src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.Sequence;
   6 import jalview.datamodel.SequenceGroup;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.AlignFrame;
   9 import jalview.gui.JvOptionPane;
  10 import jalview.gui.Preferences;
  11 import jalview.io.DataSourceType;
  12 import jalview.io.FileFormat;
  13 import jalview.util.MessageManager;
  14
  15 import java.io.File;
  16 import java.io.FileNotFoundException;
  17 import java.io.IOException;
  18 import java.util.List;
  19
  20 import javax.swing.JOptionPane;
  21
  22 public class HMMBuildThread implements Runnable
  23 {
  24   HMMERCommands cmds = new HMMERCommands();
  25   AlignFrame af;
  26   AlignmentI alignment;
  27
  28   SequenceGroup group;
  29
  30   boolean canRun = true;
  31
  32   File hmmTemp = null;
  33
  34   File stoTemp = null;
  35
  36   long barID;
  37
  38   public HMMBuildThread(AlignFrame af)
  39   {
  40     this.af = af;
  41     if (af.getViewport().getSelectionGroup() != null)
  42     {
  43       group = af.getViewport().getSelectionGroup();
  44     }
  45     alignment = af.getViewport().getAlignment();
  46
  47   }
  48
  49   @Override
  50   public void run()
  51   {
  52     barID = System.currentTimeMillis();
  53     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  54             barID);
  55     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  56     if (alignment == null && group == null)
  57     {
  58       JOptionPane.showMessageDialog(af,
  59               MessageManager.getString("label.no_sequence_data"));
  60       return;
  61     }
  62     try
  63     {
  64       hmmTemp = File.createTempFile("hmm", ".hmm");
  65       hmmTemp.deleteOnExit();
  66       stoTemp = File.createTempFile("output", ".sto");
  67       stoTemp.deleteOnExit();
  68     } catch (IOException e1)
  69     {
  70       e1.printStackTrace();
  71     }
  72
  73     try
  74     {
  75     try
  76     {
  77         SequenceI[] array;
  78         List<SequenceI> seqs = alignment
  79                 .getHMMConsensusSequences(true);
  80         cmds.setHmmSeqs(seqs);
  81         if (group != null)
  82         {
  83           array = group.getSelectionAsNewSequences(alignment);
  84         }
  85         else
  86         {
  87           if (!alignment.isAligned())
  88           {
  89             alignment.padGaps();
  90           }
  91           array = alignment.getSequencesArray();
  92         }
  93         SequenceI[] newArr = new SequenceI[array.length];
  94         int index = 0;
  95         for (SequenceI seq : array)
  96         {
  97           newArr[index] = new Sequence(seq);
  98           index++;
  99         }
 100         cmds.uniquifySequences(newArr);
 101         cmds.exportData(newArr, stoTemp, null, null);
 102         jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 103
 104     } catch (FileNotFoundException e)
 105     {
 106       // TODO Auto-generated catch block
 107       e.printStackTrace();
 108
 109     }
 110     try
 111     {
 112         boolean ran = runCommand();
 113         if (!ran)
 114         {
 115           JvOptionPane.showInternalMessageDialog(af,
 116                   MessageManager.getString("warn.hmmbuild_failed"));
 117           return;
 118         }
 119     } catch (IOException | InterruptedException e)
 120     {
 121       // TODO Auto-generated catch block
 122       e.printStackTrace();
 123     }
 124     try
 125     {
 126
 127       importData();
 128     } catch (IOException | InterruptedException e)
 129     {
 130       // TODO Auto-generated catch block
 131       e.printStackTrace();
 132     }
 133     } catch (Exception e)
 134     {
 135       e.printStackTrace();
 136     } finally
 137     {
 138       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 139               barID);
 140     }
 141   }
 142
 143
 144
 145
 146   private boolean runCommand() throws IOException, InterruptedException
 147   {
 148     File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
 149     if (!file.canExecute())
 150     {
 151       return false;
 152     }
 153     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
 154             + af.getName() + cmds.SPACE;
 155     if (!alignment.isNucleotide())
 156     {
 157       command += cmds.FORCEAMINO; // TODO check for rna
 158     }
 159     else
 160     {
 161       command += cmds.FORCEDNA;
 162     }
 163
 164     command += hmmTemp.getAbsolutePath()
 165             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 166     return cmds.runCommand(command);
 167   }
 168
 169   private void importData() throws IOException, InterruptedException
 170   {
 171     cmds.addHMMConsensusSequences(af);
 172     af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 173             FileFormat.HMMER3, null);
 174     hmmTemp.delete();
 175     stoTemp.delete();
 176   }
 177
 178   public boolean canRun()
 179   {
 180     return canRun;
 181   }
 182
 183
 184
 185 }