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