src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.analysis.SeqsetUtils;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.Sequence;
   6 import jalview.datamodel.SequenceGroup;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.AlignFrame;
   9 import jalview.gui.AlignViewport;
  10 import jalview.gui.JvOptionPane;
  11 import jalview.io.DataSourceType;
  12 import jalview.io.FileParse;
  13 import jalview.io.HMMFile;
  14 import jalview.util.MessageManager;
  15 import jalview.ws.params.ArgumentI;
  16
  17 import java.io.File;
  18 import java.io.FileNotFoundException;
  19 import java.io.IOException;
  20 import java.util.ArrayList;
  21 import java.util.List;
  22
  23 import javax.swing.JOptionPane;
  24
  25 public class HMMBuildThread extends HmmerCommand implements Runnable
  26 {
  27   AlignViewport viewport;
  28
  29   boolean multiJob = false;
  30
  31   AlignmentI alignment;
  32
  33   SequenceGroup group;
  34
  35   List<ArgumentI> params;
  36
  37   boolean forGroup = false;
  38
  39   File hmmTemp = null;
  40
  41   File stoTemp = null;
  42
  43   long barID;
  44
  45   /**
  46    * This is used for validation purposes. Do not use!
  47    *
  48    * @param viewport
  49    */
  50   public HMMBuildThread(AlignmentI alignment)
  51   {
  52     this.alignment = alignment;
  53     forGroup = false;
  54   }
  55
  56   public HMMBuildThread(AlignFrame af, List<ArgumentI> args)
  57   {
  58     this.af = af;
  59     viewport = af.getViewport();
  60     params = args;
  61   }
  62
  63   /**
  64    * Builds a HMM from an alignment, then imports and adds it to the alignment.
  65    */
  66   @Override
  67   public void run()
  68   {
  69     barID = System.currentTimeMillis();
  70     if (af != null)
  71     {
  72       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  73               barID);
  74     }
  75
  76     List<SequenceGroup> groups = new ArrayList<>();
  77     if (params != null)
  78     {
  79       for (ArgumentI arg : params)
  80       {
  81         String name = arg.getName();
  82         if (MessageManager.getString("label.hmmbuild_for").equals(name))
  83         {
  84           String value = arg.getValue();
  85           if ("Alignment".equals(value))
  86           {
  87             alignment = viewport.getAlignment();
  88             break;
  89           }
  90           else if ("All groups and alignment".equals(value))
  91           {
  92             alignment = viewport.getAlignment();
  93             groups.addAll(viewport.getAlignment().getGroups());
  94             if (groups.size() > 0)
  95             {
  96               multiJob = true;
  97             }
  98             break;
  99           }
 100           else if ("All groups".equals(value))
 101           {
 102             alignment = null;
 103             groups = viewport.getAlignment().getGroups();
 104             if (groups.size() > 0)
 105             {
 106               multiJob = true;
 107             }
 108             break;
 109           }
 110           else if ("Selected group".equals(value))
 111           {
 112             alignment = null;
 113             groups.add(viewport.getSelectionGroup());
 114             break;
 115           }
 116         }
 117         else if (MessageManager.getString("label.use_reference")
 118                 .equals(name))
 119         {
 120           if (!af.getViewport().hasReferenceAnnotation())
 121           {
 122             if (af != null)
 123             {
 124               af.setProgressBar(
 125                       MessageManager.getString("status.running_hmmbuild"),
 126                       barID);
 127             }
 128             JvOptionPane.showInternalMessageDialog(af, MessageManager
 129                     .getString("warn.no_reference_annotation"));
 130             return;
 131           }
 132         }
 133       }
 134     }
 135     else if (viewport != null)
 136     {
 137       alignment = viewport.getAlignment();
 138     }
 139
 140     if (alignment != null)
 141     {
 142       forGroup = false;
 143       runHMMBuild();
 144     }
 145
 146     if (alignment == null)
 147     {
 148       alignment = viewport.getAlignment();
 149     }
 150
 151     if (groups != null && groups.size() > 0)
 152     {
 153       for (SequenceGroup grp : groups)
 154       {
 155         group = grp;
 156         forGroup = true;
 157         runHMMBuild();
 158       }
 159     }
 160
 161     if (af != null)
 162     {
 163       af.setProgressBar("", barID);
 164     }
 165   }
 166
 167   private void runHMMBuild()
 168   {
 169     if (alignment == null && group == null)
 170     {
 171       JOptionPane.showMessageDialog(af,
 172               MessageManager.getString("warn.no_sequence_data"));
 173     }
 174     try
 175     {
 176       hmmTemp = File.createTempFile("hmm", ".hmm");
 177       hmmTemp.deleteOnExit();
 178       stoTemp = File.createTempFile("output", ".sto");
 179       stoTemp.deleteOnExit();
 180     } catch (IOException e1)
 181     {
 182       e1.printStackTrace();
 183     }
 184
 185     try
 186     {
 187       try
 188       {
 189         SequenceI[] array;
 190         List<SequenceI> hmmSeqs = null;
 191         if (forGroup)
 192         {
 193           hmmSeqs = group.getHMMConsensusSequences();
 194           if (hmmSeqs.size() > 0)
 195           {
 196             // todo why this test? means can't re-run hmmbuild on a group?
 197             return;
 198           }
 199           array = group.getSelectionAsNewSequences(alignment);
 200         }
 201         else
 202         {
 203           hmmSeqs = alignment.getHMMConsensusSequences();
 204           if (!alignment.isAligned())
 205           {
 206             alignment.padGaps();
 207           }
 208           array = alignment.getSequencesArray();
 209         }
 210
 211         if (array.length < 1)
 212         {
 213           if (af != null)
 214           {
 215             JOptionPane.showMessageDialog(af,
 216                     MessageManager.getString("warn.no_sequence_data"));
 217           }
 218           return;
 219         }
 220
 221         /*
 222          * copy over sequences excluding hmm consensus sequences
 223          */
 224         SequenceI[] newArr = new SequenceI[array.length - hmmSeqs.size()];
 225         int index = 0;
 226         for (SequenceI seq : array)
 227         {
 228           if (!seq.isHMMConsensusSequence())
 229           {
 230             newArr[index] = new Sequence(seq);
 231             index++;
 232           }
 233         }
 234
 235         uniquifySequences(newArr);
 236
 237         if (forGroup)
 238         {
 239           exportData(newArr, stoTemp, null, null, group);
 240         }
 241         else
 242         {
 243           exportData(newArr, stoTemp, null, null, alignment);
 244         }
 245
 246         SeqsetUtils.deuniquify(hash, array);
 247
 248       } catch (FileNotFoundException e)
 249       {
 250         // TODO Auto-generated catch block
 251         e.printStackTrace();
 252
 253       }
 254       try
 255       {
 256         boolean ran = runCommand();
 257         if (!ran)
 258         {
 259           return;
 260         }
 261       } catch (IOException | InterruptedException e)
 262       {
 263         // TODO Auto-generated catch block
 264         e.printStackTrace();
 265       }
 266       try
 267       {
 268
 269         importData();
 270       } catch (IOException | InterruptedException e)
 271       {
 272         // TODO Auto-generated catch block
 273         e.printStackTrace();
 274       }
 275     } catch (Exception e)
 276     {
 277       e.printStackTrace();
 278     }
 279   }
 280
 281   /**
 282    * Executes the hmmbuild command in the command line.
 283    *
 284    * @return
 285    * @throws IOException
 286    * @throws InterruptedException
 287    */
 288   private boolean runCommand() throws IOException, InterruptedException
 289   {
 290     String binaryPath = getCommandRoot(HMMBUILD);
 291     if (binaryPath == null)
 292     {
 293       return false;
 294     }
 295     String command = binaryPath + SPACE;
 296     String name = null;
 297
 298     if (params != null)
 299     {
 300       for (ArgumentI arg : params)
 301       {
 302         String argName = arg.getName();
 303         switch (argName)
 304         {
 305         case "HMM Name":
 306           name = arg.getValue();
 307           name = name.trim();
 308           break;
 309         case "Use Reference Annotation":
 310           command += "--hand ";
 311           break;
 312
 313         }
 314       }
 315     }
 316
 317     if (forGroup && multiJob)
 318     {
 319       name = group.getName() + "_HMM";
 320     }
 321
 322     if (name == null || "".equals(name))
 323     {
 324       if (af != null)
 325       {
 326         if (af.getTitle().length() < 15)
 327         {
 328           name = af.getTitle();
 329         }
 330       }
 331       if (name == null || "".equals(name))
 332       {
 333         name = "Alignment";
 334       }
 335
 336     }
 337
 338     command += "-n " + name.replace(' ', '_') + SPACE;
 339     if (!alignment.isNucleotide())
 340     {
 341       command += FORCEAMINO; // TODO check for rna
 342     }
 343     else
 344     {
 345       command += FORCEDNA;
 346     }
 347
 348     command += hmmTemp.getAbsolutePath() + SPACE + stoTemp.getAbsolutePath()
 349             + SPACE;
 350     return runCommand(command);
 351   }
 352
 353   /**
 354    * Imports the .hmm file produced by hmmbuild.
 355    *
 356    * @throws IOException
 357    * @throws InterruptedException
 358    */
 359   private void importData() throws IOException, InterruptedException
 360   {
 361     HMMFile file = new HMMFile(
 362             new FileParse(hmmTemp.getAbsolutePath(), DataSourceType.FILE));
 363     SequenceI[] seqs = file.getSeqsAsArray();
 364     SequenceI seq = seqs[0];
 365     seq.createDatasetSequence();
 366     if (group != null)
 367     {
 368       seq.insertCharAt(0, group.getStartRes(), '-');
 369       seq.insertCharAt(group.getEndRes() + 1,
 370               alignment.getWidth() - group.getEndRes() - 1, '-');
 371       seq.updateHMMMapping();
 372       SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
 373       int topIndex = alignment.findIndex(topSeq);
 374       alignment.insertSequenceAt(topIndex, seq);
 375       group.setSeqrep(seq);
 376       group.addSequence(seq, false);
 377     }
 378     else
 379     {
 380       alignment.insertSequenceAt(0, seq);
 381     }
 382
 383     if (viewport != null)
 384     {
 385       viewport.alignmentChanged(viewport.getAlignPanel());
 386       viewport.getAlignPanel().adjustAnnotationHeight();
 387       viewport.updateSequenceIdColours();
 388
 389       if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
 390       {
 391         viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
 392       }
 393     }
 394     hmmTemp.delete();
 395     stoTemp.delete();
 396   }
 397
 398   /**
 399    * Runs hmmbuild, and waits for the results to be imported before continuing
 400    */
 401   public void hmmbuildWaitTillComplete()
 402   {
 403     Thread loader = new Thread(this);
 404     loader.start();
 405
 406     while (loader.isAlive())
 407     {
 408       try
 409       {
 410         Thread.sleep(500);
 411       } catch (Exception ex)
 412       {
 413       }
 414     }
 415   }
 416 }