src/jalview/hmmer/HMMBuildThread.java

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