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         List<SequenceI> seqs = alignment
  77                 .getHMMConsensusSequences(true);
  78         cmds.setHmmSeqs(seqs);
  79         if (group != null)
  80         {
  81           SequenceI[] array = group.getSelectionAsNewSequences(alignment);
  82
  83           cmds.exportData(array, stoTemp, null, null);
  84         }
  85         else
  86         {
  87           if (!alignment.isAligned())
  88           {
  89             alignment.padGaps();
  90           }
  91           cmds.exportData(alignment.getSequencesArray(), stoTemp, null,
  92                   null);
  93         }
  94     } catch (FileNotFoundException e)
  95     {
  96       // TODO Auto-generated catch block
  97       e.printStackTrace();
  98
  99     }
 100     try
 101     {
 102         boolean ran = runCommand();
 103         if (!ran)
 104         {
 105           JvOptionPane.showInternalMessageDialog(af,
 106                   MessageManager.getString("warn.hmmbuild_failed"));
 107           return;
 108         }
 109     } catch (IOException | InterruptedException e)
 110     {
 111       // TODO Auto-generated catch block
 112       e.printStackTrace();
 113     }
 114     try
 115     {
 116
 117       importData();
 118     } catch (IOException | InterruptedException e)
 119     {
 120       // TODO Auto-generated catch block
 121       e.printStackTrace();
 122     }
 123     } catch (Exception e)
 124     {
 125       e.printStackTrace();
 126     } finally
 127     {
 128       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 129               barID);
 130     }
 131   }
 132
 133
 134
 135
 136   private boolean runCommand() throws IOException, InterruptedException
 137   {
 138     File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
 139     if (!file.canExecute())
 140     {
 141       return false;
 142     }
 143     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
 144             + af.getName() + cmds.SPACE;
 145     if (!alignment.isNucleotide())
 146     {
 147       command += cmds.FORCEAMINO; // TODO check for rna
 148     }
 149     else
 150     {
 151       command += cmds.FORCEDNA;
 152     }
 153
 154     command += hmmTemp.getAbsolutePath()
 155             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 156     return cmds.runCommand(command);
 157   }
 158
 159   private void importData() throws IOException, InterruptedException
 160   {
 161     cmds.addHMMConsensusSequences(af);
 162     af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 163             FileFormat.HMMER3, null);
 164     hmmTemp.delete();
 165     stoTemp.delete();
 166   }
 167
 168   public boolean canRun()
 169   {
 170     return canRun;
 171   }
 172
 173
 174
 175 }