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
 132     if (alignment != null)
 133     {
 134       forGroup = false;
 135       runHMMBuild();
 136     }
 137
 138     if (alignment == null)
 139     {
 140       alignment = viewport.getAlignment();
 141     }
 142
 143     if (groups != null && groups.size() > 0)
 144     {
 145       for (SequenceGroup grp : groups)
 146       {
 147         group = grp;
 148         forGroup = true;
 149         runHMMBuild();
 150       }
 151     }
 152
 153
 154     if (af != null)
 155     {
 156       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 157               barID);
 158     }
 159   }
 160
 161   private void runHMMBuild()
 162   {
 163     if (alignment == null && group == null)
 164       {
 165         JOptionPane.showMessageDialog(af,
 166               MessageManager.getString("warn.no_sequence_data"));
 167       }
 168       try
 169       {
 170         hmmTemp = File.createTempFile("hmm", ".hmm");
 171         hmmTemp.deleteOnExit();
 172         stoTemp = File.createTempFile("output", ".sto");
 173         stoTemp.deleteOnExit();
 174       } catch (IOException e1)
 175       {
 176         e1.printStackTrace();
 177       }
 178
 179     try
 180     {
 181       try
 182       {
 183         SequenceI[] array;
 184         List<SequenceI> seqs = null;
 185         if (forGroup)
 186         {
 187           seqs = group.getHMMConsensusSequences(true);
 188           if (seqs.size() > 0)
 189           {
 190             return;
 191           }
 192           array = group.getSelectionAsNewSequences(alignment);
 193         }
 194         else
 195         {
 196           seqs = alignment.getHMMConsensusSequences(true);
 197           if (!alignment.isAligned())
 198           {
 199             alignment.padGaps();
 200           }
 201           array = alignment.getSequencesArray();
 202         }
 203
 204           cmds.setHmmSeqs(seqs);
 205
 206         if (array.length < 1)
 207           {
 208           if (af != null)
 209           {
 210             JOptionPane.showMessageDialog(af,
 211                     MessageManager.getString("warn.no_sequence_data"));
 212           }
 213           return;
 214           }
 215           SequenceI[] newArr = new SequenceI[array.length];
 216           int index = 0;
 217           for (SequenceI seq : array)
 218           {
 219             newArr[index] = new Sequence(seq);
 220             index++;
 221           }
 222
 223           cmds.uniquifySequences(newArr);
 224           cmds.exportData(newArr, stoTemp, null, null);
 225           jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 226
 227       } catch (FileNotFoundException e)
 228       {
 229         // TODO Auto-generated catch block
 230         e.printStackTrace();
 231
 232       }
 233       try
 234       {
 235           boolean ran = runCommand();
 236           if (!ran)
 237           {
 238             return;
 239           }
 240       } catch (IOException | InterruptedException e)
 241       {
 242         // TODO Auto-generated catch block
 243         e.printStackTrace();
 244       }
 245       try
 246       {
 247
 248         importData();
 249       } catch (IOException | InterruptedException e)
 250       {
 251         // TODO Auto-generated catch block
 252         e.printStackTrace();
 253       }
 254       } catch (Exception e)
 255       {
 256         e.printStackTrace();
 257     }
 258   }
 259
 260
 261
 262   /**
 263    * Executes the hmmbuild command in the command line.
 264    *
 265    * @return
 266    * @throws IOException
 267    * @throws InterruptedException
 268    */
 269   private boolean runCommand() throws IOException, InterruptedException
 270   {
 271     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 272     if (!file.canExecute())
 273     {
 274       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 275       {
 276         if (!file.canExecute())
 277         {
 278           if (af != null)
 279           {
 280             JvOptionPane.showInternalMessageDialog(af,
 281                     MessageManager.getString("warn.hmmbuild_failed"));
 282           }
 283           return false;
 284         }
 285       }
 286     }
 287     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.SPACE;
 288     String name = null;
 289
 290     if (params != null)
 291     {
 292       for (ArgumentI arg : params)
 293       {
 294         String argName = arg.getName();
 295         switch (argName)
 296         {
 297         case "HMM Name":
 298           name = arg.getValue();
 299           break;
 300         case "Use Reference Annotation":
 301           command += "--hand ";
 302           break;
 303
 304         }
 305
 306       }
 307     }
 308
 309     name = name.trim();
 310
 311     if (name == null || "".equals(name))
 312     {
 313       if (forGroup)
 314       {
 315         name = group.getName();
 316       }
 317       else
 318       {
 319         if (af != null)
 320         {
 321           name = af.getTitle();
 322         }
 323         if (name == null || "".equals(name))
 324         {
 325           name = "Alignment";
 326         }
 327       }
 328     }
 329
 330     command += "-n " + name + cmds.SPACE;
 331     if (!alignment.isNucleotide())
 332     {
 333       command += cmds.FORCEAMINO; // TODO check for rna
 334     }
 335     else
 336     {
 337       command += cmds.FORCEDNA;
 338     }
 339
 340     command += hmmTemp.getAbsolutePath()
 341             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 342     return cmds.runCommand(command);
 343   }
 344
 345   /**
 346    * Imports the .hmm file produced by hmmbuild.
 347    *
 348    * @throws IOException
 349    * @throws InterruptedException
 350    */
 351   private void importData() throws IOException, InterruptedException
 352   {
 353       HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
 354               DataSourceType.FILE));
 355     SequenceI[] seqs = file.getSeqsAsArray();
 356     SequenceI seq = seqs[0];
 357     seq.createDatasetSequence();
 358     HiddenMarkovModel hmm = file.getHMM();
 359     if (group != null)
 360     {
 361       seq.insertCharAt(0, group.getStartRes(), '-');
 362       seq.insertCharAt(group.getEndRes() + 1,
 363               alignment.getWidth() - group.getEndRes(), '-');
 364       seq.updateHMMMapping();
 365       SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
 366       int topIndex = alignment.findIndex(topSeq);
 367       alignment.insertSequenceAt(topIndex, seq);
 368       group.setSeqrep(seq);
 369       group.addSequence(seq, false);
 370     }
 371     else
 372     {
 373       alignment.insertSequenceAt(0, seq);
 374     }
 375
 376     viewport.alignmentChanged(viewport.getAlignPanel());
 377     viewport.getAlignPanel().adjustAnnotationHeight();
 378     viewport.updateSequenceIdColours();
 379
 380     if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
 381     {
 382       viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
 383     }
 384     hmmTemp.delete();
 385     stoTemp.delete();
 386   }
 387
 388   /**
 389    * Runs hmmbuild, and waits for the results to be imported before continuing
 390    */
 391   public void hmmbuildWaitTillComplete()
 392   {
 393     Thread loader = new Thread(this);
 394     loader.start();
 395
 396     while (loader.isAlive())
 397     {
 398       try
 399       {
 400         Thread.sleep(500);
 401       } catch (Exception ex)
 402       {
 403       }
 404     }
 405   }
 406 }