/*
 *                  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 7, 2006
 *
 */
package org.biojava.nbio.structure.align.pairwise;


import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomImpl;
import org.biojava.nbio.structure.jama.Matrix;


/** a pair of fragments of two protein structures
 *
 * @author Andreas Prlic
 * @since 1.5
 * @version %I% %G%
 */
public class FragmentPair {


        int length;
        int pos1;
        int pos2;

        // parameter below may be used in different approaches

        int contacts;
        int cluster;
        double rms;
        int used;
        int covered;

        //filled if fragments are superimposed
        Matrix rot;
        Atom trans;

        //this unit vector indicates the rotation of j onto i
        Atom unitv;

        Atom center1;
        Atom center2;


        public FragmentPair(int length, int p1, int p2) {
                super();
                this.length = length ;
                 pos1 = p1;
                 pos2 = p2;

                 contacts = 0;
                 cluster = 0;
                 rms = 0.0;
                 used = 0;
                 covered = 0;

                 unitv = new AtomImpl();
                 unitv.setX(0);
                 unitv.setY(0);
                 unitv.setZ(1);
                 rot = null;
                 trans = new AtomImpl();
                 center1 = new AtomImpl();
                 center2 = new AtomImpl();

        }
        @Override
        public Object clone(){

                FragmentPair n = new FragmentPair(length,pos1,pos2);
                if ( center1 !=null)
                        n.setCenter1((Atom)center1.clone());

                if ( center2 != null)
                        n.setCenter2((Atom)center2.clone());

                n.setCluster(cluster);
                n.setContacts(contacts);
                n.setCovered(covered);
                n.setRms(rms);
                n.setLength(length);
                n.setRot((Matrix)rot.clone());
                n.setUnitv((Atom)unitv.clone());

                return n;
        }
        public int getCluster() {
                return cluster;
        }

        public void setCluster(int cluster) {
                this.cluster = cluster;
        }

        public int getContacts() {
                return contacts;
        }

        public void setContacts(int contacts) {
                this.contacts = contacts;
        }

        public int getCovered() {
                return covered;
        }

        public void setCovered(int covered) {
                this.covered = covered;
        }

        public int getLength() {
                return length;
        }

        public void setLength(int length) {
                this.length = length;
        }

        public int getPos1() {
                return pos1;
        }

        public void setPos1(int pos1) {
                this.pos1 = pos1;
        }

        public int getPos2() {
                return pos2;
        }

        public void setPos2(int pos2) {
                this.pos2 = pos2;
        }

        public double getRms() {
                return rms;
        }

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

        public Matrix getRot() {
                return rot;
        }

        public void setRot(Matrix rot) {
                this.rot = rot;
        }

        public Atom getTrans() {
                return trans;
        }

        public void setTrans(Atom trans) {
                this.trans = trans;
        }

        public Atom getUnitv() {
                return unitv;
        }

        public void setUnitv(Atom unitv) {
                this.unitv = unitv;
        }

        public int getUsed() {
                return used;
        }

        public void setUsed(int used) {
                this.used = used;
        }

        public Atom getCenter1() {
                return center1;
        }

        public void setCenter1(Atom center1) {
                this.center1 = center1;
        }

        public Atom getCenter2() {
                return center2;
        }

        public void setCenter2(Atom center2) {
                this.center2 = center2;
        }

        @Override
        public String toString() {
                return String.format("Fragment (%d,%d) len %d", pos1, pos2, length);
        }
}