src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.HiddenMarkovModel;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceGroup;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.gui.AlignFrame;
  11 import jalview.gui.AlignViewport;
  12 import jalview.gui.JvOptionPane;
  13 import jalview.gui.Preferences;
  14 import jalview.io.DataSourceType;
  15 import jalview.io.FileParse;
  16 import jalview.io.HMMFile;
  17 import jalview.util.MessageManager;
  18 import jalview.ws.params.ArgumentI;
  19
  20 import java.io.File;
  21 import java.io.FileNotFoundException;
  22 import java.io.IOException;
  23 import java.util.ArrayList;
  24 import java.util.List;
  25
  26 import javax.swing.JOptionPane;
  27
  28 public class HMMBuildThread implements Runnable
  29 {
  30   HMMERCommands cmds = new HMMERCommands();
  31   AlignFrame af;
  32
  33   AlignViewport viewport;
  34
  35   boolean multiJob = false;
  36   AlignmentI alignment;
  37   SequenceGroup group;
  38   List<ArgumentI> params;
  39
  40
  41   boolean forGroup = false;
  42
  43   File hmmTemp = null;
  44
  45   File stoTemp = null;
  46
  47   long barID;
  48
  49   /**
  50    * This is used for validation purposes. Do not use!
  51    *
  52    * @param viewport
  53    */
  54   public HMMBuildThread(AlignmentI alignment)
  55   {
  56     this.alignment = alignment;
  57     forGroup = false;
  58   }
  59
  60   public HMMBuildThread(AlignFrame af, List<ArgumentI> args)
  61   {
  62     this.af = af;
  63     viewport = af.getViewport();
  64     params = args;
  65   }
  66
  67   /**
  68    * Builds a HMM from an alignment, then imports and adds it to the alignment.
  69    */
  70   @Override
  71   public void run()
  72   {
  73     barID = System.currentTimeMillis();
  74     if (af != null)
  75     {
  76     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  77             barID);
  78     }
  79     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  80
  81     List<SequenceGroup> groups = new ArrayList<>();
  82     if (params != null)
  83     {
  84       for (ArgumentI arg : params)
  85       {
  86         String name = arg.getName();
  87         if (MessageManager.getString("label.hmmbuild_for").equals(name))
  88         {
  89           String value = arg.getValue();
  90           if ("Alignment".equals(value))
  91           {
  92             alignment = viewport.getAlignment();
  93             break;
  94           }
  95           else if ("All groups and alignment".equals(value))
  96           {
  97             alignment = viewport.getAlignment();
  98             groups.addAll(viewport.getAlignment().getGroups());
  99             if (groups.size() > 0)
 100             {
 101               multiJob = true;
 102             }
 103             break;
 104           }
 105           else if ("All groups".equals(value))
 106           {
 107             alignment = null;
 108             groups = viewport.getAlignment().getGroups();
 109             if (groups.size() > 0)
 110             {
 111               multiJob = true;
 112             }
 113             break;
 114           }
 115           else if ("Selected group".equals(value))
 116           {
 117             alignment = null;
 118             groups.add(viewport.getSelectionGroup());
 119             break;
 120           }
 121         }
 122         else if (MessageManager.getString("label.use_reference")
 123                 .equals(name))
 124         {
 125           if (!af.getViewport().hasReferenceAnnotation())
 126           {
 127             if (af != null)
 128             {
 129               af.setProgressBar(
 130                       MessageManager.getString("status.running_hmmbuild"),
 131                       barID);
 132             }
 133             JvOptionPane.showInternalMessageDialog(af, MessageManager
 134                     .getString("warn.no_reference_annotation"));
 135             return;
 136           }
 137         }
 138       }
 139     }
 140     else if (viewport != null)
 141     {
 142       alignment = viewport.getAlignment();
 143     }
 144
 145     if (alignment != null)
 146     {
 147       forGroup = false;
 148       runHMMBuild();
 149     }
 150
 151     if (alignment == null)
 152     {
 153       alignment = viewport.getAlignment();
 154     }
 155
 156     if (groups != null && groups.size() > 0)
 157     {
 158       for (SequenceGroup grp : groups)
 159       {
 160         group = grp;
 161         forGroup = true;
 162         runHMMBuild();
 163       }
 164     }
 165
 166
 167     if (af != null)
 168     {
 169       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 170               barID);
 171     }
 172   }
 173
 174   private void runHMMBuild()
 175   {
 176     if (alignment == null && group == null)
 177       {
 178         JOptionPane.showMessageDialog(af,
 179               MessageManager.getString("warn.no_sequence_data"));
 180       }
 181       try
 182       {
 183         hmmTemp = File.createTempFile("hmm", ".hmm");
 184         hmmTemp.deleteOnExit();
 185         stoTemp = File.createTempFile("output", ".sto");
 186         stoTemp.deleteOnExit();
 187       } catch (IOException e1)
 188       {
 189         e1.printStackTrace();
 190       }
 191
 192     try
 193     {
 194       try
 195       {
 196         SequenceI[] array;
 197         List<SequenceI> seqs = null;
 198         if (forGroup)
 199         {
 200           seqs = group.getHMMConsensusSequences(true);
 201           if (seqs.size() > 0)
 202           {
 203             return;
 204           }
 205           array = group.getSelectionAsNewSequences(alignment);
 206         }
 207         else
 208         {
 209           seqs = alignment.getHMMConsensusSequences(true);
 210           if (!alignment.isAligned())
 211           {
 212             alignment.padGaps();
 213           }
 214           array = alignment.getSequencesArray();
 215         }
 216
 217           cmds.setHmmSeqs(seqs);
 218
 219         if (array.length < 1)
 220           {
 221           if (af != null)
 222           {
 223             JOptionPane.showMessageDialog(af,
 224                     MessageManager.getString("warn.no_sequence_data"));
 225           }
 226           return;
 227           }
 228           SequenceI[] newArr = new SequenceI[array.length];
 229           int index = 0;
 230           for (SequenceI seq : array)
 231           {
 232             newArr[index] = new Sequence(seq);
 233             index++;
 234           }
 235
 236           cmds.uniquifySequences(newArr);
 237
 238         if (forGroup)
 239         {
 240           cmds.exportData(newArr, stoTemp, null, null, group);
 241         }
 242         else
 243         {
 244           cmds.exportData(newArr, stoTemp, null, null, alignment);
 245         }
 246
 247           jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 248
 249       } catch (FileNotFoundException e)
 250       {
 251         // TODO Auto-generated catch block
 252         e.printStackTrace();
 253
 254       }
 255       try
 256       {
 257           boolean ran = runCommand();
 258           if (!ran)
 259           {
 260             return;
 261           }
 262       } catch (IOException | InterruptedException e)
 263       {
 264         // TODO Auto-generated catch block
 265         e.printStackTrace();
 266       }
 267       try
 268       {
 269
 270         importData();
 271       } catch (IOException | InterruptedException e)
 272       {
 273         // TODO Auto-generated catch block
 274         e.printStackTrace();
 275       }
 276       } catch (Exception e)
 277       {
 278         e.printStackTrace();
 279     }
 280   }
 281
 282
 283
 284   /**
 285    * Executes the hmmbuild command in the command line.
 286    *
 287    * @return
 288    * @throws IOException
 289    * @throws InterruptedException
 290    */
 291   private boolean runCommand() throws IOException, InterruptedException
 292   {
 293     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 294     if (!file.canExecute())
 295     {
 296       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 297       {
 298         if (!file.canExecute())
 299         {
 300           if (af != null)
 301           {
 302             JvOptionPane.showInternalMessageDialog(af,
 303                     MessageManager.getString("warn.hmmbuild_failed"));
 304           }
 305           return false;
 306         }
 307       }
 308     }
 309     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.SPACE;
 310     String name = null;
 311
 312     if (params != null)
 313     {
 314       for (ArgumentI arg : params)
 315       {
 316         String argName = arg.getName();
 317         switch (argName)
 318         {
 319         case "HMM Name":
 320           name = arg.getValue();
 321           name = name.trim();
 322           break;
 323         case "Use Reference Annotation":
 324           command += "--hand ";
 325           break;
 326
 327         }
 328       }
 329     }
 330
 331     if (forGroup && multiJob)
 332     {
 333       name = group.getName() + "_HMM";
 334     }
 335
 336
 337     if (name == null || "".equals(name))
 338     {
 339         if (af != null)
 340         {
 341         if (af.getTitle().length() < 15)
 342         {
 343           name = af.getTitle();
 344         }
 345         }
 346         if (name == null || "".equals(name))
 347         {
 348           name = "Alignment";
 349         }
 350
 351     }
 352
 353     command += "-n " + name.replace(' ', '_') + cmds.SPACE;
 354     if (!alignment.isNucleotide())
 355     {
 356       command += cmds.FORCEAMINO; // TODO check for rna
 357     }
 358     else
 359     {
 360       command += cmds.FORCEDNA;
 361     }
 362
 363     command += hmmTemp.getAbsolutePath()
 364             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 365     return cmds.runCommand(command);
 366   }
 367
 368   /**
 369    * Imports the .hmm file produced by hmmbuild.
 370    *
 371    * @throws IOException
 372    * @throws InterruptedException
 373    */
 374   private void importData() throws IOException, InterruptedException
 375   {
 376     HMMFile file = new HMMFile(
 377             new FileParse(hmmTemp.getAbsolutePath(),
 378               DataSourceType.FILE));
 379     SequenceI[] seqs = file.getSeqsAsArray();
 380     SequenceI seq = seqs[0];
 381     seq.createDatasetSequence();
 382     HiddenMarkovModel hmm = file.getHMM();
 383     if (group != null)
 384     {
 385       seq.insertCharAt(0, group.getStartRes(), '-');
 386       seq.insertCharAt(group.getEndRes() + 1,
 387               alignment.getWidth() - group.getEndRes() - 1, '-');
 388       seq.updateHMMMapping();
 389       SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
 390       int topIndex = alignment.findIndex(topSeq);
 391       alignment.insertSequenceAt(topIndex, seq);
 392       group.setSeqrep(seq);
 393       group.addSequence(seq, false);
 394     }
 395     else
 396     {
 397       alignment.insertSequenceAt(0, seq);
 398     }
 399
 400     if (viewport != null)
 401     {
 402       viewport.alignmentChanged(viewport.getAlignPanel());
 403       viewport.getAlignPanel().adjustAnnotationHeight();
 404       viewport.updateSequenceIdColours();
 405
 406       if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
 407       {
 408         viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
 409       }
 410     }
 411     hmmTemp.delete();
 412     stoTemp.delete();
 413   }
 414
 415   /**
 416    * Runs hmmbuild, and waits for the results to be imported before continuing
 417    */
 418   public void hmmbuildWaitTillComplete()
 419   {
 420     Thread loader = new Thread(this);
 421     loader.start();
 422
 423     while (loader.isAlive())
 424     {
 425       try
 426       {
 427         Thread.sleep(500);
 428       } catch (Exception ex)
 429       {
 430       }
 431     }
 432   }
 433 }