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The protein structure modules of BioJava.
There is a newer version: 7.2.2
/*
 *                    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 Oct 2, 2009
 * Author: Andreas Prlic
 *
 */

package org.biojava.nbio.structure.align;


import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
import org.biojava.nbio.structure.align.helper.IndexPair;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.pairwise.AlternativeAlignment;
import org.biojava.nbio.structure.jama.Matrix;


/** Wrapper for the BioJava Structure Alignment Implementation
 *
 * @author Andreas Prlic
 *
 */
public class BioJavaStructureAlignment

implements StructureAlignment  {

	public static final String algorithmName = "BioJava_structure";
	private static final float versionNr = 0.1f;
	StrucAligParameters params;

	public BioJavaStructureAlignment(){
		params = new StrucAligParameters();
	}

	@Override
	public String getAlgorithmName() {
		return algorithmName;
	}

	@Override
	public ConfigStrucAligParams getParameters() {
		return null;//TODO shall we update it?
	}

	@Override
	public void setParameters(ConfigStrucAligParams o){
		//TODO what is the relation between StrucAligParameters and ConfigStrucAligParams?
		if ( ! (o instanceof StrucAligParameters)){
			throw new IllegalArgumentException("Provided parameters are not of type StrucAligParameters!");
		}
		params = (StrucAligParameters) o;
	}

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

	public String printHelp() {
		return "not implemented yet. Algorithm still under development.";
	}



	@Override
	public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException {
		StrucAligParameters params = StrucAligParameters.getDefaultParameters();
		return align(ca1,ca2,params);

	}


	@Override
	public AFPChain align(Atom[] ca1, Atom[] ca2, Object params)
			throws StructureException {
		if ( ! (params instanceof StrucAligParameters)){
			throw new IllegalArgumentException("BioJava structure alignment requires a StrucAligParameters class for the arguments.");
		}
		this.params = (StrucAligParameters) params;

		AFPChain afpChain = new AFPChain(algorithmName);
		StructurePairAligner aligner = new StructurePairAligner();
		aligner.align(ca1,ca2,this.params);

		// copy the results over into the AFPChain...
		AlternativeAlignment[] aligs = aligner.getAlignments();
		if ( aligs.length > 0){

			AlternativeAlignment altAlig = aligs[0];
			// copy the results over!
			copyResults(afpChain,altAlig,ca1,ca2);


		}

		return afpChain;

	}



	private void copyResults(AFPChain afpChain, AlternativeAlignment altAlig, Atom[] ca1, Atom[] ca2) {
		afpChain.setAlgorithmName(getAlgorithmName());
		afpChain.setVersion(getVersion());
		afpChain.setAlignScore(altAlig.getScore());
		afpChain.setOptLength(altAlig.getEqr());
		afpChain.setBlockRotationMatrix(new Matrix[]{altAlig.getRotationMatrix()});
		afpChain.setBlockShiftVector(new Atom[]{altAlig.getShift() });
		afpChain.setBlockNum(1);

		double rmsd = altAlig.getRmsd();
		afpChain.setBlockRmsd(new double[]{rmsd});


		int nAtom = altAlig.getEqr();
		int lcmp = altAlig.getPath().length;
		int[] optLen = new int[]{nAtom};
		afpChain.setOptLen(optLen);
		afpChain.setOptLength(nAtom);
		afpChain.setAlnLength(lcmp);

		int[][][] optAln = new int[1][2][lcmp];
		afpChain.setOptAln(optAln);

		afpChain.setOptRmsd(new double[]{rmsd});
		afpChain.setTotalRmsdOpt(rmsd);
		afpChain.setChainRmsd(rmsd);
		//afpChain.setProbability(-1);
		int nse1 = ca1.length;
		int nse2 = ca2.length;

		char[] alnseq1 = new char[nse1+nse2+1];
		char[] alnseq2 = new char[nse1+nse2+1] ;
		char[] alnsymb = new char[nse1+nse2+1];

		IndexPair[] path = altAlig.getPath();

		int pos = 0;
		for(int ia=0; ia