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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 Jan 29, 2006
 *
 */
package org.biojava.nbio.structure.align.pairwise;

import org.biojava.nbio.structure.align.helper.AligMatEl;
import org.biojava.nbio.structure.align.helper.IndexPair;


public class StrCompAlignment
implements Alignable
{


	AligMatEl[][] aligmat;
	int rows;
	int cols;
	IndexPair[] path;
	int pathSize;
	float gapOpenCol;
	float gapOpenRow;
	float gapExtCol;
	float gapExtRow;
	float score;

	public StrCompAlignment(int rows, int cols){
		//System.out.println("new alignment " + rows + " " + cols);
		this.rows = rows;
		this.cols = cols;
		aligmat = new AligMatEl[rows+1][cols+1];

		/*for (int i=0;i