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       exportAlignment();
  43     } catch (FileNotFoundException e)
  44     {
  45       // TODO Auto-generated catch block
  46       e.printStackTrace();
  47
  48     }
  49     try
  50     {
  51       runCommand();
  52     } catch (IOException | InterruptedException e)
  53     {
  54       // TODO Auto-generated catch block
  55       e.printStackTrace();
  56     }
  57     try
  58     {
  59       importData();
  60     } catch (IOException | InterruptedException e)
  61     {
  62       // TODO Auto-generated catch block
  63       e.printStackTrace();
  64     }
  65     } catch (Exception e)
  66     {
  67
  68     } finally
  69     {
  70       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  71               barID);
  72     }
  73   }
  74
  75
  76   private void exportAlignment() throws IOException
  77   {
  78     hmmSeqs = alignment.getHMMConsensusSequences(true);
  79     if (!alignment.isAligned())
  80     {
  81       alignment.padGaps();
  82     }
  83     HMMERCommands.exportData(alignment, true, false,
  84             new HiddenMarkovModel());
  85   }
  86
  87   private void runCommand() throws IOException, InterruptedException
  88   {
  89     final String command = HMMERCommands.HMMBUILD + HMMERCommands.NAME
  90             + af.getName() + HMMERCommands.SPACE
  91             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
  92             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
  93     HMMERCommands.runCommand(command);
  94   }
  95
  96   private void importData() throws IOException, InterruptedException
  97   {
  98     af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
  99             FileFormat.HMMER3, null);
 100     for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
 101     {
 102       SequenceI seq = entry.getValue();
 103       Integer pos = entry.getKey();
 104       HMMERCommands.addHMMConsensusSequence(af, seq, pos);
 105     }
 106     af.alignPanel.alignmentChanged();
 107   }
 108
 109
 110
 111
 112 }