/**
 *                    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 Nov 27, 2012
 * Created by Andreas Prlic
 *
 * @since 3.0.2
 */
package org.biojava.nbio.structure.symmetry.analysis;


import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.util.ResourceManager;
import org.biojava.nbio.structure.symmetry.core.*;
import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;

import java.util.List;


public class CalcBioAssemblySymmetry {
        private Structure bioAssembly;
        private QuatSymmetryParameters parameters;
        private QuatSymmetryResults results;

        private JmolSymmetryScriptGenerator scriptGenerator;

        static public String version;
        static public String build;
        static {
                try {
                        ResourceManager about = ResourceManager.getResourceManager("about");

                        version = about.getString("project_version");
                        build   = about.getString("build");

                } catch (Exception e){
                        e.printStackTrace();
                }
        }

        public CalcBioAssemblySymmetry(Structure bioAssembly, QuatSymmetryParameters parameters){
                this.bioAssembly = bioAssembly;
                this.parameters = parameters;
        }

        public QuatSymmetryParameters getParameters(){
                return parameters;
        }

        public QuatSymmetryDetector orient(){
                QuatSymmetryDetector detector = new QuatSymmetryDetector(bioAssembly, parameters);
                String defaultColoring = "";

                if (detector.hasProteinSubunits()) {
                        for (QuatSymmetryResults globalSymmetry: detector.getGlobalSymmetry()) {

                                String postFix = "g";
                                AxisAligner aligner = AxisAligner.getInstance(globalSymmetry);
                                JmolSymmetryScriptGenerator generator = JmolSymmetryScriptGenerator.getInstance(aligner, postFix);
                                generator.setOnTheFly(parameters.isOnTheFly());
                                // save the preferred result
                                if (globalSymmetry.isPreferredResult()) {
                                        this.results = globalSymmetry;
                                        this.scriptGenerator = generator;
                                }

                                // get default color by symmetry for all subunits (for asymmetric cases only)
                                if (globalSymmetry.getSymmetry().equals("C1") && ! globalSymmetry.getSubunits().isPseudoStoichiometric()) {
                                        defaultColoring = generator.colorBySymmetry();
                                }

                                if (parameters.isVerbose()) {
                                        System.out.println("Global symmetry: ");
                                        System.out.println(globalSymmetry);

//                                      System.out.println();
//                                      System.out.println(generator.getDefaultOrientation());
//                                      System.out.println(generator.getZoom());
//                                      System.out.println(generator.drawPolyhedron());
                                        System.out.println(generator.drawAxes());
                                        System.out.println(generator.colorBySubunit());
                                        System.out.println(generator.colorBySequenceCluster());
                                        System.out.println(generator.colorBySymmetry());
                                }

                        }

                        for (List<QuatSymmetryResults> localSymmetries: detector.getLocalSymmetries()) {
                                int count = 0;

                                for (QuatSymmetryResults localSymmetry: localSymmetries) {
                                        // create a unique postFix for each local symmetry to be used in the Jmol script
                                        // to avoid naming conflicts when more than one symmetry is displayed at one time.
                                        String postFix = "l" + count;
                                        AxisAligner aligner = AxisAligner.getInstance(localSymmetry);
                                        JmolSymmetryScriptGenerator generator = JmolSymmetryScriptGenerator.getInstance(aligner, postFix);
                                        generator.setOnTheFly(parameters.isOnTheFly());
                                        // sets color by symmetry for all subunits. This is
                                        // required for local symmetry, to ensure all subunits are colored.
                                        generator.setDefaultColoring(defaultColoring);
                                        // save preferred result
                                        if (localSymmetry.isPreferredResult()) {
                                                this.results = localSymmetry;
                                                this.scriptGenerator = generator;
                                        }

                                        if (parameters.isVerbose()) {
                                                System.out.println("Local symmetry: ");
                                                System.out.println(localSymmetry);

//                                              System.out.println();
//                                              System.out.println(generator.getDefaultOrientation());
//                                              System.out.println(generator.getZoom());
//                                              System.out.println(generator.drawPolyhedron());
//                                              System.out.println(generator.drawAxes());
//                                              System.out.println(generator.colorBySubunit());
//                                              System.out.println(generator.colorBySequenceCluster());
//                                              System.out.println(generator.colorBySymmetry());
                                        }
                                }
                        }
                } else {
                        System.out.println("No protein chains found for " + bioAssembly.getPDBCode() );
                }
                return detector;
        }

        /** Only works if this is not helical symmetry. Deprecated, use getSymmetry instead */
        @Deprecated
        public RotationGroup getRotationGroup() {
                return results.getRotationGroup();
        }


        public Subunits getSubunits() {
                return results.getSubunits();
        }

        /** String representation of Symmetry, e.g. C1, C2, H
         *
         * @return
         */
        public String getSymmetry() {
                return results.getSymmetry();
        }

        public JmolSymmetryScriptGenerator getScriptGenerator() {
                return scriptGenerator;
        }
}