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}