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("warn.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         if (array.length < 1)
  96         {
  97           JOptionPane.showMessageDialog(af,
  98                   MessageManager.getString("warn.no_sequence_data"));
  99           return;
 100         }
 101         SequenceI[] newArr = new SequenceI[array.length];
 102         int index = 0;
 103         for (SequenceI seq : array)
 104         {
 105           newArr[index] = new Sequence(seq);
 106           index++;
 107         }
 108
 109         cmds.uniquifySequences(newArr);
 110         cmds.exportData(newArr, stoTemp, null, null);
 111         jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 112
 113     } catch (FileNotFoundException e)
 114     {
 115       // TODO Auto-generated catch block
 116       e.printStackTrace();
 117
 118     }
 119     try
 120     {
 121         boolean ran = runCommand();
 122         if (!ran)
 123         {
 124           JvOptionPane.showInternalMessageDialog(af,
 125                   MessageManager.getString("warn.hmmbuild_failed"));
 126           return;
 127         }
 128     } catch (IOException | InterruptedException e)
 129     {
 130       // TODO Auto-generated catch block
 131       e.printStackTrace();
 132     }
 133     try
 134     {
 135
 136       importData();
 137     } catch (IOException | InterruptedException e)
 138     {
 139       // TODO Auto-generated catch block
 140       e.printStackTrace();
 141     }
 142     } catch (Exception e)
 143     {
 144       e.printStackTrace();
 145     } finally
 146     {
 147       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 148               barID);
 149     }
 150   }
 151
 152
 153
 154
 155   private boolean runCommand() throws IOException, InterruptedException
 156   {
 157     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 158     if (!file.canExecute())
 159     {
 160       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 161       {
 162         if (!file.canExecute())
 163         {
 164           return false;
 165         }
 166       }
 167     }
 168     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
 169     if (forGroup)
 170     {
 171       command += group.getName();
 172     }
 173     else
 174     {
 175       String name = af.getName();
 176       if (name == null)
 177       {
 178         name = "Alignment";
 179       }
 180       command += name;
 181     }
 182     command += cmds.SPACE;
 183     if (!alignment.isNucleotide())
 184     {
 185       command += cmds.FORCEAMINO; // TODO check for rna
 186     }
 187     else
 188     {
 189       command += cmds.FORCEDNA;
 190     }
 191
 192     command += hmmTemp.getAbsolutePath()
 193             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 194     return cmds.runCommand(command);
 195   }
 196
 197   private void importData() throws IOException, InterruptedException
 198   {
 199     cmds.addHMMConsensusSequences(af);
 200     FileLoader loader = new FileLoader();
 201     loader.LoadFileOntoAlignmentWaitTillLoaded(af.getViewport(),
 202             hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 203             FileFormat.HMMER3);
 204     hmmTemp.delete();
 205     stoTemp.delete();
 206   }
 207
 208   public boolean canRun()
 209   {
 210     return canRun;
 211   }
 212
 213
 214
 215 }