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   boolean multiJob;
  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             multiJob = true;
 100             break;
 101           }
 102           else if ("All groups".equals(value))
 103           {
 104             alignment = null;
 105             groups = viewport.getAlignment().getGroups();
 106             multiJob = true;
 107             break;
 108           }
 109           else if ("Selected group".equals(value))
 110           {
 111             alignment = null;
 112             groups.add(viewport.getSelectionGroup());
 113             break;
 114           }
 115         }
 116         else if (MessageManager.getString("label.use_reference")
 117                 .equals(name))
 118         {
 119           if (!af.getViewport().hasReferenceAnnotation())
 120           {
 121             if (af != null)
 122             {
 123               af.setProgressBar(
 124                       MessageManager.getString("status.running_hmmbuild"),
 125                       barID);
 126             }
 127             JvOptionPane.showInternalMessageDialog(af, MessageManager
 128                     .getString("warn.no_reference_annotation"));
 129             return;
 130           }
 131         }
 132       }
 133     }
 134
 135     if (alignment != null)
 136     {
 137       forGroup = false;
 138       runHMMBuild();
 139     }
 140
 141     if (alignment == null)
 142     {
 143       alignment = viewport.getAlignment();
 144     }
 145
 146     if (groups != null && groups.size() > 0)
 147     {
 148       for (SequenceGroup grp : groups)
 149       {
 150         group = grp;
 151         forGroup = true;
 152         runHMMBuild();
 153       }
 154     }
 155
 156
 157     if (af != null)
 158     {
 159       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 160               barID);
 161     }
 162   }
 163
 164   private void runHMMBuild()
 165   {
 166     if (alignment == null && group == null)
 167       {
 168         JOptionPane.showMessageDialog(af,
 169               MessageManager.getString("warn.no_sequence_data"));
 170       }
 171       try
 172       {
 173         hmmTemp = File.createTempFile("hmm", ".hmm");
 174         hmmTemp.deleteOnExit();
 175         stoTemp = File.createTempFile("output", ".sto");
 176         stoTemp.deleteOnExit();
 177       } catch (IOException e1)
 178       {
 179         e1.printStackTrace();
 180       }
 181
 182     try
 183     {
 184       try
 185       {
 186         SequenceI[] array;
 187         List<SequenceI> seqs = null;
 188         if (forGroup)
 189         {
 190           seqs = group.getHMMConsensusSequences(true);
 191           if (seqs.size() > 0)
 192           {
 193             return;
 194           }
 195           array = group.getSelectionAsNewSequences(alignment);
 196         }
 197         else
 198         {
 199           seqs = alignment.getHMMConsensusSequences(true);
 200           if (!alignment.isAligned())
 201           {
 202             alignment.padGaps();
 203           }
 204           array = alignment.getSequencesArray();
 205         }
 206
 207           cmds.setHmmSeqs(seqs);
 208
 209         if (array.length < 1)
 210           {
 211           if (af != null)
 212           {
 213             JOptionPane.showMessageDialog(af,
 214                     MessageManager.getString("warn.no_sequence_data"));
 215           }
 216           return;
 217           }
 218           SequenceI[] newArr = new SequenceI[array.length];
 219           int index = 0;
 220           for (SequenceI seq : array)
 221           {
 222             newArr[index] = new Sequence(seq);
 223             index++;
 224           }
 225
 226           cmds.uniquifySequences(newArr);
 227           cmds.exportData(newArr, stoTemp, null, null);
 228           jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 229
 230       } catch (FileNotFoundException e)
 231       {
 232         // TODO Auto-generated catch block
 233         e.printStackTrace();
 234
 235       }
 236       try
 237       {
 238           boolean ran = runCommand();
 239           if (!ran)
 240           {
 241             return;
 242           }
 243       } catch (IOException | InterruptedException e)
 244       {
 245         // TODO Auto-generated catch block
 246         e.printStackTrace();
 247       }
 248       try
 249       {
 250
 251         importData();
 252       } catch (IOException | InterruptedException e)
 253       {
 254         // TODO Auto-generated catch block
 255         e.printStackTrace();
 256       }
 257       } catch (Exception e)
 258       {
 259         e.printStackTrace();
 260     }
 261   }
 262
 263
 264
 265   /**
 266    * Executes the hmmbuild command in the command line.
 267    *
 268    * @return
 269    * @throws IOException
 270    * @throws InterruptedException
 271    */
 272   private boolean runCommand() throws IOException, InterruptedException
 273   {
 274     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 275     if (!file.canExecute())
 276     {
 277       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 278       {
 279         if (!file.canExecute())
 280         {
 281           if (af != null)
 282           {
 283             JvOptionPane.showInternalMessageDialog(af,
 284                     MessageManager.getString("warn.hmmbuild_failed"));
 285           }
 286           return false;
 287         }
 288       }
 289     }
 290     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.SPACE;
 291     String name = null;
 292
 293     if (params != null)
 294     {
 295       for (ArgumentI arg : params)
 296       {
 297         String argName = arg.getName();
 298         switch (argName)
 299         {
 300         case "HMM Name":
 301           if (!multiJob)
 302           {
 303             name = arg.getValue();
 304             name = name.trim();
 305           }
 306           break;
 307         case "Use Reference Annotation":
 308           command += "--hand ";
 309           break;
 310
 311         }
 312
 313       }
 314     }
 315
 316     if (name == null || "".equals(name))
 317     {
 318       if (forGroup)
 319       {
 320         name = group.getName();
 321       }
 322       else
 323       {
 324         if (af != null)
 325         {
 326           name = af.getTitle();
 327         }
 328         if (name == null || "".equals(name))
 329         {
 330           name = "Alignment";
 331         }
 332       }
 333     }
 334
 335
 336     command += "-n " + name.replace(' ', '_') + cmds.SPACE;
 337     if (!alignment.isNucleotide())
 338     {
 339       command += cmds.FORCEAMINO; // TODO check for rna
 340     }
 341     else
 342     {
 343       command += cmds.FORCEDNA;
 344     }
 345
 346     command += hmmTemp.getAbsolutePath()
 347             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 348     return cmds.runCommand(command);
 349   }
 350
 351   /**
 352    * Imports the .hmm file produced by hmmbuild.
 353    *
 354    * @throws IOException
 355    * @throws InterruptedException
 356    */
 357   private void importData() throws IOException, InterruptedException
 358   {
 359       HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
 360               DataSourceType.FILE));
 361     SequenceI[] seqs = file.getSeqsAsArray();
 362     SequenceI seq = seqs[0];
 363     seq.createDatasetSequence();
 364     HiddenMarkovModel hmm = file.getHMM();
 365     if (group != null)
 366     {
 367       seq.insertCharAt(0, group.getStartRes(), '-');
 368       seq.insertCharAt(group.getEndRes() + 1,
 369               alignment.getWidth() - group.getEndRes(), '-');
 370       seq.updateHMMMapping();
 371       SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
 372       int topIndex = alignment.findIndex(topSeq);
 373       alignment.insertSequenceAt(topIndex, seq);
 374       group.setSeqrep(seq);
 375       group.addSequence(seq, false);
 376     }
 377     else
 378     {
 379       alignment.insertSequenceAt(0, seq);
 380     }
 381
 382     viewport.alignmentChanged(viewport.getAlignPanel());
 383     viewport.getAlignPanel().adjustAnnotationHeight();
 384     viewport.updateSequenceIdColours();
 385
 386     if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
 387     {
 388       viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
 389     }
 390     hmmTemp.delete();
 391     stoTemp.delete();
 392   }
 393
 394   /**
 395    * Runs hmmbuild, and waits for the results to be imported before continuing
 396    */
 397   public void hmmbuildWaitTillComplete()
 398   {
 399     Thread loader = new Thread(this);
 400     loader.start();
 401
 402     while (loader.isAlive())
 403     {
 404       try
 405       {
 406         Thread.sleep(500);
 407       } catch (Exception ex)
 408       {
 409       }
 410     }
 411   }
 412 }