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