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 IntegerParameter(
 225             MessageManager.getString(HMMSearch.NUMBER_OF_ITERATIONS),
 226             MessageManager.getString("label.number_of_iterations_desc"),
 227             true, 5, 1, 20));
 228     args.add(new RadioChoiceParameter(
 229             MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
 230             Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
 231                     MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
 232                     MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
 233             MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
 234     args.add(new LogarithmicParameter(
 235             MessageManager.getString(JackHMMER.REPORTING_SEQ_EVALUE_KEY),
 236             MessageManager.getString("label.reporting_seq_e_value_desc"),
 237             false, 1D,
 238             1E-38, 10D));
 239     args.add(new LogarithmicParameter(
 240             MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
 241             MessageManager.getString(
 242                     "label.reporting_dom_e_value_desc"),
 243             false, 1D,
 244             1E-38, 10D));
 245     args.add(new DoubleParameter(
 246             MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
 247             MessageManager.getString("label.reporting_seq_score_desc"),
 248             false, 0d, 0d,
 249             1000d));
 250     args.add(new DoubleParameter(
 251             MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
 252             MessageManager.getString("label.reporting_dom_score_desc"),
 253             false, 0d, 0d,
 254             1000d));
 255     args.add(new RadioChoiceParameter(
 256             MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
 257             null,
 258             Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
 259                     MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
 260             MessageManager.getString(HmmerCommand.CUTOFF_EVALUE)));
 261     args.add(new LogarithmicParameter(
 262             MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
 263             MessageManager.getString("label.inclusion_seq_e_value_desc"),
 264             false, 1D, 1E-100, 10D));
 265     args.add(new LogarithmicParameter(
 266             MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
 267             MessageManager.getString("label.inclusion_dom_e_value_desc"),
 268             false, 1D, 1E-100, 10D));
 269     args.add(new DoubleParameter(
 270             MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
 271             MessageManager.getString("label.inclusion_seq_score_desc"),
 272             false, 0d, 0d, 1000d));
 273     args.add(new DoubleParameter(
 274             MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
 275             MessageManager.getString("label.inclusion_dom_score_desc"),
 276             false, 0d, 0d, 1000d));
 277   }
 278
 279   /**
 280    * Constructs a choice parameter for database to search; always includes 'this
 281    * alignment', and also includes any databases held under user preferences key
 282    * "HMMSEARCH_DBS" as a comma-delimited list
 283    *
 284    * @param args
 285    */
 286   protected void addChoiceOfDatabase(List<ArgumentI> args)
 287   {
 288     String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
 289     if (names == null || names.isEmpty())
 290     {
 291       return;
 292     }
 293
 294     List<String> filePaths = new ArrayList<>();
 295     List<String> fileNames = new ArrayList<>();
 296
 297     String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
 298     filePaths.add(thisAlignment);
 299     fileNames.add(thisAlignment);
 300
 301     Scanner nameScanner = new Scanner(names);
 302     nameScanner.useDelimiter(Preferences.COMMA);
 303
 304     while (nameScanner.hasNext())
 305     {
 306       String next = nameScanner.next();
 307       if ("null".equals(next))
 308       {
 309         Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
 310       }
 311       else
 312       {
 313         filePaths.add(next);
 314         int pos = next.lastIndexOf(File.separator);
 315         String fileName = next.substring(pos + 1);
 316         fileNames.add(fileName);
 317       }
 318     }
 319     nameScanner.close();
 320     ArgumentI databasesOption = new StringParameter(
 321             MessageManager.getString(HMMSearch.DATABASE_KEY),
 322             MessageManager.getString("label.database_for_hmmsearch"), true,
 323             thisAlignment,
 324             thisAlignment,
 325             filePaths, fileNames);
 326     args.add(databasesOption);
 327   }
 328
 329   /**
 330    * Answers default parameters for hmmalign, taking into account any configured
 331    * as user preferences
 332    *
 333    * @param args
 334    */
 335   private void getHMMAlignParams(List<ArgumentI> args)
 336   {
 337     addChoiceOfHmm(args);
 338
 339     boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
 340             false);
 341     args.add(new BooleanOption(
 342             MessageManager.getString("label.trim_termini"),
 343             MessageManager.getString("label.trim_termini_desc"),
 344             false, false, def, null));
 345   }
 346
 347   /**
 348    * Adds an argument representing the choice of HMM sequences (profiles)
 349    * against which to perform align or search, provided at least one is found
 350    *
 351    * @param args
 352    */
 353   protected void addChoiceOfHmm(List<ArgumentI> args)
 354   {
 355     List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
 356     if (!hmms.isEmpty())
 357     {
 358       List<String> options = new ArrayList<>();
 359       for (SequenceI hmmSeq : hmms)
 360       {
 361         options.add(hmmSeq.getName());
 362       }
 363       String defseq = options.get(0);
 364       ArgumentI arg = new StringParameter(
 365               MessageManager.getString("label.use_hmm"), null, true, defseq,
 366               defseq, options, null);
 367       args.add(arg);
 368     }
 369   }
 370
 371   /**
 372    * Adds an argument representing the choice of sequence against which to perform
 373    * jackhmmer
 374    *
 375    * @param args
 376    */
 377   protected void addChoiceOfSequence(List<ArgumentI> args)
 378   {
 379     List<SequenceI> sequences = viewport.getAlignment().getSequences();
 380
 381     List<String> options = new ArrayList<>();
 382
 383     for (SequenceI seq : sequences)
 384     {
 385       options.add(seq.getName());
 386     }
 387
 388     String defseq = options.get(0);
 389     ArgumentI arg = new StringParameter(
 390             MessageManager.getString("label.use_sequence"), null, true,
 391             defseq,
 392             defseq, options, null);
 393     args.add(arg);
 394   }
 395
 396   /**
 397    * Answers default parameters for hmmbuild, taking into account any configured
 398    * as user preferences
 399    *
 400    * @param args
 401    */
 402   private void getHMMBuildParams(List<ArgumentI> args)
 403   {
 404     /*
 405      * name to give the computed alignment HMM consensus sequence
 406      * (Jalview constructs group HMM consensus sequence names)
 407      */
 408     String defValue = "Alignment_HMM";
 409     StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
 410             MessageManager.getString("label.hmm_name_desc"), true, defValue,
 411             defValue);
 412     args.add(nameParam);
 413
 414     /*
 415      * only enable Use Reference Annotation if RF is present
 416      */
 417     if (viewport.hasReferenceAnnotation())
 418     {
 419       args.add(new BooleanOption(
 420               MessageManager.getString("label.use_reference"),
 421               MessageManager.getString("label.use_reference_desc"), true,
 422               true, true, null));
 423     }
 424
 425     /*
 426      * choice of whether to compute HMM for alignment and/or group(s)
 427      * - only if there are any groups
 428      */
 429     if (!viewport.getAlignment().getGroups().isEmpty())
 430     {
 431       List<String> options = new ArrayList<>();
 432       options.add(MessageManager.getString("label.alignment"));
 433       options.add(MessageManager.getString("label.groups_and_alignment"));
 434       options.add(MessageManager.getString("label.groups"));
 435       options.add(MessageManager.getString("label.selected_group"));
 436       args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
 437               MessageManager.getString("label.hmmbuild_for_desc"), true,
 438               MessageManager.getString("label.alignment"),
 439               MessageManager.getString("label.alignment"), options, null));
 440     }
 441   }
 442
 443   @Override
 444   public boolean presetExists(String forName)
 445   {
 446     return false;
 447   }
 448
 449   @Override
 450   public void deletePreset(String forName)
 451   {
 452   }
 453
 454   @Override
 455   public void storePreset(String presetName, String text,
 456           List<ArgumentI> jobParams)
 457   {
 458   }
 459
 460   @Override
 461   public void updatePreset(String oldName, String presetName, String text,
 462           List<ArgumentI> jobParams)
 463   {
 464   }
 465
 466   @Override
 467   public WsParamSetI parseServiceParameterFile(String forName,
 468           String description, String[] serviceURL, String parameters)
 469           throws IOException
 470   {
 471     return null;
 472   }
 473
 474   @Override
 475   public String generateServiceParameterFile(WsParamSetI pset)
 476           throws IOException
 477   {
 478     return null;
 479   }
 480
 481 }