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
 332     if (forGroup && multiJob)
 333     {
 334       name = group.getName() + "_HMM";
 335     }
 336
 337
 338     if (name == null || "".equals(name))
 339     {
 340         if (af != null)
 341         {
 342         if (af.getTitle().length() < 15)
 343         {
 344           name = af.getTitle();
 345         }
 346         }
 347         if (name == null || "".equals(name))
 348         {
 349           name = "Alignment";
 350         }
 351
 352     }
 353
 354     command += "-n " + name.replace(' ', '_') + cmds.SPACE;
 355     if (!alignment.isNucleotide())
 356     {
 357       command += cmds.FORCEAMINO; // TODO check for rna
 358     }
 359     else
 360     {
 361       command += cmds.FORCEDNA;
 362     }
 363
 364     command += hmmTemp.getAbsolutePath()
 365             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 366     return cmds.runCommand(command);
 367   }
 368
 369   /**
 370    * Imports the .hmm file produced by hmmbuild.
 371    *
 372    * @throws IOException
 373    * @throws InterruptedException
 374    */
 375   private void importData() throws IOException, InterruptedException
 376   {
 377     HMMFile file = new HMMFile(
 378             new FileParse(hmmTemp.getAbsolutePath(),
 379               DataSourceType.FILE));
 380     SequenceI[] seqs = file.getSeqsAsArray();
 381     SequenceI seq = seqs[0];
 382     seq.createDatasetSequence();
 383     HiddenMarkovModel hmm = file.getHMM();
 384     if (group != null)
 385     {
 386       seq.insertCharAt(0, group.getStartRes(), '-');
 387       seq.insertCharAt(group.getEndRes() + 1,
 388               alignment.getWidth() - group.getEndRes() - 1, '-');
 389       seq.updateHMMMapping();
 390       SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
 391       int topIndex = alignment.findIndex(topSeq);
 392       alignment.insertSequenceAt(topIndex, seq);
 393       group.setSeqrep(seq);
 394       group.addSequence(seq, false);
 395     }
 396     else
 397     {
 398       alignment.insertSequenceAt(0, seq);
 399     }
 400
 401     if (viewport != null)
 402     {
 403       viewport.alignmentChanged(viewport.getAlignPanel());
 404       viewport.getAlignPanel().adjustAnnotationHeight();
 405       viewport.updateSequenceIdColours();
 406
 407       if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
 408       {
 409         viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
 410       }
 411     }
 412     hmmTemp.delete();
 413     stoTemp.delete();
 414   }
 415
 416   /**
 417    * Runs hmmbuild, and waits for the results to be imported before continuing
 418    */
 419   public void hmmbuildWaitTillComplete()
 420   {
 421     Thread loader = new Thread(this);
 422     loader.start();
 423
 424     while (loader.isAlive())
 425     {
 426       try
 427       {
 428         Thread.sleep(500);
 429       } catch (Exception ex)
 430       {
 431       }
 432     }
 433   }
 434 }