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 */ 021 022package org.biojava.bio.program.homologene; 023 024 025public interface OrthologueFilter 026{ 027 public boolean accept(Orthologue ortho); 028 029 public final static class AcceptAll implements OrthologueFilter 030 { 031 public boolean accept(Orthologue ortho) { return true; } 032 } 033 034 public final static class Not implements OrthologueFilter 035 { 036 OrthologueFilter a; 037 038 public Not(OrthologueFilter a) 039 { 040 this.a = a; 041 } 042 043 public boolean accept(Orthologue ortho) 044 { 045 return !a.accept(ortho); 046 } 047 } 048 049 public final static class Or implements OrthologueFilter 050 { 051 OrthologueFilter a; 052 OrthologueFilter b; 053 054 public Or(OrthologueFilter a, OrthologueFilter b) 055 { 056 this.a = a; 057 this.b = b; 058 } 059 060 public boolean accept(Orthologue ortho) 061 { 062 return ((a.accept(ortho)) || (b.accept(ortho))); 063 } 064 } 065 066 public final static class And implements OrthologueFilter 067 { 068 OrthologueFilter a; 069 OrthologueFilter b; 070 071 public And(OrthologueFilter a, OrthologueFilter b) 072 { 073 this.a = a; 074 this.b = b; 075 } 076 077 public boolean accept(Orthologue ortho) 078 { 079 return ((a.accept(ortho)) && (b.accept(ortho))); 080 } 081 } 082 083 public final static class Xor implements OrthologueFilter 084 { 085 OrthologueFilter a; 086 OrthologueFilter b; 087 088 public Xor(OrthologueFilter a, OrthologueFilter b) 089 { 090 this.a = a; 091 this.b = b; 092 } 093 094 public boolean accept(Orthologue ortho) 095 { 096 return ((a.accept(ortho)) ^ (b.accept(ortho))); 097 } 098 } 099 100 public class ByTaxonID implements OrthologueFilter 101 { 102 int taxonID; 103 104 public ByTaxonID(int taxonID) 105 { 106 this.taxonID = taxonID; 107 } 108 109 public boolean accept(Orthologue ortho) 110 { 111 try { 112 return (taxonID == ortho.getTaxonID()); 113 } 114 catch (Exception e) { 115 return false; 116 } 117 } 118 } 119 120 public class ByTaxon implements OrthologueFilter 121 { 122 Taxon taxon; 123 124 public ByTaxon(Taxon taxon) 125 { 126 this.taxon = taxon; 127 } 128 129 public boolean accept(Orthologue ortho) 130 { 131 try { 132 return (taxon == ortho.getTaxon()); 133 } 134 catch (Exception e) { 135 return false; 136 } 137 } 138 } 139 140 public class ByLocusID implements OrthologueFilter 141 { 142 String locusID; 143 144 public ByLocusID(String locusID) 145 { 146 this.locusID = locusID; 147 } 148 149 public boolean accept(Orthologue ortho) 150 { 151 try { 152 return (locusID.equals(ortho.getLocusID())); 153 } 154 catch (Exception e) { 155 return false; 156 } 157 } 158 } 159 160 public class ByHomologeneID implements OrthologueFilter 161 { 162 String homologeneID; 163 164 public ByHomologeneID(String homologeneID) 165 { 166 this.homologeneID = homologeneID; 167 } 168 169 public boolean accept(Orthologue ortho) 170 { 171 try { 172 return (homologeneID.equals(ortho.getHomologeneID())); 173 } 174 catch (Exception e) { 175 return false; 176 } 177 } 178 } 179 180 public class ByAccession implements OrthologueFilter 181 { 182 String regex; 183 184 public ByAccession(String regex) 185 { 186 this.regex = regex; 187 } 188 189 public boolean accept(Orthologue ortho) 190 { 191 try { 192 return ortho.getAccession().matches(regex); 193 } 194 catch (Exception e) { 195 return false; 196 } 197 } 198 } 199 200 public class ByTitle implements OrthologueFilter 201 { 202 String regex; 203 204 public ByTitle(String regex) 205 { 206 this.regex = regex; 207 } 208 209 public boolean accept(Orthologue ortho) 210 { 211 try { 212 return ortho.getTitle().matches(regex); 213 } 214 catch (Exception e) { 215 return false; 216 } 217 } 218 } 219} 220