jalviewX
File FileFormat.java
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28% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| FileFormat | 30 | 62 | 54 | 44 |
Contributing tests
This file is covered by 177 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.io; | |
| 22 | ||
| 23 | import jalview.datamodel.AlignmentI; | |
| 24 | import jalview.datamodel.PDBEntry; | |
| 25 | import jalview.ext.jmol.JmolParser; | |
| 26 | import jalview.structure.StructureImportSettings; | |
| 27 | ||
| 28 | import java.io.IOException; | |
| 29 | ||
| 30 | public enum FileFormat implements FileFormatI | |
| 31 | { | |
| 32 | Fasta("Fasta", "fa, fasta, mfa, fastq", true, true) | |
| 33 | { | |
| 34 | 149 |  @Override |
| 35 | public AlignmentFileReaderI getReader(FileParse source) | |
| 36 | throws IOException | |
| 37 | { | |
| 38 | 149 | return new FastaFile(source); |
| 39 | } | |
| 40 | ||
| 41 | 4 | @Override |
| 42 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 43 | { | |
| 44 | 4 | return new FastaFile(); |
| 45 | } | |
| 46 | }, | |
| 47 | Pfam("PFAM", "pfam", true, true) | |
| 48 | { | |
| 49 | 9 | @Override |
| 50 | public AlignmentFileReaderI getReader(FileParse source) | |
| 51 | throws IOException | |
| 52 | { | |
| 53 | 9 | return new PfamFile(source); |
| 54 | } | |
| 55 | ||
| 56 | 1 | @Override |
| 57 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 58 | { | |
| 59 | 1 | return new PfamFile(); |
| 60 | } | |
| 61 | }, | |
| 62 | Stockholm("Stockholm", "sto,stk", true, true) | |
| 63 | { | |
| 64 | 37 | @Override |
| 65 | public AlignmentFileReaderI getReader(FileParse source) | |
| 66 | throws IOException | |
| 67 | { | |
| 68 | 37 | return new StockholmFile(source); |
| 69 | } | |
| 70 | ||
| 71 | 6 | @Override |
| 72 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 73 | { | |
| 74 | 6 | return new StockholmFile(al); |
| 75 | } | |
| 76 | ||
| 77 | }, | |
| 78 | ||
| 79 | PIR("PIR", "pir", true, true) | |
| 80 | { | |
| 81 | 1 | @Override |
| 82 | public AlignmentFileReaderI getReader(FileParse source) | |
| 83 | throws IOException | |
| 84 | { | |
| 85 | 1 | return new PIRFile(source); |
| 86 | } | |
| 87 | ||
| 88 | 1 | @Override |
| 89 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 90 | { | |
| 91 | 1 | return new PIRFile(); |
| 92 | } | |
| 93 | }, | |
| 94 | BLC("BLC", "BLC", true, true) | |
| 95 | { | |
| 96 | 1 | @Override |
| 97 | public AlignmentFileReaderI getReader(FileParse source) | |
| 98 | throws IOException | |
| 99 | { | |
| 100 | 1 | return new BLCFile(source); |
| 101 | } | |
| 102 | ||
| 103 | 1 | @Override |
| 104 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 105 | { | |
| 106 | 1 | return new BLCFile(); |
| 107 | } | |
| 108 | }, | |
| 109 | AMSA("AMSA", "amsa", true, true) | |
| 110 | { | |
| 111 | 1 | @Override |
| 112 | public AlignmentFileReaderI getReader(FileParse source) | |
| 113 | throws IOException | |
| 114 | { | |
| 115 | 1 | return new AMSAFile(source); |
| 116 | } | |
| 117 | ||
| 118 | 1 | @Override |
| 119 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 120 | { | |
| 121 | 1 | return new AMSAFile(al); |
| 122 | } | |
| 123 | }, | |
| 124 | Html("HTML", "html", true, false) | |
| 125 | { | |
| 126 | 0 | @Override |
| 127 | public AlignmentFileReaderI getReader(FileParse source) | |
| 128 | throws IOException | |
| 129 | { | |
| 130 | 0 | return new HtmlFile(source); |
| 131 | } | |
| 132 | ||
| 133 | 0 | @Override |
| 134 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 135 | { | |
| 136 | 0 | return new HtmlFile(); |
| 137 | } | |
| 138 | ||
| 139 | 0 | @Override |
| 140 | public boolean isComplexAlignFile() | |
| 141 | { | |
| 142 | 0 | return true; |
| 143 | } | |
| 144 | ||
| 145 | }, | |
| 146 | Rnaml("RNAML", "xml,rnaml", true, false) | |
| 147 | { | |
| 148 | 1 | @Override |
| 149 | public AlignmentFileReaderI getReader(FileParse source) | |
| 150 | throws IOException | |
| 151 | { | |
| 152 | 1 | return new RnamlFile(source); |
| 153 | } | |
| 154 | ||
| 155 | 0 | @Override |
| 156 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 157 | { | |
| 158 | 0 | return new RnamlFile(); |
| 159 | } | |
| 160 | ||
| 161 | }, | |
| 162 | Json("JSON", "json", true, true) | |
| 163 | { | |
| 164 | 6 | @Override |
| 165 | public AlignmentFileReaderI getReader(FileParse source) | |
| 166 | throws IOException | |
| 167 | { | |
| 168 | 6 | return new JSONFile(source); |
| 169 | } | |
| 170 | ||
| 171 | 4 | @Override |
| 172 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 173 | { | |
| 174 | 4 | return new JSONFile(); |
| 175 | } | |
| 176 | ||
| 177 | 0 | @Override |
| 178 | public boolean isComplexAlignFile() | |
| 179 | { | |
| 180 | 0 | return true; |
| 181 | } | |
| 182 | ||
| 183 | }, | |
| 184 | Pileup("PileUp", "pileup", true, true) | |
| 185 | { | |
| 186 | 1 | @Override |
| 187 | public AlignmentFileReaderI getReader(FileParse source) | |
| 188 | throws IOException | |
| 189 | { | |
| 190 | 1 | return new PileUpfile(source); |
| 191 | } | |
| 192 | ||
| 193 | 1 | @Override |
| 194 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 195 | { | |
| 196 | 1 | return new PileUpfile(); |
| 197 | } | |
| 198 | ||
| 199 | }, | |
| 200 | MSF("MSF", "msf", true, true) | |
| 201 | { | |
| 202 | 1 | @Override |
| 203 | public AlignmentFileReaderI getReader(FileParse source) | |
| 204 | throws IOException | |
| 205 | { | |
| 206 | 1 | return new MSFfile(source); |
| 207 | } | |
| 208 | ||
| 209 | 1 | @Override |
| 210 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 211 | { | |
| 212 | 1 | return new MSFfile(); |
| 213 | } | |
| 214 | ||
| 215 | }, | |
| 216 | Clustal("Clustal", "aln", true, true) | |
| 217 | { | |
| 218 | 1 | @Override |
| 219 | public AlignmentFileReaderI getReader(FileParse source) | |
| 220 | throws IOException | |
| 221 | { | |
| 222 | 1 | return new ClustalFile(source); |
| 223 | } | |
| 224 | ||
| 225 | 28 | @Override |
| 226 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 227 | { | |
| 228 | 28 | return new ClustalFile(); |
| 229 | } | |
| 230 | }, | |
| 231 | Phylip("PHYLIP", "phy", true, true) | |
| 232 | { | |
| 233 | 7 | @Override |
| 234 | public AlignmentFileReaderI getReader(FileParse source) | |
| 235 | throws IOException | |
| 236 | { | |
| 237 | 7 | return new PhylipFile(source); |
| 238 | } | |
| 239 | ||
| 240 | 3 | @Override |
| 241 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 242 | { | |
| 243 | 3 | return new PhylipFile(); |
| 244 | } | |
| 245 | }, | |
| 246 | Jnet("JnetFile", "", false, false) | |
| 247 | { | |
| 248 | 0 | @Override |
| 249 | public AlignmentFileReaderI getReader(FileParse source) | |
| 250 | throws IOException | |
| 251 | { | |
| 252 | 0 | JPredFile af = new JPredFile(source); |
| 253 | 0 | af.removeNonSequences(); |
| 254 | 0 | return af; |
| 255 | } | |
| 256 | ||
| 257 | 0 | @Override |
| 258 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 259 | { | |
| 260 | 0 | return null; // todo is this called? |
| 261 | } | |
| 262 | ||
| 263 | }, | |
| 264 | Features("GFF or Jalview features", "gff2,gff3", true, false) | |
| 265 | { | |
| 266 | 1 | @Override |
| 267 | public AlignmentFileReaderI getReader(FileParse source) | |
| 268 | throws IOException | |
| 269 | { | |
| 270 | 1 | return new FeaturesFile(source); |
| 271 | } | |
| 272 | ||
| 273 | 0 | @Override |
| 274 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 275 | { | |
| 276 | 0 | return new FeaturesFile(); |
| 277 | } | |
| 278 | }, | |
| 279 | ScoreMatrix("Substitution matrix", "", false, false) | |
| 280 | { | |
| 281 | 0 | @Override |
| 282 | public AlignmentFileReaderI getReader(FileParse source) | |
| 283 | throws IOException | |
| 284 | { | |
| 285 | 0 | return new ScoreMatrixFile(source); |
| 286 | } | |
| 287 | ||
| 288 | 0 | @Override |
| 289 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 290 | { | |
| 291 | 0 | return null; |
| 292 | } | |
| 293 | }, | |
| 294 | PDB("PDB", "pdb,ent", true, false) | |
| 295 | { | |
| 296 | 0 | @Override |
| 297 | public AlignmentFileReaderI getReader(FileParse source) | |
| 298 | throws IOException | |
| 299 | { | |
| 300 | 0 | boolean isParseWithJMOL = StructureImportSettings |
| 301 | .getDefaultStructureFileFormat() != PDBEntry.Type.PDB; | |
| 302 | 0 | if (isParseWithJMOL) |
| 303 | { | |
| 304 | 0 | return new JmolParser(source); |
| 305 | } | |
| 306 | else | |
| 307 | { | |
| 308 | 0 | StructureImportSettings.setShowSeqFeatures(true); |
| 309 | 0 | return new mc_view.PDBfile( |
| 310 | StructureImportSettings.isVisibleChainAnnotation(), | |
| 311 | StructureImportSettings.isProcessSecondaryStructure(), | |
| 312 | StructureImportSettings.isExternalSecondaryStructure(), | |
| 313 | source); | |
| 314 | } | |
| 315 | } | |
| 316 | ||
| 317 | 0 | @Override |
| 318 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 319 | { | |
| 320 | 0 | return new JmolParser(); // todo or null? |
| 321 | } | |
| 322 | ||
| 323 | 21 | @Override |
| 324 | public boolean isStructureFile() | |
| 325 | { | |
| 326 | 21 | return true; |
| 327 | } | |
| 328 | }, | |
| 329 | MMCif("mmCIF", "cif", true, false) | |
| 330 | { | |
| 331 | 0 | @Override |
| 332 | public AlignmentFileReaderI getReader(FileParse source) | |
| 333 | throws IOException | |
| 334 | { | |
| 335 | 0 | return new JmolParser(source); |
| 336 | } | |
| 337 | ||
| 338 | 0 | @Override |
| 339 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 340 | { | |
| 341 | 0 | return new JmolParser(); // todo or null? |
| 342 | } | |
| 343 | ||
| 344 | 0 | @Override |
| 345 | public boolean isStructureFile() | |
| 346 | { | |
| 347 | 0 | return true; |
| 348 | } | |
| 349 | }, | |
| 350 | Jalview("Jalview", "jar,jvp", true, true) | |
| 351 | { | |
| 352 | 0 | @Override |
| 353 | public AlignmentFileReaderI getReader(FileParse source) | |
| 354 | throws IOException | |
| 355 | { | |
| 356 | 0 | return null; |
| 357 | } | |
| 358 | ||
| 359 | 0 | @Override |
| 360 | public AlignmentFileWriterI getWriter(AlignmentI al) | |
| 361 | { | |
| 362 | 0 | return null; |
| 363 | } | |
| 364 | ||
| 365 | 216 | @Override |
| 366 | public boolean isTextFormat() | |
| 367 | { | |
| 368 | 216 | return false; |
| 369 | } | |
| 370 | ||
| 371 | 15 | @Override |
| 372 | public boolean isIdentifiable() | |
| 373 | { | |
| 374 | 15 | return false; |
| 375 | } | |
| 376 | }; | |
| 377 | ||
| 378 | private boolean writable; | |
| 379 | ||
| 380 | private boolean readable; | |
| 381 | ||
| 382 | private String extensions; | |
| 383 | ||
| 384 | private String name; | |
| 385 | ||
| 386 | 0 | @Override |
| 387 | public boolean isComplexAlignFile() | |
| 388 | { | |
| 389 | 0 | return false; |
| 390 | } | |
| 391 | ||
| 392 | 1614 | @Override |
| 393 | public boolean isReadable() | |
| 394 | { | |
| 395 | 1614 | return readable; |
| 396 | } | |
| 397 | ||
| 398 | 5226 | @Override |
| 399 | public boolean isWritable() | |
| 400 | { | |
| 401 | 5226 | return writable; |
| 402 | } | |
| 403 | ||
| 404 | /** | |
| 405 | * Constructor | |
| 406 | * | |
| 407 | * @param shortName | |
| 408 | * @param extensions | |
| 409 | * comma-separated list of file extensions associated with the format | |
| 410 | * @param isReadable | |
| 411 | * @param isWritable | |
| 412 | */ | |
| 413 | 19 | private FileFormat(String shortName, String extensions, |
| 414 | boolean isReadable, boolean isWritable) | |
| 415 | { | |
| 416 | 19 | this.name = shortName; |
| 417 | 19 | this.extensions = extensions; |
| 418 | 19 | this.readable = isReadable; |
| 419 | 19 | this.writable = isWritable; |
| 420 | } | |
| 421 | ||
| 422 | 206 | @Override |
| 423 | public String getExtensions() | |
| 424 | { | |
| 425 | 206 | return extensions; |
| 426 | } | |
| 427 | ||
| 428 | /** | |
| 429 | * Answers the display name of the file format (as for example shown in menu | |
| 430 | * options). This name should not be locale (language) dependent. | |
| 431 | */ | |
| 432 | 5344 | @Override |
| 433 | public String getName() | |
| 434 | { | |
| 435 | 5344 | return name; |
| 436 | } | |
| 437 | ||
| 438 | 2375 | @Override |
| 439 | public boolean isTextFormat() | |
| 440 | { | |
| 441 | 2375 | return true; |
| 442 | } | |
| 443 | ||
| 444 | 275 | @Override |
| 445 | public boolean isStructureFile() | |
| 446 | { | |
| 447 | 275 | return false; |
| 448 | } | |
| 449 | ||
| 450 | /** | |
| 451 | * By default, answers true, indicating the format is one that can be | |
| 452 | * identified by IdentifyFile. Formats that cannot be identified should | |
| 453 | * override this method to return false. | |
| 454 | */ | |
| 455 | 274 | public boolean isIdentifiable() |
| 456 | { | |
| 457 | 274 | return true; |
| 458 | } | |
| 459 | } |