001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.structure.align.model;
022
023import org.biojava.nbio.structure.jama.Matrix;
024
025import java.io.Serializable;
026
027/** A class to represent a FATCAT AFP
028 *
029 * @author Andreas Prlic
030 *
031 */
032
033public class AFP implements Serializable {
034
035        /**
036         *
037         */
038        private static final long serialVersionUID = 3901209995477111829L;
039        int p1;
040        int p2;
041        int fragLen;
042        double rmsd;
043        Matrix m;
044        double[] t;
045        double score;
046
047        long id;
048
049        @Override
050public String toString(){
051
052                // we use the metric of
053
054                // Manfred J. Sippl
055                // On Distance and Similarity in Fold Space
056                // Bioinformatics, 24, pp. 872-873  (2008)
057
058
059                StringBuffer buf = new StringBuffer();
060                buf.append("AFP: p1:");
061                buf.append(p1);
062                buf.append(" p2: ");
063                buf.append(p2);
064                buf.append(" len " );
065                buf.append(fragLen);
066                buf.append(" rmsd ");
067                buf.append(rmsd);
068                buf.append(" score ");
069                buf.append(score);
070                return buf.toString();
071        }
072
073
074        public long getId()
075        {
076                return id;
077        }
078
079        public void setId(long id)
080        {
081                this.id = id;
082        }
083
084        public int getP1() {
085                return p1;
086        }
087        public void setP1(int p1) {
088                this.p1 = p1;
089        }
090        public int getP2() {
091                return p2;
092        }
093        public void setP2(int p2) {
094                this.p2 = p2;
095        }
096        public int getFragLen() {
097                return fragLen;
098        }
099        public void setFragLen(int fragLen) {
100                this.fragLen = fragLen;
101        }
102        public double getRmsd() {
103                return rmsd;
104        }
105        public void setRmsd(double rmsd) {
106                this.rmsd = rmsd;
107        }
108        public Matrix getM() {
109                return m;
110        }
111        public void setM(Matrix m) {
112                this.m = m;
113        }
114        public double[] getT() {
115                return t;
116        }
117        public void setT(double[] t) {
118                this.t = t;
119        }
120        public double getScore() {
121                return score;
122        }
123        public void setScore(double score) {
124                this.score = score;
125        }
126
127
128
129
130}