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.JvOptionPane;
  14 import jalview.gui.Preferences;
  15 import jalview.gui.SplitFrame;
  16 import jalview.io.DataSourceType;
  17 import jalview.io.StockholmFile;
  18 import jalview.util.MessageManager;
  19 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  20
  21 import java.io.File;
  22 import java.io.IOException;
  23 import java.util.ArrayList;
  24 import java.util.List;
  25 import java.util.Map;
  26
  27 import javax.swing.JInternalFrame;
  28 import javax.swing.JOptionPane;
  29
  30 public class HMMAlignThread implements Runnable
  31 {
  32
  33   /**
  34    * feature settings from view that job was associated with
  35    */
  36   protected FeatureRendererSettings featureSettings = null;
  37
  38   HMMERCommands cmds = new HMMERCommands();
  39
  40   AlignFrame af;
  41
  42   AlignmentI alignment;
  43
  44   AlignmentI dataset;
  45
  46   List<AlignmentOrder> orders;
  47
  48   AlignmentView msa;
  49
  50   HiddenMarkovModel hmm;
  51
  52   boolean newFrame;
  53
  54   long barID;
  55
  56   Map<Integer, SequenceI> hmmSeqs;
  57
  58   File hmmTemp = null;
  59
  60   File outTemp = null;
  61
  62   File inputTemp = null;
  63
  64   List<AlignmentOrder> allOrders;
  65
  66   SequenceI[][] allResults;
  67
  68   public HMMAlignThread(AlignFrame af, boolean createNewFrame)
  69   {
  70     this.af = af;
  71     alignment = af.getViewport().getAlignment();
  72     if (alignment.getDataset() != null)
  73     {
  74       dataset = alignment.getDataset();
  75     }
  76     newFrame = createNewFrame;
  77     featureSettings = af.getFeatureRenderer().getSettings();
  78   }
  79
  80   @Override
  81   public void run()
  82   {
  83     if (af.getSelectedHMM() == null)
  84     {
  85       JOptionPane.showMessageDialog(af,
  86               MessageManager.getString("warn.no_selected_hmm"));
  87       return;
  88     }
  89     else
  90     {
  91       hmm = af.getSelectedHMM();
  92     }
  93     barID = System.currentTimeMillis();
  94     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
  95             barID);
  96     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  97
  98     // if (!alignment.isAligned())
  99     // {
 100     // alignment.padGaps();
 101     // }
 102     prepareAlignment();
 103     SequenceI[][] subAlignments = msa.getVisibleContigs('-');
 104     allOrders = new ArrayList<>();
 105     allResults = new SequenceI[subAlignments.length][];
 106     int job = 0;
 107     for (SequenceI[] seqs : subAlignments)
 108     {
 109       cmds.uniquifySequences(seqs);
 110       try
 111       {
 112         createTemporaryFiles();
 113       } catch (IOException e2)
 114       {
 115         e2.printStackTrace();
 116       }
 117       try
 118       {
 119         cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
 120                 hmmTemp.getAbsoluteFile());
 121       } catch (IOException e1)
 122       {
 123         e1.printStackTrace();
 124       }
 125       try
 126       {
 127         boolean ran = runCommand();
 128         if (!ran)
 129         {
 130           JvOptionPane.showInternalMessageDialog(af,
 131                   MessageManager.getString("warn.hmmalign_failed"));
 132           return;
 133         }
 134       } catch (IOException | InterruptedException e)
 135       {
 136         e.printStackTrace();
 137       }
 138       try
 139       {
 140         importData(job);
 141       } catch (IOException | InterruptedException e)
 142       {
 143         // TODO Auto-generated catch block
 144         e.printStackTrace();
 145       }
 146       job++;
 147     }
 148
 149     displayResults(newFrame);
 150
 151     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
 152             barID);
 153
 154   }
 155
 156   private void createTemporaryFiles() throws IOException
 157   {
 158     hmmTemp = File.createTempFile("hmm", ".hmm");
 159     hmmTemp.deleteOnExit();
 160     outTemp = File.createTempFile("output", ".sto");
 161     outTemp.deleteOnExit();
 162     inputTemp = File.createTempFile("input", ".sto");
 163     inputTemp.deleteOnExit();
 164   }
 165
 166   private boolean runCommand() throws IOException, InterruptedException
 167   {
 168     File file = new File(cmds.HMMERFOLDER + "/binaries/hmmalign.exe");
 169     if (!file.canExecute())
 170     {
 171       return false;
 172     }
 173     String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
 174     String version = Cache.getProperty("HMMER_VERSION");
 175     if (!"3.1b2".equals(version))
 176     {
 177       command += cmds.ALLCOL;
 178     }
 179     boolean trim = true;
 180     String bool = Cache.getProperty("TRIM_TERMINI");
 181     if ("false".equals(bool))
 182     {
 183       trim = false;
 184     }
 185     if (trim)
 186     {
 187       command += cmds.TRIM;
 188     }
 189     command += " -o " + inputTemp.getAbsolutePath() + cmds.SPACE
 190             + hmmTemp.getAbsolutePath() + cmds.SPACE
 191             + outTemp.getAbsolutePath();
 192     return cmds.runCommand(command);
 193   }
 194
 195   private void importData(int index)
 196           throws IOException, InterruptedException
 197   {
 198     StockholmFile file = new StockholmFile(inputTemp.getAbsolutePath(),
 199             DataSourceType.FILE);
 200     SequenceI[] result = file.getSeqsAsArray();
 201     AlignmentOrder msaorder = new AlignmentOrder(result);
 202     jalview.analysis.AlignmentSorter.recoverOrder(result);
 203     jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
 204     allOrders.add(msaorder);
 205     allResults[index] = result;
 206     hmmTemp.delete();
 207     outTemp.delete();
 208     inputTemp.delete();
 209   }
 210
 211   private void prepareAlignment()
 212   {
 213     // hmmSeqs = alignment.getHMMConsensusSequences(true);
 214     msa = af.gatherSequencesForAlignment();
 215   }
 216
 217   private void displayResults(boolean newFrame)
 218   {
 219     AlignmentOrder[] arrOrders = allOrders
 220             .toArray(new AlignmentOrder[allOrders.size()]);
 221     Object[] newview = msa.getUpdatedView(allResults,
 222             arrOrders, '-');
 223     SequenceI[] alignment = (SequenceI[]) newview[0];
 224     HiddenColumns hidden = (HiddenColumns) newview[1];
 225     Alignment al = new Alignment(alignment);
 226     al.setProperty("Alignment Program", "hmmalign");
 227     if (dataset != null)
 228     {
 229       al.setDataset(dataset);
 230     }
 231
 232     if (newFrame)
 233     {
 234       displayInNewFrame(al, allOrders, hidden);
 235     }
 236   }
 237
 238   private void displayInNewFrame(AlignmentI al,
 239           List<AlignmentOrder> alorders, HiddenColumns hidden)
 240   {
 241     AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
 242             AlignFrame.DEFAULT_HEIGHT);
 243
 244     // initialise with same renderer settings as in parent alignframe.
 245     af.getFeatureRenderer().transferSettings(this.featureSettings);
 246
 247     if (allOrders.size() > 0)
 248     {
 249       addSortByMenuItems(af, allOrders);
 250     }
 251
 252     // TODO: refactor retrieve and show as new splitFrame as Desktop method
 253
 254     /*
 255      * If alignment was requested from one half of a SplitFrame, show in a
 256      * SplitFrame with the other pane similarly aligned.
 257      */
 258     AlignFrame requestedBy = this.af;
 259     if (requestedBy != null && requestedBy.getSplitViewContainer() != null
 260             && requestedBy.getSplitViewContainer()
 261                     .getComplement(requestedBy) != null)
 262     {
 263       AlignmentI complement = requestedBy.getSplitViewContainer()
 264               .getComplement(requestedBy);
 265       String complementTitle = requestedBy.getSplitViewContainer()
 266               .getComplementTitle(requestedBy);
 267       // becomes null if the alignment window was closed before the alignment
 268       // job finished.
 269       AlignmentI copyComplement = new Alignment(complement);
 270       // todo should this be done by copy constructor?
 271       copyComplement.setGapCharacter(complement.getGapCharacter());
 272       // share the same dataset (and the mappings it holds)
 273       copyComplement.setDataset(complement.getDataset());
 274       copyComplement.alignAs(al);
 275       if (copyComplement.getHeight() > 0)
 276       {
 277         af.setTitle(this.af.getTitle());
 278         AlignFrame af2 = new AlignFrame(copyComplement,
 279                 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 280         af2.setTitle(complementTitle);
 281         String linkedTitle = MessageManager
 282                 .getString("label.linked_view_title");
 283         JInternalFrame splitFrame = new SplitFrame(
 284                 al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
 285         Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 286         return;
 287       }
 288     }
 289
 290     /*
 291      * Not from SplitFrame, or failed to created a complementary alignment
 292      */
 293     Desktop.addInternalFrame(af, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
 294             AlignFrame.DEFAULT_HEIGHT);
 295   }
 296
 297   /**
 298    * Add sort order options to the AlignFrame menus.
 299    *
 300    * @param af
 301    * @param alorders
 302    */
 303   protected void addSortByMenuItems(AlignFrame af,
 304           List<AlignmentOrder> alorders)
 305   {
 306     // update orders
 307     if (alorders.size() == 1)
 308     {
 309       af.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
 310     }
 311     else
 312     {
 313       // construct a non-redundant ordering set
 314       List<String> names = new ArrayList<>();
 315       for (int i = 0, l = alorders.size(); i < l; i++)
 316       {
 317         String orderName = " Region " + i;
 318         int j = i + 1;
 319
 320         while (j < l)
 321         {
 322           if (alorders.get(i).equals(alorders.get(j)))
 323           {
 324             alorders.remove(j);
 325             l--;
 326             orderName += "," + j;
 327           }
 328           else
 329           {
 330             j++;
 331           }
 332         }
 333
 334         if (i == 0 && j == 1)
 335         {
 336           names.add("");
 337         }
 338         else
 339         {
 340           names.add(orderName);
 341         }
 342       }
 343       for (int i = 0, l = alorders.size(); i < l; i++)
 344       {
 345         af.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
 346                 alorders.get(i));
 347       }
 348     }
 349   }
 350
 351   }
 352
 353