src/jalview/hmmer/HMMAlignThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.Alignment;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.AlignmentOrder;
   7 import jalview.datamodel.AlignmentView;
   8 import jalview.datamodel.HiddenColumns;
   9 import jalview.datamodel.HiddenMarkovModel;
  10 import jalview.datamodel.SequenceI;
  11 import jalview.gui.AlignFrame;
  12 import jalview.gui.Desktop;
  13 import jalview.gui.Preferences;
  14 import jalview.gui.SplitFrame;
  15 import jalview.io.DataSourceType;
  16 import jalview.io.StockholmFile;
  17 import jalview.util.MessageManager;
  18 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  19
  20 import java.io.File;
  21 import java.io.IOException;
  22 import java.util.ArrayList;
  23 import java.util.List;
  24 import java.util.Map;
  25
  26 import javax.swing.JInternalFrame;
  27 import javax.swing.JOptionPane;
  28
  29 public class HMMAlignThread implements Runnable
  30 {
  31
  32   /**
  33    * feature settings from view that job was associated with
  34    */
  35   protected FeatureRendererSettings featureSettings = null;
  36
  37   HMMERCommands cmds = new HMMERCommands();
  38
  39   AlignFrame af;
  40
  41   AlignmentI alignment;
  42
  43   AlignmentI dataset;
  44
  45   List<AlignmentOrder> orders;
  46
  47   AlignmentView msa;
  48
  49   HiddenMarkovModel hmm;
  50
  51   boolean newFrame;
  52
  53   long barID;
  54
  55   Map<Integer, SequenceI> hmmSeqs;
  56
  57   File hmmTemp = null;
  58
  59   File outTemp = null;
  60
  61   File inputTemp = null;
  62
  63   List<AlignmentOrder> allOrders;
  64
  65   SequenceI[][] allResults;
  66
  67   public HMMAlignThread(AlignFrame af, boolean createNewFrame)
  68   {
  69     this.af = af;
  70     alignment = af.getViewport().getAlignment();
  71     if (alignment.getDataset() != null)
  72     {
  73       dataset = alignment.getDataset();
  74     }
  75     newFrame = createNewFrame;
  76     featureSettings = af.getFeatureRenderer().getSettings();
  77   }
  78
  79   @Override
  80   public void run()
  81   {
  82     if (af.getViewport().getSelectedHMM() == null)
  83     {
  84       JOptionPane.showMessageDialog(af,
  85               MessageManager.getString("warn.no_selected_hmm"));
  86       return;
  87     }
  88     else
  89     {
  90       hmm = af.getViewport().getSelectedHMM();
  91     }
  92     barID = System.currentTimeMillis();
  93     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  94             barID);
  95     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  96
  97     // if (!alignment.isAligned())
  98     // {
  99     // alignment.padGaps();
 100     // }
 101     prepareAlignment();
 102     SequenceI[][] subAlignments = msa.getVisibleContigs('-');
 103     allOrders = new ArrayList<>();
 104     allResults = new SequenceI[subAlignments.length][];
 105     int job = 0;
 106     for (SequenceI[] seqs : subAlignments)
 107     {
 108       cmds.uniquifySequences(seqs);
 109       try
 110       {
 111         createTemporaryFiles();
 112       } catch (IOException e2)
 113       {
 114         e2.printStackTrace();
 115       }
 116       try
 117       {
 118         cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
 119                 hmmTemp.getAbsoluteFile());
 120       } catch (IOException e1)
 121       {
 122         e1.printStackTrace();
 123       }
 124       try
 125       {
 126         runCommand();
 127       } catch (IOException | InterruptedException e)
 128       {
 129         e.printStackTrace();
 130       }
 131       try
 132       {
 133         importData(job);
 134       } catch (IOException | InterruptedException e)
 135       {
 136         // TODO Auto-generated catch block
 137         e.printStackTrace();
 138       }
 139       job++;
 140     }
 141
 142     displayResults(newFrame);
 143
 144     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
 145             barID);
 146
 147   }
 148
 149   private void createTemporaryFiles() throws IOException
 150   {
 151     hmmTemp = File.createTempFile("hmm", ".hmm");
 152     hmmTemp.deleteOnExit();
 153     outTemp = File.createTempFile("output", ".sto");
 154     outTemp.deleteOnExit();
 155     inputTemp = File.createTempFile("input", ".sto");
 156     inputTemp.deleteOnExit();
 157   }
 158
 159   private void runCommand() throws IOException, InterruptedException
 160   {
 161     String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
 162     if (!hmm.getFileHeader().contains("HMMER3/f"))
 163     {
 164       command += cmds.ALLCOL;
 165     }
 166     command += cmds.TRIM + " -o" + inputTemp.getAbsolutePath() + cmds.SPACE
 167             + hmmTemp.getAbsolutePath() + cmds.SPACE
 168             + outTemp.getAbsolutePath();
 169     cmds.runCommand(command);
 170   }
 171
 172   private void importData(int index)
 173           throws IOException, InterruptedException
 174   {
 175     StockholmFile file = new StockholmFile(inputTemp.getAbsolutePath(),
 176             DataSourceType.FILE);
 177     SequenceI[] result = file.getSeqsAsArray();
 178     AlignmentOrder msaorder = new AlignmentOrder(result);
 179     // always recover the order - makes parseResult()'s life easier.
 180     jalview.analysis.AlignmentSorter.recoverOrder(result);
 181     jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
 182     allOrders.add(msaorder);
 183     allResults[index] = result;
 184
 185     /*
 186     if (newFrame)
 187     {
 188       FileLoader loader = new FileLoader();
 189       AlignFrame aFrame = new AlignFrame(new Alignment(new SequenceI[1]),
 190               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 191       Desktop.addInternalFrame(aFrame, aFrame.getTitle(),
 192               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 193       aFrame.setTitle(
 194               af.getName() + "Aligned to " + hmm.getName() + "'s HMM");
 195       af.getViewport().setAlignment(null);
 196
 197       aFrame.loadJalviewDataFile(inputTemp.getAbsolutePath(),
 198               DataSourceType.FILE, FileFormat.Stockholm, null);
 199
 200
 201
 202       Map<Integer, SequenceI> copy = new HashMap<>(
 203               hmmSeqs);
 204       addSeqs(aFrame, copy);
 205       SequenceI seq = aFrame.getViewport().getAlignment()
 206               .getSequenceAt(0);
 207       seq.getHMM().mapToReferenceAnnotation(aFrame, seq);
 208       addSeqs(af, hmmSeqs);
 209     }
 210     else
 211     {
 212       af.getViewport().getAlignment().getSequences().clear();
 213       af.setIsRecurring(true);
 214       af.loadJalviewDataFile(inputTemp.getAbsolutePath(),
 215               DataSourceType.FILE, FileFormat.Stockholm, null);
 216       af.setIsRecurring(false);
 217       addSeqs(af, hmmSeqs);
 218     }
 219     */
 220     hmmTemp.delete();
 221     outTemp.delete();
 222     inputTemp.delete();
 223   }
 224
 225   private void prepareAlignment()
 226   {
 227     // hmmSeqs = alignment.getHMMConsensusSequences(true);
 228     msa = af.gatherSequencesForAlignment();
 229   }
 230
 231   private void displayResults(boolean newFrame)
 232   {
 233     AlignmentOrder[] arrOrders = allOrders
 234             .toArray(new AlignmentOrder[allOrders.size()]);
 235     Object[] newview = msa.getUpdatedView(allResults,
 236             arrOrders, '-');
 237     SequenceI[] alignment = (SequenceI[]) newview[0];
 238     HiddenColumns hidden = (HiddenColumns) newview[1];
 239     Alignment al = new Alignment(alignment);
 240     al.setProperty("Alignment Program", "hmmalign");
 241     if (dataset != null)
 242     {
 243       al.setDataset(dataset);
 244     }
 245
 246     if (newFrame)
 247     {
 248       displayInNewFrame(al, allOrders, hidden);
 249     }
 250   }
 251
 252   private void displayInNewFrame(AlignmentI al,
 253           List<AlignmentOrder> alorders, HiddenColumns hidden)
 254   {
 255     AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
 256             AlignFrame.DEFAULT_HEIGHT);
 257
 258     // initialise with same renderer settings as in parent alignframe.
 259     af.getFeatureRenderer().transferSettings(this.featureSettings);
 260
 261     if (allOrders.size() > 0)
 262     {
 263       addSortByMenuItems(af, allOrders);
 264     }
 265
 266     // TODO: refactor retrieve and show as new splitFrame as Desktop method
 267
 268     /*
 269      * If alignment was requested from one half of a SplitFrame, show in a
 270      * SplitFrame with the other pane similarly aligned.
 271      */
 272     AlignFrame requestedBy = this.af;
 273     if (requestedBy != null && requestedBy.getSplitViewContainer() != null
 274             && requestedBy.getSplitViewContainer()
 275                     .getComplement(requestedBy) != null)
 276     {
 277       AlignmentI complement = requestedBy.getSplitViewContainer()
 278               .getComplement(requestedBy);
 279       String complementTitle = requestedBy.getSplitViewContainer()
 280               .getComplementTitle(requestedBy);
 281       // becomes null if the alignment window was closed before the alignment
 282       // job finished.
 283       AlignmentI copyComplement = new Alignment(complement);
 284       // todo should this be done by copy constructor?
 285       copyComplement.setGapCharacter(complement.getGapCharacter());
 286       // share the same dataset (and the mappings it holds)
 287       copyComplement.setDataset(complement.getDataset());
 288       copyComplement.alignAs(al);
 289       if (copyComplement.getHeight() > 0)
 290       {
 291         af.setTitle(this.af.getTitle());
 292         AlignFrame af2 = new AlignFrame(copyComplement,
 293                 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 294         af2.setTitle(complementTitle);
 295         String linkedTitle = MessageManager
 296                 .getString("label.linked_view_title");
 297         JInternalFrame splitFrame = new SplitFrame(
 298                 al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
 299         Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 300         return;
 301       }
 302     }
 303
 304     /*
 305      * Not from SplitFrame, or failed to created a complementary alignment
 306      */
 307     Desktop.addInternalFrame(af, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
 308             AlignFrame.DEFAULT_HEIGHT);
 309   }
 310
 311   /**
 312    * Add sort order options to the AlignFrame menus.
 313    *
 314    * @param af
 315    * @param alorders
 316    */
 317   protected void addSortByMenuItems(AlignFrame af,
 318           List<AlignmentOrder> alorders)
 319   {
 320     // update orders
 321     if (alorders.size() == 1)
 322     {
 323       af.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
 324     }
 325     else
 326     {
 327       // construct a non-redundant ordering set
 328       List<String> names = new ArrayList<>();
 329       for (int i = 0, l = alorders.size(); i < l; i++)
 330       {
 331         String orderName = " Region " + i;
 332         int j = i + 1;
 333
 334         while (j < l)
 335         {
 336           if (alorders.get(i).equals(alorders.get(j)))
 337           {
 338             alorders.remove(j);
 339             l--;
 340             orderName += "," + j;
 341           }
 342           else
 343           {
 344             j++;
 345           }
 346         }
 347
 348         if (i == 0 && j == 1)
 349         {
 350           names.add("");
 351         }
 352         else
 353         {
 354           names.add(orderName);
 355         }
 356       }
 357       for (int i = 0, l = alorders.size(); i < l; i++)
 358       {
 359         af.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
 360                 alorders.get(i));
 361       }
 362     }
 363   }
 364
 365   }
 366
 367