src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.HiddenMarkovModel;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignFrame;
   8 import jalview.gui.Preferences;
   9 import jalview.io.DataSourceType;
  10 import jalview.io.FileFormat;
  11 import jalview.util.MessageManager;
  12
  13 import java.io.FileNotFoundException;
  14 import java.io.IOException;
  15 import java.util.Map;
  16
  17 public class HMMBuildThread implements Runnable
  18 {
  19
  20   AlignFrame af;
  21   AlignmentI alignment;
  22
  23   long barID;
  24
  25   Map<Integer, SequenceI> hmmSeqs;
  26
  27   public HMMBuildThread(AlignFrame af)
  28   {
  29     this.af = af;
  30     alignment = af.getViewport().getAlignment();
  31   }
  32
  33   @Override
  34   public void run()
  35   {
  36     barID = System.currentTimeMillis();
  37     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  38             barID);
  39     HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  40
  41     try
  42     {
  43     try
  44     {
  45         hmmSeqs = alignment.getHMMConsensusSequences(true);
  46         HMMERCommands.exportData(alignment, true, false,
  47                 new HiddenMarkovModel());
  48     } catch (FileNotFoundException e)
  49     {
  50       // TODO Auto-generated catch block
  51       e.printStackTrace();
  52
  53     }
  54     try
  55     {
  56       runCommand();
  57     } catch (IOException | InterruptedException e)
  58     {
  59       // TODO Auto-generated catch block
  60       e.printStackTrace();
  61     }
  62     try
  63     {
  64       importData();
  65     } catch (IOException | InterruptedException e)
  66     {
  67       // TODO Auto-generated catch block
  68       e.printStackTrace();
  69     }
  70     } catch (Exception e)
  71     {
  72
  73     } finally
  74     {
  75       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  76               barID);
  77     }
  78   }
  79
  80
  81
  82
  83   private void runCommand() throws IOException, InterruptedException
  84   {
  85     final String command = HMMERCommands.HMMERFOLDER
  86             + HMMERCommands.HMMBUILD + HMMERCommands.NAME
  87             + af.getName() + HMMERCommands.SPACE
  88             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
  89             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
  90     HMMERCommands.runCommand(command);
  91   }
  92
  93   private void importData() throws IOException, InterruptedException
  94   {
  95     af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
  96             FileFormat.HMMER3, null);
  97     for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
  98     {
  99       SequenceI seq = entry.getValue();
 100       Integer pos = entry.getKey();
 101       HMMERCommands.addHMMConsensusSequence(af, seq, pos);
 102     }
 103     af.alignPanel.alignmentChanged();
 104   }
 105
 106
 107
 108
 109 }