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.File;
  14 import java.io.FileNotFoundException;
  15 import java.io.IOException;
  16 import java.util.Map;
  17
  18 public class HMMBuildThread implements Runnable
  19 {
  20   HMMERCommands cmds = new HMMERCommands();
  21   AlignFrame af;
  22   AlignmentI alignment;
  23
  24   long barID;
  25
  26   Map<Integer, SequenceI> hmmSeqs;
  27
  28   public HMMBuildThread(AlignFrame af)
  29   {
  30     this.af = af;
  31     alignment = af.getViewport().getAlignment();
  32   }
  33
  34   @Override
  35   public void run()
  36   {
  37     barID = System.currentTimeMillis();
  38     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  39             barID);
  40     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  41     try
  42     {
  43       cmds.HMMBUFFER = File.createTempFile("hmm", ".hmm").getAbsolutePath()
  44               + cmds.SPACE;
  45       cmds.ALIGNMENTBUFFER = File.createTempFile("output", ".sto")
  46               .getAbsolutePath() + cmds.SPACE;
  47     } catch (IOException e1)
  48     {
  49       e1.printStackTrace();
  50     }
  51
  52     try
  53     {
  54     try
  55     {
  56         hmmSeqs = alignment.getHMMConsensusSequences(true);
  57         cmds.exportData(alignment, true, false,
  58                 new HiddenMarkovModel());
  59     } catch (FileNotFoundException e)
  60     {
  61       // TODO Auto-generated catch block
  62       e.printStackTrace();
  63
  64     }
  65     try
  66     {
  67       runCommand();
  68     } catch (IOException | InterruptedException e)
  69     {
  70       // TODO Auto-generated catch block
  71       e.printStackTrace();
  72     }
  73     try
  74     {
  75       importData();
  76     } catch (IOException | InterruptedException e)
  77     {
  78       // TODO Auto-generated catch block
  79       e.printStackTrace();
  80     }
  81     } catch (Exception e)
  82     {
  83
  84     } finally
  85     {
  86       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  87               barID);
  88     }
  89   }
  90
  91
  92
  93
  94   private void runCommand() throws IOException, InterruptedException
  95   {
  96     final String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
  97             + af.getName() + cmds.SPACE + cmds.HMMBUFFER
  98             + cmds.ALIGNMENTBUFFER;
  99     cmds.runCommand(command);
 100   }
 101
 102   private void importData() throws IOException, InterruptedException
 103   {
 104     af.loadJalviewDataFile(cmds.HMMBUFFER, DataSourceType.FILE,
 105             FileFormat.HMMER3, null);
 106     for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
 107     {
 108       SequenceI seq = entry.getValue();
 109       Integer pos = entry.getKey();
 110       cmds.addHMMConsensusSequence(af, seq, pos);
 111     }
 112     af.alignPanel.alignmentChanged();
 113   }
 114
 115
 116
 117
 118 }