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     viewport = af.getViewport();
  65     alignment = viewport.getAlignment();
  66
  67   }
  68
  69   @Override
  70   public void run()
  71   {
  72     barID = System.currentTimeMillis();
  73     if (af != null)
  74     {
  75     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  76             barID);
  77     }
  78     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  79     if (alignment == null && group == null)
  80     {
  81       JOptionPane.showMessageDialog(af,
  82               MessageManager.getString("warn.no_sequence_data"));
  83       return;
  84     }
  85     try
  86     {
  87       hmmTemp = File.createTempFile("hmm", ".hmm");
  88       hmmTemp.deleteOnExit();
  89       stoTemp = File.createTempFile("output", ".sto");
  90       stoTemp.deleteOnExit();
  91     } catch (IOException e1)
  92     {
  93       e1.printStackTrace();
  94     }
  95
  96     try
  97     {
  98     try
  99     {
 100         SequenceI[] array;
 101         List<SequenceI> seqs = alignment
 102                 .getHMMConsensusSequences(true);
 103         cmds.setHmmSeqs(seqs);
 104         if (forGroup)
 105         {
 106           array = group.getSelectionAsNewSequences(alignment);
 107         }
 108         else
 109         {
 110           if (!alignment.isAligned())
 111           {
 112             alignment.padGaps();
 113           }
 114           array = alignment.getSequencesArray();
 115         }
 116         if (array.length < 1)
 117         {
 118           if (af != null)
 119           {
 120             JOptionPane.showMessageDialog(af,
 121                   MessageManager.getString("warn.no_sequence_data"));
 122           }
 123           return;
 124         }
 125         SequenceI[] newArr = new SequenceI[array.length];
 126         int index = 0;
 127         for (SequenceI seq : array)
 128         {
 129           newArr[index] = new Sequence(seq);
 130           index++;
 131         }
 132
 133         cmds.uniquifySequences(newArr);
 134         cmds.exportData(newArr, stoTemp, null, null);
 135         jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
 136
 137     } catch (FileNotFoundException e)
 138     {
 139       // TODO Auto-generated catch block
 140       e.printStackTrace();
 141
 142     }
 143     try
 144     {
 145         boolean ran = runCommand();
 146         if (!ran)
 147         {
 148           if (af != null)
 149           {
 150             JvOptionPane.showInternalMessageDialog(af,
 151                   MessageManager.getString("warn.hmmbuild_failed"));
 152           }
 153           return;
 154         }
 155     } catch (IOException | InterruptedException e)
 156     {
 157       // TODO Auto-generated catch block
 158       e.printStackTrace();
 159     }
 160     try
 161     {
 162
 163       importData();
 164     } catch (IOException | InterruptedException e)
 165     {
 166       // TODO Auto-generated catch block
 167       e.printStackTrace();
 168     }
 169     } catch (Exception e)
 170     {
 171       e.printStackTrace();
 172     } finally
 173     {
 174       if (af != null)
 175       {
 176         af.setProgressBar(
 177                 MessageManager.getString("status.running_hmmbuild"),
 178               barID);
 179       }
 180     }
 181   }
 182
 183
 184
 185
 186   private boolean runCommand() throws IOException, InterruptedException
 187   {
 188     File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
 189     if (!file.canExecute())
 190     {
 191       file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
 192       {
 193         if (!file.canExecute())
 194         {
 195           return false;
 196         }
 197       }
 198     }
 199     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
 200     if (forGroup)
 201     {
 202       command += group.getName();
 203     }
 204     else
 205     {
 206       String name = null;
 207       if (af != null)
 208       {
 209         name = af.getName();
 210       }
 211       if (name == null)
 212       {
 213         name = "Alignment";
 214       }
 215       command += name;
 216     }
 217     command += cmds.SPACE;
 218     if (!alignment.isNucleotide())
 219     {
 220       command += cmds.FORCEAMINO; // TODO check for rna
 221     }
 222     else
 223     {
 224       command += cmds.FORCEDNA;
 225     }
 226
 227     command += hmmTemp.getAbsolutePath()
 228             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 229     return cmds.runCommand(command);
 230   }
 231
 232   private void importData() throws IOException, InterruptedException
 233   {
 234     if (af != null)
 235     {
 236       cmds.addHMMConsensusSequences(af);
 237
 238       FileLoader loader = new FileLoader();
 239       loader.LoadFileOntoAlignmentWaitTillLoaded(viewport,
 240               hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 241               FileFormat.HMMER3);
 242     }
 243     else
 244     {
 245       HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
 246               DataSourceType.FILE));
 247       alignment.addSequence(file.getSeqsAsArray()[0]);
 248     }
 249     hmmTemp.delete();
 250     stoTemp.delete();
 251   }
 252
 253   public void hmmbuildWaitTillComplete()
 254   {
 255     Thread loader = new Thread(this);
 256     loader.start();
 257
 258     while (loader.isAlive())
 259     {
 260       try
 261       {
 262         Thread.sleep(500);
 263       } catch (Exception ex)
 264       {
 265       }
 266     }
 267   }
 268 }