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