
                                iter.remove();
                        }
                }
        }
}