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The protein structure modules of BioJava.

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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 1, 2006
 *
 */
package org.biojava.nbio.structure.align.helper;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;


/** A utility class that defines which set of atoms are considered
 * to be on equivalent positions.
 *
 *
 */
public class JointFragments {


		double rms;

		List idxlist;
		public JointFragments(){
			idxlist = new ArrayList();
			rms = 999;
		}

		/**
		 * Stores the alignment between the residues of several fragments.
		 * Each int[] stores the residue numbers of several equivalent residues.
		 */
		public void setIdxlist(List idxs) {
			Iterator iter = idxs.iterator();
			while (iter.hasNext()){
				int[] e = iter.next();
				idxlist.add(e);
			}
		}



		public double getRms() {
			return rms;
		}

		public void setRms(double rms) {
			this.rms = rms;
		}

		public List getIdxlist(){
			return idxlist;
		}
		public void add(int p1, int p2,int start,int end){
			//System.out.println("JointFragments add " +p1 + " " + p2 + " " + start + " " + end);
			for ( int k = start;k< end ; k++){
				//e = (f[0]+k,f[1]+k)
				//e = (f[0]+k,f[1]+k);
				int[] e = new int[] {p1+k,p2+k};

				// check if already known ...
				Iterator iter = idxlist.iterator();
				while (iter.hasNext()){
					int[] kno = iter.next();
					if ((kno[0] == e[0]) && ( kno[1] == e[1])){
						System.err.println("already known index pair, not adding a 2nd time." + e[0] + " " + e[1]);
						return;
					}
				}
				idxlist.add(e);
				Collections.sort(idxlist, new IdxComparator());
			}
		}


		@Override
		public String toString(){
			String s = "Joint Fragment idxlist len: " +idxlist.size();
			return s;
		}


}