src/jalview/io/FileFormat.java

   1 package jalview.io;
   2
   3 import jalview.ext.jmol.JmolParser;
   4 import jalview.structure.StructureImportSettings;
   5
   6 import java.io.IOException;
   7
   8 public enum FileFormat implements FileFormatI
   9 {
  10   Fasta
  11   {
  12     @Override
  13     public AlignmentFileI getAlignmentFile(String inFile,
  14             DataSourceType sourceType) throws IOException
  15     {
  16       return new FastaFile(inFile, sourceType);
  17     }
  18
  19     @Override
  20     public AlignmentFileI getAlignmentFile(FileParse source)
  21             throws IOException
  22     {
  23       return new FastaFile(source);
  24     }
  25
  26     @Override
  27     public AlignmentFileI getAlignmentFile()
  28     {
  29       return new FastaFile();
  30     }
  31   },
  32   Pfam
  33   {
  34     @Override
  35     public AlignmentFileI getAlignmentFile(String inFile,
  36             DataSourceType sourceType) throws IOException
  37     {
  38       return new PfamFile(inFile, sourceType);
  39     }
  40
  41     @Override
  42     public AlignmentFileI getAlignmentFile(FileParse source)
  43             throws IOException
  44     {
  45       return new PfamFile(source);
  46     }
  47
  48     @Override
  49     public AlignmentFileI getAlignmentFile()
  50     {
  51       return new PfamFile();
  52     }
  53   },
  54   Stockholm
  55   {
  56     @Override
  57     public AlignmentFileI getAlignmentFile(String inFile,
  58             DataSourceType sourceType) throws IOException
  59     {
  60       return new StockholmFile(inFile, sourceType);
  61     }
  62     @Override
  63     public AlignmentFileI getAlignmentFile(FileParse source)
  64             throws IOException
  65     {
  66       return new StockholmFile(source);
  67     }
  68
  69     @Override
  70     public AlignmentFileI getAlignmentFile()
  71     {
  72       return new StockholmFile();
  73     }
  74
  75   },
  76   SimpleBlast
  77   {
  78     @Override
  79     public AlignmentFileI getAlignmentFile(String inFile,
  80             DataSourceType sourceType) throws IOException
  81     {
  82       return new SimpleBlastFile(inFile, sourceType);
  83     }
  84
  85     @Override
  86     public AlignmentFileI getAlignmentFile(FileParse source)
  87             throws IOException
  88     {
  89       return new SimpleBlastFile(source);
  90     }
  91
  92     @Override
  93     public AlignmentFileI getAlignmentFile()
  94     {
  95       return new SimpleBlastFile();
  96     }
  97   },
  98
  99   PIR
 100   {
 101     @Override
 102     public AlignmentFileI getAlignmentFile(String inFile,
 103             DataSourceType sourceType) throws IOException
 104     {
 105       return new PIRFile(inFile, sourceType);
 106     }
 107     @Override
 108     public AlignmentFileI getAlignmentFile(FileParse source)
 109             throws IOException
 110     {
 111       return new PIRFile(source);
 112     }
 113
 114     @Override
 115     public AlignmentFileI getAlignmentFile()
 116     {
 117       return new PIRFile();
 118     }
 119   },
 120   BLC
 121   {
 122     @Override
 123     public AlignmentFileI getAlignmentFile(String inFile,
 124             DataSourceType sourceType) throws IOException
 125     {
 126       return new BLCFile(inFile, sourceType);
 127     }    @Override
 128     public AlignmentFileI getAlignmentFile(FileParse source)
 129             throws IOException
 130     {
 131       return new BLCFile(source);
 132     }
 133
 134     @Override
 135     public AlignmentFileI getAlignmentFile()
 136     {
 137       return new BLCFile();
 138     }
 139
 140   },
 141   Html
 142   {
 143     @Override
 144     public AlignmentFileI getAlignmentFile(String inFile,
 145             DataSourceType sourceType) throws IOException
 146     {
 147       return new HtmlFile(inFile, sourceType);
 148     }    @Override
 149     public AlignmentFileI getAlignmentFile(FileParse source)
 150             throws IOException
 151     {
 152       return new HtmlFile(source);
 153     }
 154
 155     @Override
 156     public AlignmentFileI getAlignmentFile()
 157     {
 158       return new HtmlFile();
 159     }
 160
 161     @Override
 162     public boolean isComplexAlignFile()
 163     {
 164       return true;
 165     }
 166
 167   },
 168   Rnaml
 169   {
 170     @Override
 171     public AlignmentFileI getAlignmentFile(String inFile,
 172             DataSourceType sourceType) throws IOException
 173     {
 174       return new RnamlFile(inFile, sourceType);
 175     }    @Override
 176     public AlignmentFileI getAlignmentFile(FileParse source)
 177             throws IOException
 178     {
 179       return new RnamlFile(source);
 180     }
 181
 182     @Override
 183     public AlignmentFileI getAlignmentFile()
 184     {
 185       return new RnamlFile();
 186     }
 187
 188   },
 189   Json
 190   {
 191     @Override
 192     public AlignmentFileI getAlignmentFile(String inFile,
 193             DataSourceType sourceType) throws IOException
 194     {
 195       return new JSONFile(inFile, sourceType);
 196     }    @Override
 197     public AlignmentFileI getAlignmentFile(FileParse source)
 198             throws IOException
 199     {
 200       return new JSONFile(source);
 201     }
 202
 203     @Override
 204     public AlignmentFileI getAlignmentFile()
 205     {
 206       return new JSONFile();
 207     }
 208
 209     @Override
 210     public boolean isComplexAlignFile()
 211     {
 212       return true;
 213     }
 214
 215   },
 216   Pileup
 217   {
 218     @Override
 219     public AlignmentFileI getAlignmentFile(String inFile,
 220             DataSourceType sourceType) throws IOException
 221     {
 222       return new PileUpfile(inFile, sourceType);
 223     }    @Override
 224     public AlignmentFileI getAlignmentFile(FileParse source)
 225             throws IOException
 226     {
 227       return new PileUpfile(source);
 228     }
 229
 230     @Override
 231     public AlignmentFileI getAlignmentFile()
 232     {
 233       return new PileUpfile();
 234     }
 235
 236   },
 237   MSF
 238   {
 239     @Override
 240     public AlignmentFileI getAlignmentFile(String inFile,
 241             DataSourceType sourceType) throws IOException
 242     {
 243       return new MSFfile(inFile, sourceType);
 244     }    @Override
 245     public AlignmentFileI getAlignmentFile(FileParse source)
 246             throws IOException
 247     {
 248       return new MSFfile(source);
 249     }
 250
 251     @Override
 252     public AlignmentFileI getAlignmentFile()
 253     {
 254       return new MSFfile();
 255     }
 256
 257   },
 258   Clustal
 259   {
 260     @Override
 261     public AlignmentFileI getAlignmentFile(String inFile,
 262             DataSourceType sourceType) throws IOException
 263     {
 264       return new ClustalFile(inFile, sourceType);
 265     }    @Override
 266     public AlignmentFileI getAlignmentFile(FileParse source)
 267             throws IOException
 268     {
 269       return new ClustalFile(source);
 270     }
 271
 272     @Override
 273     public AlignmentFileI getAlignmentFile()
 274     {
 275       return new ClustalFile();
 276     }
 277
 278   },
 279   Phylip
 280   {
 281     @Override
 282     public AlignmentFileI getAlignmentFile(String inFile,
 283             DataSourceType sourceType) throws IOException
 284     {
 285       return new PhylipFile(inFile, sourceType);
 286     }
 287
 288     @Override
 289     public AlignmentFileI getAlignmentFile(FileParse source)
 290             throws IOException
 291     {
 292       return new PhylipFile(source);
 293     }
 294
 295     @Override
 296     public AlignmentFileI getAlignmentFile()
 297     {
 298       return new PhylipFile();
 299     }
 300
 301   },
 302   Jnet
 303   {
 304     @Override
 305     public AlignmentFileI getAlignmentFile(String inFile,
 306             DataSourceType sourceType) throws IOException
 307     {
 308       JPredFile af = new JPredFile(inFile, sourceType);
 309       af.removeNonSequences();
 310       return af;
 311     }
 312
 313     @Override
 314     public AlignmentFileI getAlignmentFile(FileParse source)
 315             throws IOException
 316     {
 317       JPredFile af = new JPredFile(source);
 318       af.removeNonSequences();
 319       return af;
 320     }
 321
 322     @Override
 323     public AlignmentFileI getAlignmentFile()
 324     {
 325       return null; // todo is this called?
 326     }
 327
 328   },
 329   Features
 330   {
 331     @Override
 332     public AlignmentFileI getAlignmentFile(String inFile,
 333             DataSourceType sourceType) throws IOException
 334     {
 335       return new FeaturesFile(true, inFile, sourceType);
 336     }
 337
 338     @Override
 339     public AlignmentFileI getAlignmentFile(FileParse source)
 340             throws IOException
 341     {
 342       return new FeaturesFile(source);
 343     }
 344
 345     @Override
 346     public AlignmentFileI getAlignmentFile()
 347     {
 348       return new FeaturesFile();
 349     }
 350   },
 351   PDB
 352   {
 353
 354     @Override
 355     public AlignmentFileI getAlignmentFile(String inFile,
 356             DataSourceType sourceType) throws IOException
 357     {
 358       // TODO obtain config value from preference settings.
 359       // Set value to 'true' to test PDB processing with Jmol: JAL-1213
 360       boolean isParseWithJMOL = !StructureImportSettings
 361               .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
 362       if (isParseWithJMOL)
 363       {
 364         return new JmolParser(
 365                 StructureImportSettings.isVisibleChainAnnotation(),
 366                 StructureImportSettings.isPredictSecondaryStructure(),
 367                 StructureImportSettings.isExternalSecondaryStructure(),
 368                 inFile,
 369                 sourceType);
 370       }
 371       else
 372       {
 373         StructureImportSettings.setShowSeqFeatures(true);
 374         return new MCview.PDBfile(
 375                 StructureImportSettings.isVisibleChainAnnotation(),
 376                 StructureImportSettings.isPredictSecondaryStructure(),
 377                 StructureImportSettings.isExternalSecondaryStructure(),
 378                 inFile,
 379                 sourceType);
 380       }
 381     }
 382
 383     @Override
 384     public AlignmentFileI getAlignmentFile(FileParse source)
 385             throws IOException
 386     {
 387       boolean isParseWithJMOL = !StructureImportSettings
 388               .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
 389       if (isParseWithJMOL)
 390       {
 391         return new JmolParser(
 392                 StructureImportSettings.isVisibleChainAnnotation(),
 393                 StructureImportSettings.isPredictSecondaryStructure(),
 394                 StructureImportSettings.isExternalSecondaryStructure(),
 395                 source);
 396       }
 397       else
 398       {
 399         StructureImportSettings.setShowSeqFeatures(true);
 400         return new MCview.PDBfile(
 401                 StructureImportSettings.isVisibleChainAnnotation(),
 402                 StructureImportSettings.isPredictSecondaryStructure(),
 403                 StructureImportSettings.isExternalSecondaryStructure(),
 404                 source);
 405       }
 406     }
 407
 408     @Override
 409     public AlignmentFileI getAlignmentFile()
 410     {
 411       return new JmolParser(); // todo or null?
 412     }
 413
 414   },
 415   MMCif
 416   {
 417
 418     @Override
 419     public AlignmentFileI getAlignmentFile(String inFile,
 420             DataSourceType sourceType) throws IOException
 421     {
 422       return new JmolParser(
 423               StructureImportSettings.isVisibleChainAnnotation(),
 424               StructureImportSettings.isPredictSecondaryStructure(),
 425               StructureImportSettings.isExternalSecondaryStructure(),
 426               inFile, sourceType);
 427     }
 428
 429     @Override
 430     public AlignmentFileI getAlignmentFile(FileParse source)
 431             throws IOException
 432     {
 433       return new JmolParser(
 434               StructureImportSettings.isVisibleChainAnnotation(),
 435               StructureImportSettings.isPredictSecondaryStructure(),
 436               StructureImportSettings.isExternalSecondaryStructure(),
 437               source);
 438     }
 439
 440     @Override
 441     public AlignmentFileI getAlignmentFile()
 442     {
 443       return new JmolParser(); // todo or null?
 444     }
 445   },
 446   Jalview
 447   {
 448
 449     @Override
 450     public AlignmentFileI getAlignmentFile(String inFile,
 451             DataSourceType sourceType) throws IOException
 452     {
 453       return null;
 454     }
 455
 456     @Override
 457     public AlignmentFileI getAlignmentFile(FileParse source)
 458             throws IOException
 459     {
 460       return null;
 461     }
 462
 463     @Override
 464     public AlignmentFileI getAlignmentFile()
 465     {
 466       return null;
 467     }
 468   };
 469
 470   @Override
 471   public boolean isComplexAlignFile()
 472   {
 473     return false;
 474   }
 475
 476   @Override
 477   public String getShortDescription()
 478   {
 479     return toString();
 480   }
 481 }