src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.gui.AlignFrame;
   7 import jalview.gui.Preferences;
   8 import jalview.io.DataSourceType;
   9 import jalview.io.FileFormat;
  10 import jalview.util.MessageManager;
  11
  12 import java.io.File;
  13 import java.io.FileNotFoundException;
  14 import java.io.IOException;
  15 import java.util.Map;
  16
  17 public class HMMBuildThread implements Runnable
  18 {
  19   HMMERCommands cmds = new HMMERCommands();
  20   AlignFrame af;
  21   AlignmentI alignment;
  22
  23   File hmmTemp = null;
  24
  25   File stoTemp = null;
  26
  27   long barID;
  28
  29   Map<Integer, SequenceI> hmmSeqs;
  30
  31   public HMMBuildThread(AlignFrame af)
  32   {
  33     this.af = af;
  34     alignment = af.getViewport().getAlignment();
  35   }
  36
  37   @Override
  38   public void run()
  39   {
  40     barID = System.currentTimeMillis();
  41     System.out.println(System.getProperty("java.io.tmpdir"));
  42     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  43             barID);
  44     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  45     try
  46     {
  47       hmmTemp = File.createTempFile("hmm", ".hmm");
  48       hmmTemp.deleteOnExit();
  49       stoTemp = File.createTempFile("output", ".sto");
  50       stoTemp.deleteOnExit();
  51     } catch (IOException e1)
  52     {
  53       e1.printStackTrace();
  54     }
  55
  56     try
  57     {
  58     try
  59     {
  60         hmmSeqs = alignment.getHMMConsensusSequences(true);
  61         if (!alignment.isAligned())
  62         {
  63           alignment.padGaps();
  64         }
  65         cmds.exportData(alignment.getSequencesArray(), stoTemp, null, null);
  66     } catch (FileNotFoundException e)
  67     {
  68       // TODO Auto-generated catch block
  69       e.printStackTrace();
  70
  71     }
  72     try
  73     {
  74       runCommand();
  75     } catch (IOException | InterruptedException e)
  76     {
  77       // TODO Auto-generated catch block
  78       e.printStackTrace();
  79     }
  80     try
  81     {
  82
  83       importData();
  84     } catch (IOException | InterruptedException e)
  85     {
  86       // TODO Auto-generated catch block
  87       e.printStackTrace();
  88     }
  89     } catch (Exception e)
  90     {
  91
  92     } finally
  93     {
  94       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  95               barID);
  96     }
  97   }
  98
  99
 100
 101
 102   private void runCommand() throws IOException, InterruptedException
 103   {
 104     final String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
 105             + af.getName() + cmds.SPACE + hmmTemp.getAbsolutePath()
 106             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 107     cmds.runCommand(command);
 108   }
 109
 110   private void importData() throws IOException, InterruptedException
 111   {
 112     af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 113             FileFormat.HMMER3, null);
 114     for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
 115     {
 116       SequenceI seq = entry.getValue();
 117       Integer pos = entry.getKey();
 118       cmds.addHMMConsensusSequence(af, seq, pos);
 119     }
 120     af.alignPanel.alignmentChanged();
 121     hmmTemp.delete();
 122     stoTemp.delete();
 123   }
 124
 125
 126
 127
 128 }