src/jalview/hmmer/HMMERParamStore.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.gui.Preferences;
   6 import jalview.util.MessageManager;
   7 import jalview.viewmodel.AlignmentViewport;
   8 import jalview.ws.params.ArgumentI;
   9 import jalview.ws.params.ParamDatastoreI;
  10 import jalview.ws.params.WsParamSetI;
  11 import jalview.ws.params.simple.BooleanOption;
  12 import jalview.ws.params.simple.DoubleParameter;
  13 import jalview.ws.params.simple.FileParameter;
  14 import jalview.ws.params.simple.IntegerParameter;
  15 import jalview.ws.params.simple.LogarithmicParameter;
  16 import jalview.ws.params.simple.Option;
  17 import jalview.ws.params.simple.RadioChoiceParameter;
  18 import jalview.ws.params.simple.StringParameter;
  19
  20 import java.io.File;
  21 import java.io.IOException;
  22 import java.util.ArrayList;
  23 import java.util.Arrays;
  24 import java.util.List;
  25 import java.util.Scanner;
  26
  27 public final class HMMERParamStore implements ParamDatastoreI
  28 {
  29   private static final String HMMBUILD = "hmmbuild";
  30
  31   private static final String HMMALIGN = "hmmalign";
  32
  33   private static final String HMMSEARCH = "hmmsearch";
  34
  35   private static final String JACKHMMER = "jackhmmer";
  36
  37   private String name;
  38
  39   private List<WsParamSetI> presets = new ArrayList<>();
  40
  41   private AlignmentViewport viewport;
  42
  43   private HMMERParamStore(String nam, AlignmentViewport av)
  44   {
  45     this.viewport = av;
  46     this.name = nam;
  47   }
  48
  49   public static HMMERParamStore forBuild(AlignmentViewport viewport)
  50   {
  51     return new HMMERParamStore(HMMBUILD, viewport);
  52   }
  53
  54   public static HMMERParamStore forAlign(AlignmentViewport viewport)
  55   {
  56     return new HMMERParamStore(HMMALIGN, viewport);
  57   }
  58
  59   public static HMMERParamStore forSearch(AlignmentViewport viewport)
  60   {
  61     return new HMMERParamStore(HMMSEARCH, viewport);
  62   }
  63
  64   public static HMMERParamStore forJackhmmer(AlignmentViewport viewport)
  65   {
  66     return new HMMERParamStore(JACKHMMER, viewport);
  67   }
  68
  69   @Override
  70   public List<WsParamSetI> getPresets()
  71   {
  72     return presets;
  73   }
  74
  75   @Override
  76   public WsParamSetI getPreset(String nam)
  77   {
  78     return null;
  79   }
  80
  81   @Override
  82   public List<ArgumentI> getServiceParameters()
  83   {
  84     List<ArgumentI> args = new ArrayList<>();
  85     switch (name)
  86     {
  87     case HMMSEARCH:
  88       getHMMSearchParams(args);
  89       break;
  90     case HMMALIGN:
  91       getHMMAlignParams(args);
  92       break;
  93     case HMMBUILD:
  94       getHMMBuildParams(args);
  95       break;
  96     case JACKHMMER:
  97       getJackhmmerParams(args);
  98     default:
  99     }
 100
 101     return args;
 102   }
 103
 104   /**
 105    * Answers default parameters for hmmsearch, taking into account any
 106    * configured as user preferences
 107    *
 108    * @param args
 109    */
 110   private void getHMMSearchParams(List<ArgumentI> args)
 111   {
 112     /*
 113      * 'Options'
 114      */
 115     args.add(new BooleanOption(
 116             MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
 117             MessageManager.getString("label.auto_align_seqs_desc"), false,
 118             false, false, null));
 119     args.add(new BooleanOption(
 120             MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
 121             MessageManager.getString("label.use_accessions_desc"), false,
 122             false, true, null));
 123     args.add(new BooleanOption(
 124             MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
 125             MessageManager.getString("label.trim_termini_desc"), false,
 126             false, true, null));
 127     args.add(new BooleanOption(
 128             MessageManager.getString(HMMSearch.RETURN_N_NEW_SEQ),
 129             MessageManager.getString("label.check_for_new_sequences_desc"),
 130             false, false, false, null));
 131
 132     /*
 133      * 'Parameters'
 134      */
 135     addChoiceOfHmm(args);
 136
 137     // addChoiceOfDatabase(args);
 138
 139     String thisAlignment = MessageManager
 140             .getString(HMMSearch.THIS_ALIGNMENT_KEY);
 141     String database = MessageManager.getString("label.database");
 142     args.add(new FileParameter(database, "", false, "", ""));
 143     args.add(new IntegerParameter(
 144             MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
 145             MessageManager.getString("label.number_of_results_desc"), true,
 146             100, 0, 100000));
 147     args.add(new RadioChoiceParameter(
 148             MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
 149             Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
 150                     MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
 151             MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
 152     args.add(new LogarithmicParameter(
 153             MessageManager.getString(HMMSearch.REPORTING_SEQ_EVALUE_KEY),
 154             MessageManager.getString("label.reporting_seq_e_value_desc"),
 155             false, 1D,
 156             1E-100, 10D));
 157     args.add(new LogarithmicParameter(
 158             MessageManager.getString(HMMSearch.REPORTING_DOM_EVALUE_KEY),
 159             MessageManager.getString("label.reporting_dom_e_value_desc"),
 160             false, 1D,
 161             1E-100, 10D));
 162     args.add(
 163             new DoubleParameter(
 164                     MessageManager
 165                             .getString(HMMSearch.REPORTING_SEQ_SCORE_KEY),
 166                     MessageManager.getString(
 167                             "label.reporting_seq_score_desc"),
 168                     false,
 169                     0d, 0d, 1000d));
 170     args.add(
 171             new DoubleParameter(
 172                     MessageManager
 173                             .getString(HMMSearch.REPORTING_DOM_SCORE_KEY),
 174                     MessageManager.getString(
 175                             "label.reporting_dom_score_desc"),
 176                     false,
 177                     0d, 0d, 1000d));
 178     args.add(new RadioChoiceParameter(
 179             MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
 180             null,
 181             Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
 182                     MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
 183             MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
 184     args.add(new LogarithmicParameter(
 185             MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
 186             MessageManager.getString("label.inclusion_seq_e_value_desc"),
 187             false, 1D,
 188             1E-100, 10D));
 189     args.add(new LogarithmicParameter(
 190             MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
 191             MessageManager.getString("label.inclusion_dom_e_value_desc"),
 192             false, 1D,
 193             1E-100, 10D));
 194     args.add(new DoubleParameter(
 195             MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
 196             MessageManager.getString("label.inclusion_seq_score_desc"),
 197             false, 0d, 0d,
 198             1000d));
 199     args.add(new DoubleParameter(
 200             MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
 201             MessageManager.getString("label.inclusion_dom_score_desc"),
 202             false, 0d, 0d,
 203             1000d));
 204   }
 205
 206   /**
 207    * Answers default parameters for jackhmmer, taking into account any configured
 208    * as user preferences
 209    *
 210    * @param args
 211    */
 212   private void getJackhmmerParams(List<ArgumentI> args)
 213   {
 214
 215     /*
 216      * 'Parameters'
 217      */
 218     addChoiceOfSequence(args);
 219
 220     // addChoiceOfDatabase(args);
 221
 222     String database = MessageManager.getString("label.database");
 223     args.add(new FileParameter(database, "", false, "", ""));
 224     args.add(new RadioChoiceParameter(
 225             MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
 226             Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
 227                     MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
 228                     MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
 229             MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
 230     args.add(new LogarithmicParameter(
 231             MessageManager.getString(JackHMMER.REPORTING_SEQ_EVALUE_KEY),
 232             MessageManager.getString("label.reporting_seq_e_value_desc"),
 233             false, 1D,
 234             1E-38, 10D));
 235     args.add(new LogarithmicParameter(
 236             MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
 237             MessageManager.getString(
 238                     "label.reporting_dom_e_value_desc"),
 239             false, 1D,
 240             1E-38, 10D));
 241     args.add(new DoubleParameter(
 242             MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
 243             MessageManager.getString("label.reporting_seq_score_desc"),
 244             false, 0d, 0d,
 245             1000d));
 246     args.add(new DoubleParameter(
 247             MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
 248             MessageManager.getString("label.reporting_dom_score_desc"),
 249             false, 0d, 0d,
 250             1000d));
 251     args.add(new RadioChoiceParameter(
 252             MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
 253             null,
 254             Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
 255                     MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
 256             MessageManager.getString(HmmerCommand.CUTOFF_EVALUE)));
 257     args.add(new LogarithmicParameter(
 258             MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
 259             MessageManager.getString("label.inclusion_seq_e_value_desc"),
 260             false, 1D, 1E-100, 10D));
 261     args.add(new LogarithmicParameter(
 262             MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
 263             MessageManager.getString("label.inclusion_dom_e_value_desc"),
 264             false, 1D, 1E-100, 10D));
 265     args.add(new DoubleParameter(
 266             MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
 267             MessageManager.getString("label.inclusion_seq_score_desc"),
 268             false, 0d, 0d, 1000d));
 269     args.add(new DoubleParameter(
 270             MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
 271             MessageManager.getString("label.inclusion_dom_score_desc"),
 272             false, 0d, 0d, 1000d));
 273   }
 274
 275   /**
 276    * Constructs a choice parameter for database to search; always includes 'this
 277    * alignment', and also includes any databases held under user preferences key
 278    * "HMMSEARCH_DBS" as a comma-delimited list
 279    *
 280    * @param args
 281    */
 282   protected void addChoiceOfDatabase(List<ArgumentI> args)
 283   {
 284     String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
 285     if (names == null || names.isEmpty())
 286     {
 287       return;
 288     }
 289
 290     List<String> filePaths = new ArrayList<>();
 291     List<String> fileNames = new ArrayList<>();
 292
 293     String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
 294     filePaths.add(thisAlignment);
 295     fileNames.add(thisAlignment);
 296
 297     Scanner nameScanner = new Scanner(names);
 298     nameScanner.useDelimiter(Preferences.COMMA);
 299
 300     while (nameScanner.hasNext())
 301     {
 302       String next = nameScanner.next();
 303       if ("null".equals(next))
 304       {
 305         Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
 306       }
 307       else
 308       {
 309         filePaths.add(next);
 310         int pos = next.lastIndexOf(File.separator);
 311         String fileName = next.substring(pos + 1);
 312         fileNames.add(fileName);
 313       }
 314     }
 315     nameScanner.close();
 316     ArgumentI databasesOption = new StringParameter(
 317             MessageManager.getString(HMMSearch.DATABASE_KEY),
 318             MessageManager.getString("label.database_for_hmmsearch"), true,
 319             thisAlignment,
 320             thisAlignment,
 321             filePaths, fileNames);
 322     args.add(databasesOption);
 323   }
 324
 325   /**
 326    * Answers default parameters for hmmalign, taking into account any configured
 327    * as user preferences
 328    *
 329    * @param args
 330    */
 331   private void getHMMAlignParams(List<ArgumentI> args)
 332   {
 333     addChoiceOfHmm(args);
 334
 335     boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
 336             false);
 337     args.add(new BooleanOption(
 338             MessageManager.getString("label.trim_termini"),
 339             MessageManager.getString("label.trim_termini_desc"),
 340             false, false, def, null));
 341   }
 342
 343   /**
 344    * Adds an argument representing the choice of HMM sequences (profiles)
 345    * against which to perform align or search, provided at least one is found
 346    *
 347    * @param args
 348    */
 349   protected void addChoiceOfHmm(List<ArgumentI> args)
 350   {
 351     List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
 352     if (!hmms.isEmpty())
 353     {
 354       List<String> options = new ArrayList<>();
 355       for (SequenceI hmmSeq : hmms)
 356       {
 357         options.add(hmmSeq.getName());
 358       }
 359       String defseq = options.get(0);
 360       ArgumentI arg = new StringParameter(
 361               MessageManager.getString("label.use_hmm"), null, true, defseq,
 362               defseq, options, null);
 363       args.add(arg);
 364     }
 365   }
 366
 367   /**
 368    * Adds an argument representing the choice of sequence against which to perform
 369    * jackhmmer
 370    *
 371    * @param args
 372    */
 373   protected void addChoiceOfSequence(List<ArgumentI> args)
 374   {
 375     List<SequenceI> sequences = viewport.getAlignment().getSequences();
 376
 377     List<String> options = new ArrayList<>();
 378
 379     for (SequenceI seq : sequences)
 380     {
 381       options.add(seq.getName());
 382     }
 383
 384     String defseq = options.get(0);
 385     ArgumentI arg = new StringParameter(
 386             MessageManager.getString("label.use_sequence"), null, true,
 387             defseq,
 388             defseq, options, null);
 389     args.add(arg);
 390   }
 391
 392   /**
 393    * Answers default parameters for hmmbuild, taking into account any configured
 394    * as user preferences
 395    *
 396    * @param args
 397    */
 398   private void getHMMBuildParams(List<ArgumentI> args)
 399   {
 400     /*
 401      * name to give the computed alignment HMM consensus sequence
 402      * (Jalview constructs group HMM consensus sequence names)
 403      */
 404     String defValue = "Alignment_HMM";
 405     StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
 406             MessageManager.getString("label.hmm_name_desc"), true, defValue,
 407             defValue);
 408     args.add(nameParam);
 409
 410     /*
 411      * only enable Use Reference Annotation if RF is present
 412      */
 413     if (viewport.hasReferenceAnnotation())
 414     {
 415       args.add(new BooleanOption(
 416               MessageManager.getString("label.use_reference"),
 417               MessageManager.getString("label.use_reference_desc"), true,
 418               true, true, null));
 419     }
 420
 421     /*
 422      * choice of whether to compute HMM for alignment and/or group(s)
 423      * - only if there are any groups
 424      */
 425     if (!viewport.getAlignment().getGroups().isEmpty())
 426     {
 427       List<String> options = new ArrayList<>();
 428       options.add(MessageManager.getString("label.alignment"));
 429       options.add(MessageManager.getString("label.groups_and_alignment"));
 430       options.add(MessageManager.getString("label.groups"));
 431       options.add(MessageManager.getString("label.selected_group"));
 432       args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
 433               MessageManager.getString("label.hmmbuild_for_desc"), true,
 434               MessageManager.getString("label.alignment"),
 435               MessageManager.getString("label.alignment"), options, null));
 436     }
 437   }
 438
 439   @Override
 440   public boolean presetExists(String forName)
 441   {
 442     return false;
 443   }
 444
 445   @Override
 446   public void deletePreset(String forName)
 447   {
 448   }
 449
 450   @Override
 451   public void storePreset(String presetName, String text,
 452           List<ArgumentI> jobParams)
 453   {
 454   }
 455
 456   @Override
 457   public void updatePreset(String oldName, String presetName, String text,
 458           List<ArgumentI> jobParams)
 459   {
 460   }
 461
 462   @Override
 463   public WsParamSetI parseServiceParameterFile(String forName,
 464           String description, String[] serviceURL, String parameters)
 465           throws IOException
 466   {
 467     return null;
 468   }
 469
 470   @Override
 471   public String generateServiceParameterFile(WsParamSetI pset)
 472           throws IOException
 473   {
 474     return null;
 475   }
 476
 477 }