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/*
 *                    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 Mar 15, 2010
 * Author: Andreas Prlic
 *
 */

package demo;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.ce.CeParameters;
import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.model.AfpChainWriter;
import org.biojava.nbio.structure.align.util.AFPChainScorer;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
import org.biojava.nbio.structure.chem.DownloadChemCompProvider;

public class DemoCE
{


	public static void main(String[] args){
		//String name1 = "4hhb.A";
		//String name2 = "4hhb.B";

		String name1 = "d1pqsa_";
		String name2 = "d1poha_";

		//String name1 = "5AZQ.A";
		//String name2 = "4ODC.A";

		AtomCache cache = new AtomCache();

		DownloadChemCompProvider prov = new DownloadChemCompProvider();
		prov.setDownloadAll(true);

		ChemCompGroupFactory.setChemCompProvider(prov);

		Structure structure1 = null;
		Structure structure2 = null;

		try {

			StructureAlignment algorithm  = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);

			structure1 = cache.getStructure(name1);
			structure2 = cache.getStructure(name2);

			Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
			Atom[] ca2 = StructureTools.getAtomCAArray(structure2);

			// get default parameters
			CeParameters params = new CeParameters();

			// add more print
			params.setShowAFPRanges(true);

			// set the maximum gap size to unlimited
			params.setMaxGapSize(-1);

			AFPChain afpChain = algorithm.align(ca1,ca2,params);

			afpChain.setName1(name1);
			afpChain.setName2(name2);

			// show a nice summary print
			System.out.println(AfpChainWriter.toWebSiteDisplay(afpChain, ca1, ca2));

			// print rotation matrices
			System.out.println(afpChain.toRotMat());
			//System.out.println(afpChain.toCE(ca1, ca2));

			// print XML representation
			//System.out.println(AFPChainXMLConverter.toXML(afpChain,ca1,ca2));

			StructureAlignmentDisplay.display(afpChain, ca1, ca2);


			double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);
			afpChain.setTMScore(tmScore);
			System.out.println(AfpChainWriter.toScoresList(afpChain));

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

}