/*
 *                  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 Jan 28, 2006
 *
 */
package org.biojava.nbio.structure.align.pairwise;


import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.align.StrucAligParameters;
import org.biojava.nbio.structure.align.helper.AligMatEl;
import org.biojava.nbio.structure.align.helper.IndexPair;
import org.biojava.nbio.structure.align.helper.JointFragments;
import org.biojava.nbio.structure.jama.Matrix;

import java.io.Serializable;
import java.text.DecimalFormat;
import java.util.List;
import java.util.logging.Logger;

/**
 * Implements a class which handles one possible (alternative) solution.
 *
 * Alternative alignments arise from different seed
 * alignments or seed FPairs. The AltAlg class contains methods
 * for refinement (Dynamic Programming based) and filtering
 * (i.e. removing probably wrongly matched APairs). In the refinement
 * phase, different seed alignments can converge to the same solution.
 *
 * @author Andreas Prlic,
 * @author Peter Lackner (original Python and C code)
 * @since 3:04:26 PM
 * @version %I% %G%
 */
public class AlternativeAlignment implements Serializable{


	/**
	 *
	 */
	private static final long serialVersionUID = -6226717654562221241L;

	int[] idx1;
	int[] idx2;
	String[] pdbresnum1;
	String[] pdbresnum2;
	//short[] alig1;
	//short[] alig2;

	int nfrags;
	Atom center;
	Matrix rot;
	Atom tr;


	// the scores...
	int gaps0;
	int eqr0;
	int rms0;
	int joined;
	int percId;
	int cluster;
	float score;
	IndexPair[] aligpath;
	int fromia;
	Matrix currentRotMatrix;
	Atom currentTranMatrix;

	double rms;

	Matrix distanceMatrix;

	public static Logger logger =  Logger.getLogger("org.biojava.nbio.structure.align");


	public AlternativeAlignment() {
		super();

		nfrags = 0;
		aligpath = new IndexPair[0];
		//alig1 = new short[0];
		//alig2 = new short[0];
		idx1 = new int[0];
		idx2 = new int[0];

		center = new AtomImpl();
		rot = null;
		tr = new AtomImpl();
		eqr0 = -99;
		rms0 = 99;
		joined = 0;
		gaps0 = -99;
		fromia = 0;

		currentRotMatrix = new Matrix(0,0);
		currentTranMatrix = new AtomImpl();

		distanceMatrix = new Matrix(0,0);
	}




	/** print the idx positions of this alignment
	 *
	 * @return a String representation
	 */
	@Override
	public String toString(){
		DecimalFormat d2 = new DecimalFormat();
		// the result can be localized. To change this and enforce UK local do...
		//(DecimalFormat)NumberFormat.getInstance(java.util.Locale.UK);
		d2.setMaximumIntegerDigits(3);
		d2.setMinimumFractionDigits(2);
		d2.setMaximumFractionDigits(2);
		StringBuffer s = new StringBuffer();
		s.append("#" + getAltAligNumber() +
				" cluster:" + cluster +
				" eqr:" + getEqr() +
				" rmsd:" + d2.format(getRmsd()) +
				" %id:" + getPercId() +
				" gaps:" + getGaps() +
				" score:" + d2.format(score)	);

		return s.toString();
	}


	/** get the number of the cluster this alignment belongs to
	 *
	 * @return an int giving the number of the cluster
	 */
	public int getCluster() {
		return cluster;
	}



	/** set the number of the cluster this alignment belongs to.
	 * All alignments in a cluster are quite similar.
	 *
	 * @param cluster the number of the cluster
	 */
	public void setCluster(int cluster) {
		this.cluster = cluster;
	}




	public double getRmsd() {
		return rms;
	}

	/** the rms in the structurally equivalent regions
	 *
	 * @param rms
	 */
	public void setRms(double rms) {
		this.rms = rms;
	}

	/** the alignment score
	 *
	 * @return the score of this alignment
	 */
	public float getScore() {
		return score;
	}

	public void setScore(float score) {
		this.score = score;
	}


	/** return the number of gaps in this alignment
	 *
	 * @return the number of Gaps
	 */
	public int getGaps(){
		return gaps0;
	}

	/** returns the number of euqivalent residues in this alignment
	 *
	 * @return the number of equivalent residues
	 */
	public int getEqr(){
		return eqr0 ;
	}

	/** the positions of the structure equivalent positions in atom set 1
	 *
	 * @return the array of the positions
	 */
	public int[] getIdx1(){
		return idx1;
	}

	/** the positions of the structure equivalent atoms in atom set 2
	 *
	 * @return the array of the positions
	 */
	public int[] getIdx2(){
		return idx2;
	}

	public int getPercId() {
		return percId;
	}

	public void setPercId(int percId) {
		this.percId = percId;
	}

	/** Set apairs according to a seed position.
	 *
	 * @param l
	 * @param i
	 * @param j
	 */
	public void  apairs_from_seed(int l,int i, int j){
		aligpath = new IndexPair[l];
		idx1 = new int[l];
		idx2 = new int[l];
		for (int x = 0 ; x < l ; x++) {
			idx1[x]=i+x;
			idx2[x]=j+x;
			aligpath[x] = new IndexPair((short)(i+x),(short)(j+x));
		}
	}

	/** Set apairs according to a list of (i,j) tuples.
	 *
	 * @param jf a JoingFragment
	 */
	public void apairs_from_idxlst(JointFragments jf) {
		List<int[]> il = jf.getIdxlist();
		//System.out.println("Alt Alig apairs_from_idxlst");

		aligpath = new IndexPair[il.size()];
		idx1 = new int[il.size()];
		idx2 = new int[il.size()];
		for (int i =0 ; i < il.size();i++) {
			int[] p = il.get(i);
			//System.out.print(" idx1 " + p[0] + " idx2 " + p[1]);
			idx1[i] = p[0];
			idx2[i] = p[1];
			aligpath[i] = new IndexPair((short)p[0],(short)p[1]);

		}
		eqr0  = idx1.length;
		//System.out.println("eqr " + eqr0);
		gaps0 = count_gaps(idx1,idx2);

	}


	/** returns the sequential number of this alternative alignment
	 *
	 * @return the sequential number of this alternative alignment
	 */
	public int getAltAligNumber() {
		return fromia;
	}

	public void setAltAligNumber(int fromia) {
		this.fromia = fromia;
	}

	/** rotate and shift atoms with currentRotMatrix and current Tranmatrix
	 *
	 * @param ca
	 */
	private void rotateShiftAtoms(Atom[] ca){

		for (int i  = 0 ; i < ca.length; i++){
			Atom c = ca[i];

			Calc.rotate(c,currentRotMatrix);
			Calc.shift(c,currentTranMatrix);
			//System.out.println("after " + c);
			ca[i] = c;
		}
		//System.out.println("after " + ca[0]);
	}

	public void finish(StrucAligParameters params,Atom[]ca1,Atom[]ca2) throws StructureException{

		Atom[] ca3 = new Atom[ca2.length];
		for ( int i = 0 ; i < ca2.length;i++){
			ca3[i] = (Atom) ca2[i].clone();

		}
		// do the inital superpos...

		super_pos_alig(ca1,ca3,idx1,idx2,true);
		rotateShiftAtoms(ca3);

		calcScores(ca1,ca2);
		logger.fine("eqr " + eqr0 + " " + gaps0 + " "  +idx1[0] + " " +idx1[1]);

		getPdbRegions(ca1,ca2);

	}

	public static Matrix getDistanceMatrix(Atom[] ca1, Atom[]ca2){

		int r = ca1.length;
		int c = ca2.length;

		Matrix out = new Matrix(r,c);

		for (int i=0; i<r; i++) {
			Atom a1 = ca1[i];
			for (int j=0;j<c;j++){
				Atom b1 = ca2[j];


				double d = Calc.getDistance(a1,b1);
				out.set(i,j,d);

			}
		}
		return out;
	}

	private Alignable getInitalStrCompAlignment(
			Atom[] ca1,
			Atom[]ca2,
			StrucAligParameters params
			){

		int rows = ca1.length;
		int cols = ca2.length;

		float gapOpen = params.getGapOpen();
		float gapExtension = params.getGapExtension();
		float co = params.getCreate_co();

		Alignable al = new StrCompAlignment(rows,cols);
		al.setGapExtCol(gapExtension);
		al.setGapExtRow(gapExtension);
		al.setGapOpenCol(gapOpen);
		al.setGapOpenRow(gapOpen);

		AligMatEl[][] aligmat = al.getAligMat();

		//System.out.println(rows + " " + cols );

		aligmat[0][cols]    = new AligMatEl();
		aligmat[rows][0]    = new AligMatEl();
		aligmat[rows][cols] = new AligMatEl();

		for (int i = 0; i < rows; i++) {
			Atom a1 = ca1[i];

			aligmat[i][0]    = new AligMatEl();
			//aligmat[i][cols] = new AligMatEl();

			for (int j = 0; j < cols; j++) {
				//System.out.println("index " + i + " " + j);
				aligmat[0][j] = new AligMatEl();

				Atom b1 = ca2[j];
				double d = 999;

				d = Calc.getDistance(a1,b1);


				AligMatEl e = new AligMatEl();
				if (d > co) {
					e.setValue(0);
				} else {
					double s =  2 * co / ( 1 + ( d/co) * (d/co)) - co;
					e.setValue((int) Math.round(Gotoh.ALIGFACTOR * s));
				}
				aligmat[i+1][j+1] = e;
			}
		}

		return al;
	}

	/*private Alignable getAlignableFromSimMatrix (Matrix sim,StrucAligParameters params){
		//System.out.println("align_NPE");

		float gapOpen = params.getGapOpen();
		float gapExtension = params.getGapExtension();

		int rows = sim.getRowDimension();
		int cols = sim.getColumnDimension();

		Alignable al = new StrCompAlignment(rows,cols);
		al.setGapExtCol(gapExtension);
		al.setGapExtRow(gapExtension);
		al.setGapOpenCol(gapOpen);
		al.setGapOpenRow(gapOpen);
		//System.out.println("size of aligmat: " + rows+1 + " " + cols+1);
		//AligMatEl[][] aligmat = new AligMatEl[rows+1][cols+1];
		AligMatEl[][] aligmat = al.getAligMat();

		for (int i = 0; i < rows; i++) {
			for (int j = 0; j < cols; j++) {

				int e=0;
				//if ( ( i < rows) &&
				//        ( j < cols)) {
				//TODO: the ALIGFACTOR calc should be hidden in Gotoh!!

				e = (int)Math.round(Gotoh.ALIGFACTOR * sim.get(i,j));
				//}
				//System.out.println(e);
				//AligMatEl am = new AligMatEl();
				aligmat[i+1][j+1].setValue(e);
				//.setValue(e);
				//am.setTrack(new IndexPair((short)-99,(short)-99));
				//igmat[i+1][j+1] = am;

			}
		}
		//al.setAligMat(aligmat);


		return al;
	}*/
	/** Refinement procedure based on superposition and dynamic programming.
	 * Performs an iterative refinement. Several methods apply such a procedure,
	 * e.g. CE or ProSup. Here we additionally test for circular permutation,
	 * which are in the same frame of superposition as the optimal alignment.
	 * This feature may be switched off by setting permsize to -1.
	 *
	 * @param params the parameters
	 * @param ca1 atoms of structure 1
	 * @param ca2 atoms of structure 2
	 * @throws StructureException
	 */

	public void refine(StrucAligParameters params,Atom[]ca1,Atom[]ca2) throws StructureException{
		// System.out.println("refine Alternative Alignment #"+ getAltAligNumber()+" l1:" + ca1.length + " l2:" + ca2.length);
		//		for ( int i= 0 ; i < idx1.length;i++){
		//		System.out.println(idx1[i] + " " + idx2[i]);
		//		}

		// avoid any operations on the original Atoms ...
		Atom[] ca3 = new Atom[ca2.length];
		for ( int i = 0 ; i < ca2.length;i++){
			ca3[i] = (Atom) ca2[i].clone();

		}
		//Atom[] ca3 = (Atom[]) ca2.clone();

		// do the inital superpos...

		super_pos_alig(ca1,ca3,idx1,idx2,false);

		//JmolDisplay jmol1 = new JmolDisplay(ca1,ca2,"after first alig " );
		//jmol1.selectEquiv(idx1,idx2);
		//int[] jmoltmp1 = idx1;
		//int[] jmoltmp2 = idx2;

		int lenalt =idx1.length;
		int lenneu = aligpath.length;
		//Matrix rmsalt = currentRotMatrix;



		int ml = Math.max(ca1.length, ca3.length);
		idx1 = new int[ml];
		idx2 = new int[ml];

		//int m1l = ca1.length;
		//int m2l = ca3.length;

		//Matrix sim = new Matrix(ca1.length,ca3.length,0);

		int maxiter = params.getMaxIter();
		for (int iter = 0 ; iter< maxiter; iter++){

			float  subscore = 0.0f;

			rotateShiftAtoms(ca3);

			// do the dynamic alignment...
			Alignable ali = getInitalStrCompAlignment(ca1,ca3, params);

			new Gotoh(ali);

			this.score = ali.getScore();
			//System.out.println("score " + score);
			IndexPair[] path = ali.getPath();

			int pathsize = ali.getPathSize();


			// now for a superimposable permutation. First we need to check the size and
			// position of the quadrant left out by the optimal path
			int firsta = path[0].getRow();
			int firstb = path[0].getCol();
			int lasta  = path[pathsize-1].getRow();
			int lastb  = path[pathsize-1].getCol();

			int quada_beg, quada_end, quadb_beg,quadb_end;

			if ( firsta == 0){
				quada_beg = lasta +1;
				quada_end = ca1.length -1;
				quadb_beg = 0;
				quadb_end = firstb-1;
			} else {
				quada_beg = 0;
				quada_end = firsta-1;
				quadb_beg = lastb+1;
				quadb_end = ca3.length -1;
			}

			// if the unaligned quadrant is larger than permsize
			int permsize = params.getPermutationSize();

			if ( permsize > 0 &&
					(quada_end - quada_beg >= permsize) &&
					( quadb_end - quadb_beg >= permsize)) {
				AligMatEl[][] aligmat = ali.getAligMat();
				Matrix submat = new Matrix(quada_end-quada_beg, quadb_end - quadb_beg) ;
				//then we copy the score values of the quadrant into a new matrix

				//System.out.println(quada_beg + " " + quada_end + " " +quadb_beg+" " + quadb_end);
				//System.out.println(sim.getRowDimension() + " " + sim.getColumnDimension());
				Atom[] tmp1 = new Atom[quada_end - quada_beg ];
				Atom[] tmp2 = new Atom[quadb_end - quadb_beg ];

				for ( int s = quada_beg; s < quada_end; s++){
					//System.out.println(s + " " +( quada_end-s));
					tmp1[quada_end - s -1] = ca1[s];
					for ( int t = quadb_beg; t < quadb_end; t++){
						if ( s == quada_beg )
							tmp2[quadb_end - t -1 ] = ca3[t];

						//System.out.println(s+" " +t);
						//double val = sim.get(s,t);
						double val = aligmat[s][t].getValue();
						submat.set(s-quada_beg,t-quadb_beg,val);
					}
				}
				// and perform a dp alignment again. (Note, that we fix the superposition).

				//Alignable subali = getAlignableFromSimMatrix(submat,params);
				Alignable subali = getInitalStrCompAlignment(tmp1, tmp2, params);
				subscore = subali.getScore();
				//System.out.println("join score" + score + " " + subscore);
				this.score = score+subscore;

				IndexPair[] subpath = subali.getPath();
				int subpathsize = subali.getPathSize();
				for ( int p=0;p<subpath.length;p++){
					IndexPair sp = subpath[p];
					sp.setRow((short)(sp.getRow()+quada_beg));
					sp.setCol((short)(sp.getCol()+quadb_beg));
				}

				// now we join the two solutions
				if ( subpathsize > permsize){
					IndexPair[] wholepath = new IndexPair[pathsize+subpathsize];
					for ( int t=0; t < pathsize; t++){
						wholepath[t] = path[t];
					}
					for ( int t=0 ; t < subpathsize; t++){
						wholepath[t+pathsize] = subpath[t];
					}
					pathsize += subpathsize;
					path = wholepath;
					ali.setPath(path);
					ali.setPathSize(pathsize);
				}

			}


			int j =0 ;
			//System.out.println("pathsize,path " + pathsize + " " + path.length);

			for (int i=0; i < pathsize; i++){
				int x = path[i].getRow();
				int y = path[i].getCol();
				//System.out.println(x+ " " + y);
				double d = Calc.getDistance(ca1[x], ca3[y]);
				//double d = dismat.get(x,y);
				// now we apply the evaluation distance cutoff
				if ( d < params.getEvalCutoff()){
					//System.out.println("j:"+j+ " " + x+" " + y + " " + d );

					idx1[j] = x;
					idx2[j] = y;
					j+=1;
				}
			}

			lenneu = j;
			//System.out.println("lenalt,neu:" + lenalt + " " + lenneu);


			int[] tmpidx1 = new int[j];
			int[] tmpidx2 = new int[j];
			//String idx1str ="idx1: ";
			//String idx2str ="idx2: ";
			for (int i = 0 ; i<j;i++){
				//idx1str += idx1[i]+ " ";
				//idx2str += idx2[i]+ " ";
				tmpidx1[i] = idx1[i];
				tmpidx2[i] = idx2[i];
			}
			//System.out.println(idx1str);
			//System.out.println(idx2str);
			//jmol.selectEquiv(idx1,idx2);

			//if ( j > 0)
			//  System.out.println("do new superimpos " + idx1.length + " " + idx2.length + " " + idx1[0] + " " + idx2[0]);
			super_pos_alig(ca1,ca3,tmpidx1,tmpidx2,false);

			this.aligpath = path;

			if (lenneu == lenalt)
				break;

		}



		idx1 = (int[]) FragmentJoiner.resizeArray(idx1,lenneu);
		idx2 = (int[]) FragmentJoiner.resizeArray(idx2,lenneu);
		//		new ... get rms...
		// now use the original atoms to get the rotmat relative to the original structure...
		super_pos_alig(ca1,ca2,idx1,idx2,true);
		eqr0 = idx1.length;
		gaps0 = count_gaps(idx1,idx2);

		getPdbRegions(ca1,ca2);
		//System.out.println("eqr " + eqr0 + " aligpath len:"+aligpath.length+ " gaps:" + gaps0 + " score " + score);
	}

	private void getPdbRegions(Atom[] ca1, Atom[] ca2){
		pdbresnum1 = new String[idx1.length];
		pdbresnum2 = new String[idx2.length];

		for (int i =0 ; i < idx1.length;i++){
			Atom a1 = ca1[idx1[i]];
			Atom a2 = ca2[idx2[i]];
			Group p1 = a1.getGroup();
			Group p2 = a2.getGroup();
			Chain c1 = p1.getChain();
			Chain c2 = p2.getChain();

			String cid1 = c1.getChainID();
			String cid2 = c2.getChainID();

			String pdb1 = p1.getResidueNumber().toString();
			String pdb2 = p2.getResidueNumber().toString();


			if ( ! cid1.equals(" "))
				pdb1 += ":" + cid1;


			if ( ! cid2.equals(" "))
				pdb2 += ":" + cid2;


			pdbresnum1[i] = pdb1;
			pdbresnum2[i] = pdb2;
		}
	}


	public String[] getPDBresnum1() {
		return pdbresnum1;
	}




	public void setPDBresnum1(String[] pdbresnum1) {
		this.pdbresnum1 = pdbresnum1;
	}




	public String[] getPDBresnum2() {
		return pdbresnum2;
	}




	public void setPDBresnum2(String[] pdbresnum2) {
		this.pdbresnum2 = pdbresnum2;
	}




	/** Count the number of gaps in an alignment represented by idx1,idx2.
	 *
	 * @param idx1
	 * @param idx2
	 * @return the number of gaps in this alignment
	 */
	private int count_gaps(int[] i1, int[] i2){

		int i0 = i1[0];
		int j0 = i2[0];
		int gaps = 0;
		for (int i =1 ; i<i1.length;i++ ){
			if ( Math.abs(i1[i]-i0) != 1 ||
					( Math.abs(i2[i]-j0) != 1)){
				gaps +=1;
			}
			i0 = i1[i];
			j0 = i2[i];
		}

		return gaps;
	}



	public void calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)throws StructureException {

		super_pos_alig(ca1,ca2,idx1,idx2,false);

	}

	/** Superimposes two molecules according to residue index list idx1 and idx2.
	 *  Does not change the original coordinates.
	 *  as an internal result the rotation matrix and shift vectors for are set
	 *
	 * @param ca1 Atom set 1
	 * @param ca2 Atom set 2
	 * @param idx1 idx positions in set1
	 * @param idx2 idx positions in set2
	 * @param getRMS a flag if the RMS should be calculated
	 * @throws StructureException
	 */



	private void super_pos_alig(Atom[]ca1,Atom[]ca2,int[] idx1, int[] idx2, boolean getRMS) throws StructureException{

		//System.out.println("superpos alig ");
		Atom[] ca1subset = new Atom[idx1.length];
		Atom[] ca2subset = new Atom[idx2.length];

		for (int i = 0 ; i < idx1.length;i++){
			//System.out.println("idx1 "+ idx1[i] + " " + idx2[i]);
			int pos1 =  idx1[i];
			int pos2 =  idx2[i];

			ca1subset[i] =  ca1[pos1];
			ca2subset[i] = (Atom) ca2[pos2].clone();
		}

		SVDSuperimposer svd = new SVDSuperimposer(ca1subset,ca2subset);
		this.currentRotMatrix  = svd.getRotation();
		this.currentTranMatrix = svd.getTranslation();
		//currentRotMatrix.print(3,3);
		if ( getRMS) {
			rotateShiftAtoms(ca2subset);
			this.rms = SVDSuperimposer.getRMS(ca1subset,ca2subset);
		}


	}


	/** returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
	 *
	 * @return the rotation Matrix
	 */
	public Matrix getRotationMatrix(){
		return currentRotMatrix;
	}

	/** returns the shift vector that has to be applied on structure to to shift on structure one
	 *
	 * @return the shift vector
	 */
	public Atom getShift(){
		return currentTranMatrix;
	}



	/** calculates  scores for this alignment ( %id )
	 * @param ca1 set of Atoms for molecule 1
	 * @param ca2 set of Atoms for molecule 2

	 */
	public void calcScores(Atom[] ca1, Atom[] ca2){
		eqr0 = idx1.length;
		gaps0 = count_gaps(idx1,idx2);

		percId = 0;
		// calc the % id
		for (int i=0 ; i< idx1.length; i++){
			Atom a1 = ca1[idx1[i]];
			Atom a2 = ca2[idx2[i]];

			Group g1 = a1.getGroup();
			Group g2 = a2.getGroup();
			if ( g1.getPDBName().equals(g2.getPDBName())){
				percId++;
			}

		}
	}



	/** create an artifical Structure object that contains the two
	 * structures superimposed onto each other. Each structure is in a separate model.
	 * Model 1 is structure 1 and Model 2 is structure 2.
	 *
	 * @param s1 the first structure. its coordinates will not be changed
	 * @param s2 the second structure, it will be cloned and the cloned coordinates will be rotated according to the alignment results.
	 * @return composite structure containing the 2 aligned structures as a models 1 and 2
	 */
	public Structure getAlignedStructure(Structure s1, Structure s2){
		// do not change the original coords ..
		Structure s3 = s2.clone();

		currentRotMatrix.print(3,3);

		Calc.rotate(s3, currentRotMatrix);
		Calc.shift( s3, currentTranMatrix);

		Structure newpdb = new StructureImpl();
		newpdb.setPDBCode("Java");
		newpdb.setName("Aligned with BioJava");


		newpdb.addModel(s1.getChains(0));
		newpdb.addModel(s3.getChains(0));

		return newpdb;

	}

	/** converts the alignment to a PDB file
	 * each of the structures will be represented as a model.
	 *
	 *
	 * @param s1
	 * @param s2
	 * @return a PDB file as a String
	 */
	public String toPDB(Structure s1, Structure s2){


		Structure newpdb = getAlignedStructure(s1, s2);

		return newpdb.toPDB();
	}



	/** The distance matrix this alignment is based on
	 *
	 * @return a Matrix object.
	 */
	public Matrix getDistanceMatrix() {
		return distanceMatrix;
	}



	/** The distance matrix this alignment is based on
	 *
	 * @param distanceMatrix
	 */
	public void setDistanceMatrix(Matrix distanceMatrix) {
		this.distanceMatrix = distanceMatrix;
	}




	public IndexPair[] getPath() {
		return aligpath;
	}



}

