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The protein structure modules of BioJava.
There is a newer version: 7.1.3
/* This class is based on the original FATCAT implementation by
 *  * Yuzhen Ye & Adam Godzik (2003)
 * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
 * Bioinformatics vol.19 suppl. 2. ii246-ii255.
 * https://www.ncbi.nlm.nih.gov/pubmed/14534198
 * 
 *
 * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this 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.
 *
 *
 * Created by Andreas Prlic - RCSB PDB
 *
 */

package org.biojava.nbio.structure.align.fatcat;


import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
import org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters;
import org.biojava.nbio.structure.align.model.AFPChain;


public class FatCatFlexible  extends FatCat implements StructureAlignment{



	public static final String algorithmName = "jFatCat_flexible";

	FatCatParameters params;

	public FatCatFlexible(){
		super();
		params = new FatCatParameters();
	}

	@Override
	public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException {

		AFPChain afpChain = alignFlexible(ca1, ca2, params);
		afpChain.setAlgorithmName(algorithmName);
		afpChain.setVersion(VERSION+"");
		return afpChain;
	}

	@Override
	public AFPChain align(Atom[] ca1, Atom[] ca2, Object param)
	throws StructureException {

		if ( ! (param instanceof FatCatParameters)){
			throw new IllegalArgumentException("FatCat algorithm needs FatCatParameters object as argument.");
		}

		params = (FatCatParameters) param;

		AFPChain afpChain= alignFlexible(ca1, ca2, params);
		afpChain.setAlgorithmName(algorithmName);
		afpChain.setVersion(VERSION+"");
		return afpChain;
	}

	@Override
	public String getAlgorithmName() {

		return algorithmName;
	}

	@Override
	public String getVersion(){
		return VERSION+"";
	}

	@Override
	public ConfigStrucAligParams getParameters() {

		return params;
	}

//	public StructureAlignmentJmol display(AFPChain afpChain, Atom[] ca1,
//			Atom[] ca2, List hetatms, List nucs,
//			List hetatms2, List nucs2) throws StructureException {
//
//		StructureAlignmentJmol gui =  super.display(afpChain, ca1, ca2, hetatms, nucs, hetatms2, nucs2);
//		gui.setTitle(getAlgorithmName() + " : " + afpChain.getName1() + " vs. " + afpChain.getName2());
//		return gui;
//	}

	@Override
	public void setParameters(ConfigStrucAligParams parameters) {
		if (! (parameters instanceof FatCatParameters)){
			throw new IllegalArgumentException("Provided parameters are not of type FatCatParameters!");
		}
		params = (FatCatParameters) parameters;
	}



}