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.Sequence;
   7 import jalview.datamodel.SequenceGroup;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.gui.AlignFrame;
  10 import jalview.gui.AlignViewport;
  11 import jalview.gui.JvOptionPane;
  12 import jalview.gui.Preferences;
  13 import jalview.io.DataSourceType;
  14 import jalview.io.FileFormat;
  15 import jalview.io.FileLoader;
  16 import jalview.io.FileParse;
  17 import jalview.io.HMMFile;
  18 import jalview.util.MessageManager;
  19
  20 import java.io.File;
  21 import java.io.FileNotFoundException;
  22 import java.io.IOException;
  23 import java.util.List;
  24
  25 import javax.swing.JOptionPane;
  26
  27 public class HMMBuildThread implements Runnable
  28 {
  29   HMMERCommands cmds = new HMMERCommands();
  30   AlignFrame af;
  31
  32   AlignViewport viewport;
  33   AlignmentI alignment;
  34   SequenceGroup group;
  35
  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)
  57   {
  58     this.af = af;
  59     if (af.getViewport().getSelectionGroup() != null)
  60     {
  61       group = af.getViewport().getSelectionGroup();
  62       forGroup = true;
  63     }
  64     viewport = af.getViewport();
  65     alignment = viewport.getAlignment();
  66
  67   }
  68
  69   /**
  70    * Builds a HMM from an alignment, then imports and adds it to the alignment.
  71    */
  72   @Override
  73   public void run()
  74   {
  75     barID = System.currentTimeMillis();
  76     if (af != null)
  77     {
  78     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  79             barID);
  80     }
  81     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  82     if (alignment == null && group == null)
  83     {
  84       JOptionPane.showMessageDialog(af,
  85               MessageManager.getString("warn.no_sequence_data"));
  86       return;
  87     }
  88     try
  89     {
  90       hmmTemp = File.createTempFile("hmm", ".hmm");
  91       hmmTemp.deleteOnExit();
  92       stoTemp = File.createTempFile("output", ".sto");
  93       stoTemp.deleteOnExit();
  94     } catch (IOException e1)
  95     {
  96       e1.printStackTrace();
  97     }
  98
  99     try
 100     {
 101     try
 102     {
 103         SequenceI[] array;
 104         List<SequenceI> seqs = alignment
 105                 .getHMMConsensusSequences(true);
 106         cmds.setHmmSeqs(seqs);
 107         if (forGroup)
 108         {
 109           array = group.getSelectionAsNewSequences(alignment);
 110         }
 111         else
 112         {
 113           if (!alignment.isAligned())
 114           {
 115             alignment.padGaps();
 116           }
 117           array = alignment.getSequencesArray();
 118         }
 119         if (array.length < 1)
 120         {
 121           if (af != null)
 122           {
 123             JOptionPane.showMessageDialog(af,
 124                   MessageManager.getString("warn.no_sequence_data"));
 125           }
 126           return;
 127         }
 128         SequenceI[] newArr = new SequenceI[array.length];
 129         int index = 0;
 130         for (SequenceI seq : array)
 131         {
 132           newArr[index] = new Sequence(seq);
 133           index++;
 134         }
 135
 136         cmds.uniquifySequences(newArr);
 137         cmds.exportData(newArr, stoTemp, null, null);
 138         jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 139
 140     } catch (FileNotFoundException e)
 141     {
 142       // TODO Auto-generated catch block
 143       e.printStackTrace();
 144
 145     }
 146     try
 147     {
 148         boolean ran = runCommand();
 149         if (!ran)
 150         {
 151           if (af != null)
 152           {
 153             JvOptionPane.showInternalMessageDialog(af,
 154                   MessageManager.getString("warn.hmmbuild_failed"));
 155           }
 156           return;
 157         }
 158     } catch (IOException | InterruptedException e)
 159     {
 160       // TODO Auto-generated catch block
 161       e.printStackTrace();
 162     }
 163     try
 164     {
 165
 166       importData();
 167     } catch (IOException | InterruptedException e)
 168     {
 169       // TODO Auto-generated catch block
 170       e.printStackTrace();
 171     }
 172     } catch (Exception e)
 173     {
 174       e.printStackTrace();
 175     } finally
 176     {
 177       if (af != null)
 178       {
 179         af.setProgressBar(
 180                 MessageManager.getString("status.running_hmmbuild"),
 181               barID);
 182       }
 183     }
 184   }
 185
 186
 187
 188   /**
 189    * Executes the hmmbuild command in the command line.
 190    *
 191    * @return
 192    * @throws IOException
 193    * @throws InterruptedException
 194    */
 195   private boolean runCommand() throws IOException, InterruptedException
 196   {
 197     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 198     if (!file.canExecute())
 199     {
 200       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 201       {
 202         if (!file.canExecute())
 203         {
 204           return false;
 205         }
 206       }
 207     }
 208     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
 209     if (forGroup)
 210     {
 211       command += group.getName();
 212     }
 213     else
 214     {
 215       String name = null;
 216       if (af != null)
 217       {
 218         name = af.getTitle();
 219       }
 220       if (name == null)
 221       {
 222         name = "Alignment";
 223       }
 224       command += name;
 225     }
 226     command += cmds.SPACE;
 227     if (!alignment.isNucleotide())
 228     {
 229       command += cmds.FORCEAMINO; // TODO check for rna
 230     }
 231     else
 232     {
 233       command += cmds.FORCEDNA;
 234     }
 235
 236     command += hmmTemp.getAbsolutePath()
 237             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 238     return cmds.runCommand(command);
 239   }
 240
 241   /**
 242    * Imports the .hmm file produced by hmmbuild.
 243    *
 244    * @throws IOException
 245    * @throws InterruptedException
 246    */
 247   private void importData() throws IOException, InterruptedException
 248   {
 249     if (af != null)
 250     {
 251       cmds.addHMMConsensusSequences(af);
 252
 253       FileLoader loader = new FileLoader();
 254       loader.LoadFileOntoAlignmentWaitTillLoaded(viewport,
 255               hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 256               FileFormat.HMMER3);
 257     }
 258     else
 259     {
 260       HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
 261               DataSourceType.FILE));
 262       alignment.addSequence(file.getSeqsAsArray()[0]);
 263     }
 264     hmmTemp.delete();
 265     stoTemp.delete();
 266   }
 267
 268   /**
 269    * Runs hmmbuild, and waits for the results to be imported before continuing
 270    */
 271   public void hmmbuildWaitTillComplete()
 272   {
 273     Thread loader = new Thread(this);
 274     loader.start();
 275
 276     while (loader.isAlive())
 277     {
 278       try
 279       {
 280         Thread.sleep(500);
 281       } catch (Exception ex)
 282       {
 283       }
 284     }
 285   }
 286 }