src/jalview/hmmer/HMMBuildThread.java

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