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.io.FileLoader;
  14 import jalview.util.MessageManager;
  15
  16 import java.io.File;
  17 import java.io.FileNotFoundException;
  18 import java.io.IOException;
  19 import java.util.List;
  20
  21 import javax.swing.JOptionPane;
  22
  23 public class HMMBuildThread implements Runnable
  24 {
  25   HMMERCommands cmds = new HMMERCommands();
  26   AlignFrame af;
  27   AlignmentI alignment;
  28   SequenceGroup group;
  29
  30   boolean forGroup = false;
  31   boolean canRun = true;
  32
  33   File hmmTemp = null;
  34
  35   File stoTemp = null;
  36
  37   long barID;
  38
  39   public HMMBuildThread(AlignFrame af)
  40   {
  41     this.af = af;
  42     if (af.getViewport().getSelectionGroup() != null)
  43     {
  44       group = af.getViewport().getSelectionGroup();
  45       forGroup = true;
  46     }
  47     alignment = af.getViewport().getAlignment();
  48
  49   }
  50
  51   @Override
  52   public void run()
  53   {
  54     barID = System.currentTimeMillis();
  55     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  56             barID);
  57     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  58     if (alignment == null && group == null)
  59     {
  60       JOptionPane.showMessageDialog(af,
  61               MessageManager.getString("label.no_sequence_data"));
  62       return;
  63     }
  64     try
  65     {
  66       hmmTemp = File.createTempFile("hmm", ".hmm");
  67       hmmTemp.deleteOnExit();
  68       stoTemp = File.createTempFile("output", ".sto");
  69       stoTemp.deleteOnExit();
  70     } catch (IOException e1)
  71     {
  72       e1.printStackTrace();
  73     }
  74
  75     try
  76     {
  77     try
  78     {
  79         SequenceI[] array;
  80         List<SequenceI> seqs = alignment
  81                 .getHMMConsensusSequences(true);
  82         cmds.setHmmSeqs(seqs);
  83         if (forGroup)
  84         {
  85           array = group.getSelectionAsNewSequences(alignment);
  86         }
  87         else
  88         {
  89           if (!alignment.isAligned())
  90           {
  91             alignment.padGaps();
  92           }
  93           array = alignment.getSequencesArray();
  94         }
  95
  96         SequenceI[] newArr = new SequenceI[array.length];
  97         int index = 0;
  98         for (SequenceI seq : array)
  99         {
 100           newArr[index] = new Sequence(seq);
 101           index++;
 102         }
 103
 104         cmds.uniquifySequences(newArr);
 105         cmds.exportData(newArr, stoTemp, null, null);
 106         jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 107
 108     } catch (FileNotFoundException e)
 109     {
 110       // TODO Auto-generated catch block
 111       e.printStackTrace();
 112
 113     }
 114     try
 115     {
 116         boolean ran = runCommand();
 117         if (!ran)
 118         {
 119           JvOptionPane.showInternalMessageDialog(af,
 120                   MessageManager.getString("warn.hmmbuild_failed"));
 121           return;
 122         }
 123     } catch (IOException | InterruptedException e)
 124     {
 125       // TODO Auto-generated catch block
 126       e.printStackTrace();
 127     }
 128     try
 129     {
 130
 131       importData();
 132     } catch (IOException | InterruptedException e)
 133     {
 134       // TODO Auto-generated catch block
 135       e.printStackTrace();
 136     }
 137     } catch (Exception e)
 138     {
 139       e.printStackTrace();
 140     } finally
 141     {
 142       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 143               barID);
 144     }
 145   }
 146
 147
 148
 149
 150   private boolean runCommand() throws IOException, InterruptedException
 151   {
 152     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 153     if (!file.canExecute())
 154     {
 155       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 156       {
 157         if (!file.canExecute())
 158         {
 159           return false;
 160         }
 161       }
 162     }
 163     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
 164     if (forGroup)
 165     {
 166       command += group.getName();
 167     }
 168     else
 169     {
 170       String name = af.getName();
 171       if (name == null)
 172       {
 173         name = "Alignment";
 174       }
 175       command += name;
 176     }
 177     command += cmds.SPACE;
 178     if (!alignment.isNucleotide())
 179     {
 180       command += cmds.FORCEAMINO; // TODO check for rna
 181     }
 182     else
 183     {
 184       command += cmds.FORCEDNA;
 185     }
 186
 187     command += hmmTemp.getAbsolutePath()
 188             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 189     return cmds.runCommand(command);
 190   }
 191
 192   private void importData() throws IOException, InterruptedException
 193   {
 194     cmds.addHMMConsensusSequences(af);
 195     FileLoader loader = new FileLoader();
 196     loader.LoadFileOntoAlignmentWaitTillLoaded(af.getViewport(),
 197             hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 198             FileFormat.HMMER3);
 199     hmmTemp.delete();
 200     stoTemp.delete();
 201   }
 202
 203   public boolean canRun()
 204   {
 205     return canRun;
 206   }
 207
 208
 209
 210 }