src/jalview/hmmer/HMMBuildThread.java

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