src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.Sequence;
   7 import jalview.datamodel.SequenceGroup;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.gui.AlignFrame;
  10 import jalview.gui.AlignViewport;
  11 import jalview.gui.JvOptionPane;
  12 import jalview.gui.Preferences;
  13 import jalview.io.DataSourceType;
  14 import jalview.io.FileFormat;
  15 import jalview.io.FileLoader;
  16 import jalview.io.FileParse;
  17 import jalview.io.HMMFile;
  18 import jalview.util.MessageManager;
  19
  20 import java.io.File;
  21 import java.io.FileNotFoundException;
  22 import java.io.IOException;
  23 import java.util.List;
  24
  25 import javax.swing.JOptionPane;
  26
  27 public class HMMBuildThread implements Runnable
  28 {
  29   HMMERCommands cmds = new HMMERCommands();
  30   AlignFrame af;
  31
  32   AlignViewport viewport;
  33   AlignmentI alignment;
  34   SequenceGroup group;
  35
  36
  37   boolean forGroup = false;
  38
  39   File hmmTemp = null;
  40
  41   File stoTemp = null;
  42
  43   long barID;
  44
  45   /**
  46    * This is used for validation purposes. Do not use!
  47    *
  48    * @param viewport
  49    */
  50   public HMMBuildThread(AlignmentI alignment)
  51   {
  52     this.alignment = alignment;
  53     forGroup = false;
  54   }
  55
  56   public HMMBuildThread(AlignFrame af)
  57   {
  58     this.af = af;
  59     if (af.getViewport().getSelectionGroup() != null)
  60     {
  61       group = af.getViewport().getSelectionGroup();
  62       forGroup = true;
  63     }
  64     alignment = af.getViewport().getAlignment();
  65
  66   }
  67
  68   @Override
  69   public void run()
  70   {
  71     barID = System.currentTimeMillis();
  72     if (af != null)
  73     {
  74     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  75             barID);
  76     }
  77     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  78     if (alignment == null && group == null)
  79     {
  80       JOptionPane.showMessageDialog(af,
  81               MessageManager.getString("warn.no_sequence_data"));
  82       return;
  83     }
  84     try
  85     {
  86       hmmTemp = File.createTempFile("hmm", ".hmm");
  87       hmmTemp.deleteOnExit();
  88       stoTemp = File.createTempFile("output", ".sto");
  89       stoTemp.deleteOnExit();
  90     } catch (IOException e1)
  91     {
  92       e1.printStackTrace();
  93     }
  94
  95     try
  96     {
  97     try
  98     {
  99         SequenceI[] array;
 100         List<SequenceI> seqs = alignment
 101                 .getHMMConsensusSequences(true);
 102         cmds.setHmmSeqs(seqs);
 103         if (forGroup)
 104         {
 105           array = group.getSelectionAsNewSequences(alignment);
 106         }
 107         else
 108         {
 109           if (!alignment.isAligned())
 110           {
 111             alignment.padGaps();
 112           }
 113           array = alignment.getSequencesArray();
 114         }
 115         if (array.length < 1)
 116         {
 117           if (af != null)
 118           {
 119             JOptionPane.showMessageDialog(af,
 120                   MessageManager.getString("warn.no_sequence_data"));
 121           }
 122           return;
 123         }
 124         SequenceI[] newArr = new SequenceI[array.length];
 125         int index = 0;
 126         for (SequenceI seq : array)
 127         {
 128           newArr[index] = new Sequence(seq);
 129           index++;
 130         }
 131
 132         cmds.uniquifySequences(newArr);
 133         cmds.exportData(newArr, stoTemp, null, null);
 134         jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 135
 136     } catch (FileNotFoundException e)
 137     {
 138       // TODO Auto-generated catch block
 139       e.printStackTrace();
 140
 141     }
 142     try
 143     {
 144         boolean ran = runCommand();
 145         if (!ran)
 146         {
 147           if (af != null)
 148           {
 149             JvOptionPane.showInternalMessageDialog(af,
 150                   MessageManager.getString("warn.hmmbuild_failed"));
 151           }
 152           return;
 153         }
 154     } catch (IOException | InterruptedException e)
 155     {
 156       // TODO Auto-generated catch block
 157       e.printStackTrace();
 158     }
 159     try
 160     {
 161
 162       importData();
 163     } catch (IOException | InterruptedException e)
 164     {
 165       // TODO Auto-generated catch block
 166       e.printStackTrace();
 167     }
 168     } catch (Exception e)
 169     {
 170       e.printStackTrace();
 171     } finally
 172     {
 173       if (af != null)
 174       {
 175         af.setProgressBar(
 176                 MessageManager.getString("status.running_hmmbuild"),
 177               barID);
 178       }
 179     }
 180   }
 181
 182
 183
 184
 185   private boolean runCommand() throws IOException, InterruptedException
 186   {
 187     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 188     if (!file.canExecute())
 189     {
 190       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 191       {
 192         if (!file.canExecute())
 193         {
 194           return false;
 195         }
 196       }
 197     }
 198     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
 199     if (forGroup)
 200     {
 201       command += group.getName();
 202     }
 203     else
 204     {
 205       String name = null;
 206       if (af != null)
 207       {
 208         name = af.getName();
 209       }
 210       if (name == null)
 211       {
 212         name = "Alignment";
 213       }
 214       command += name;
 215     }
 216     command += cmds.SPACE;
 217     if (!alignment.isNucleotide())
 218     {
 219       command += cmds.FORCEAMINO; // TODO check for rna
 220     }
 221     else
 222     {
 223       command += cmds.FORCEDNA;
 224     }
 225
 226     command += hmmTemp.getAbsolutePath()
 227             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 228     return cmds.runCommand(command);
 229   }
 230
 231   private void importData() throws IOException, InterruptedException
 232   {
 233     if (af != null)
 234     {
 235       cmds.addHMMConsensusSequences(af);
 236
 237       FileLoader loader = new FileLoader();
 238       loader.LoadFileOntoAlignmentWaitTillLoaded(viewport,
 239               hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 240               FileFormat.HMMER3);
 241     }
 242     else
 243     {
 244       HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
 245               DataSourceType.FILE));
 246       alignment.addSequence(file.getSeqsAsArray()[0]);
 247     }
 248     hmmTemp.delete();
 249     stoTemp.delete();
 250   }
 251
 252   public void hmmbuildWaitTillComplete()
 253   {
 254     Thread loader = new Thread(this);
 255     loader.start();
 256
 257     while (loader.isAlive())
 258     {
 259       try
 260       {
 261         Thread.sleep(500);
 262       } catch (Exception ex)
 263       {
 264       }
 265     }
 266   }
 267 }