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.bio.seq.io.agave; 022import java.util.ArrayList; 023import java.util.Iterator; 024import java.util.List; 025 026import org.biojava.bio.Annotation; 027 028/** 029 * Basic implementation of AGAVEAnnotFilter 030 * @author Hanning Ni Doubletwist Inc 031*/ 032public class SimpleAnnotFilter implements AGAVEAnnotFilter{ 033 034 public static final AGAVEAnnotFilterFactory SIMPLE_ANNOT_FILTER_FACTORY 035 = new AGAVEAnnotFilterFactory() { 036 public AGAVEAnnotFilter getInstance() { 037 return new SimpleAnnotFilter(); 038 } 039 }; 040 041 SimpleAnnotFilter() { 042 } 043 044 /** 045 * 046 */ 047 public String getAccession(Annotation annot) 048 { 049 return (String) null ; 050 } 051 052 /** 053 * 054 */ 055 public String getKeyword(Annotation annot) 056 { 057 return (String) null; 058 } 059 public String getElementId(Annotation annot) 060 { 061 return (String) null ; 062 } 063 /** 064 * 065 */ 066 public String getOrganism(Annotation annot) 067 { 068 return (String) null ; 069 } 070 071 public String getLabel(Annotation annot) 072 { 073 return (String) null; 074 } 075 076 /** 077 * 078 */ 079 public String getDescription(Annotation annot) 080 { 081 return (String) null; 082 } 083 084 public String getMatchAlign(Annotation annot) 085 { 086 return (String) null ; 087 } 088 089 public AGAVEMatchRegion getMatchRegion(Annotation annot) 090 { 091 return (AGAVEMatchRegion) null ; 092 } 093 094 public AGAVEQueryRegion getQueryRegion(Annotation annot) 095 { 096 return (AGAVEQueryRegion) null ; 097 } 098 099 public String getClassifySystem(Annotation annot) 100 { 101 return (String) null ; 102 } 103 104 public String getClassifyId(Annotation annot) 105 { 106 return (String) null ; 107 } 108 109 public String getClassifyType(Annotation annot) 110 { 111 return (String) null ; 112 } 113 114 public String[] getExonIds(Annotation annot) 115 { 116 return (String[])null ; 117 } 118 119 public String getChromNum(Annotation annot) 120 { 121 return (String)null ; 122 } 123 124 public AGAVEIdAlias[] getIdAlias(Annotation annot) 125 { 126 return (AGAVEIdAlias[])null ; 127 } 128 /** 129 * 130 */ 131 public String getNote(Annotation annot) 132 { 133 return (String) null ; 134 } 135 136 public AGAVEDbId[] getAltIds(Annotation annot) 137 { 138 return (AGAVEDbId[])null ; 139 } 140 141 public AGAVEMapLocation[] getMapLocation(Annotation annot) 142 { 143 return (AGAVEMapLocation[]) null ; 144 } 145 146 public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot) 147 { 148 return (AGAVERelatedAnnot[]) null ; 149 } 150 151 public String[] getElementIds(Annotation annot) 152 { 153 return (String[]) null ; 154 } 155 156 public String getGroupOrder(Annotation annot) 157 { 158 return (String) null ; 159 } 160 161 public String getMatchDesc(Annotation annot) 162 { 163 return (String) null ; 164 } 165 166 public String getFeatureType(Annotation annot) 167 { 168 return (String) null ; 169 } 170 public String getResultType(Annotation annot) 171 { 172 return (String) null ; 173 } 174 175 public String getConfidence(Annotation annot) 176 { 177 return (String) null ; 178 } 179 180 public String getAlignLength(Annotation annot) 181 { 182 return (String) null ; 183 } 184 185 public String getAlignUnits(Annotation annot) 186 { 187 return (String) null ; 188 } 189 190 191 public AGAVEXrefs[] getXrefs(Annotation annot) 192 { 193 return (AGAVEXrefs[])null ; 194 } 195 /** 196 * 197 */ 198 public String getVersion(Annotation annot) 199 { 200 return (String) null ; 201 } 202 203 public String getSequenceId(Annotation annot) 204 { 205 return (String) null ; 206 } 207 208 public String getTaxonId(Annotation annot) 209 { 210 return (String) null ; 211 } 212 213 public String getCloneId(Annotation annot) 214 { 215 return (String) null ; 216 } 217 218 public String getCloneLibrary(Annotation annot) 219 { 220 return (String) null ; 221 } 222 223 public String getChromosome(Annotation annot) 224 { 225 return (String) null ; 226 } 227 228 public String getMapPosition(Annotation annot) 229 { 230 return (String) null ; 231 } 232 233 public String getEcNumber(Annotation annot) 234 { 235 return (String) null ; 236 } 237 238 public String getCreateDate(Annotation annot) 239 { 240 return (String) null ; 241 } 242 243 public String getUpdateDate(Annotation annot) 244 { 245 return (String) null ; 246 } 247 248 249 /** 250 * 251 */ 252 public String getOS(Annotation annot) 253 { 254 return (String) null ; 255 } 256 257 /** 258 * 259 */ 260 public String getMolType(Annotation annot) 261 { 262 return (String) null; 263 } 264 265 public AGAVEDbId getDbId(Annotation annot) 266 { 267 return (AGAVEDbId) null ; 268 } 269 /** 270 * ThomasD made this a bit safer... 271 */ 272 public AGAVEProperty[] getProperty(Annotation annot, String type) 273 { 274 List set = new ArrayList(); 275 for (Iterator i = annot.keys().iterator(); i.hasNext();) 276 { 277 Object key = i.next(); 278 Object value = annot.getProperty(key); 279 if (key instanceof String && value instanceof String) { 280 set.add(new AGAVEProperty(type, (String) key, null, (String) value )); 281 } 282 } 283 return (AGAVEProperty[]) set.toArray(new AGAVEProperty[set.size()]); 284 } 285}