src/jalview/hmmer/HMMBuildThread.java

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