src/jalview/hmmer/HMMBuildThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceGroup;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignFrame;
   8 import jalview.gui.Preferences;
   9 import jalview.io.DataSourceType;
  10 import jalview.io.FileFormat;
  11 import jalview.util.MessageManager;
  12
  13 import java.io.File;
  14 import java.io.FileNotFoundException;
  15 import java.io.IOException;
  16 import java.util.List;
  17
  18 import javax.swing.JOptionPane;
  19
  20 public class HMMBuildThread implements Runnable
  21 {
  22   HMMERCommands cmds = new HMMERCommands();
  23   AlignFrame af;
  24   AlignmentI alignment;
  25
  26   SequenceGroup group;
  27
  28   boolean canRun = true;
  29
  30   File hmmTemp = null;
  31
  32   File stoTemp = null;
  33
  34   long barID;
  35
  36   public HMMBuildThread(AlignFrame af)
  37   {
  38     this.af = af;
  39     if (af.getViewport().getSelectionGroup() != null)
  40     {
  41       group = af.getViewport().getSelectionGroup();
  42     }
  43     alignment = af.getViewport().getAlignment();
  44
  45   }
  46
  47   @Override
  48   public void run()
  49   {
  50     barID = System.currentTimeMillis();
  51     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  52             barID);
  53     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  54     if (alignment == null && group == null)
  55     {
  56       JOptionPane.showMessageDialog(af,
  57               MessageManager.getString("label.no_sequence_data"));
  58       return;
  59     }
  60     try
  61     {
  62       hmmTemp = File.createTempFile("hmm", ".hmm");
  63       hmmTemp.deleteOnExit();
  64       stoTemp = File.createTempFile("output", ".sto");
  65       stoTemp.deleteOnExit();
  66     } catch (IOException e1)
  67     {
  68       e1.printStackTrace();
  69     }
  70
  71     try
  72     {
  73     try
  74     {
  75         List<SequenceI> seqs = alignment
  76                 .getHMMConsensusSequences(true);
  77         cmds.setHmmSeqs(seqs);
  78         if (group != null)
  79         {
  80           SequenceI[] array = group.getSelectionAsNewSequences(alignment);
  81
  82           cmds.exportData(array, stoTemp, null, null);
  83         }
  84         else
  85         {
  86           if (!alignment.isAligned())
  87           {
  88             alignment.padGaps();
  89           }
  90           cmds.exportData(alignment.getSequencesArray(), stoTemp, null,
  91                   null);
  92         }
  93     } catch (FileNotFoundException e)
  94     {
  95       // TODO Auto-generated catch block
  96       e.printStackTrace();
  97
  98     }
  99     try
 100     {
 101       runCommand();
 102     } catch (IOException | InterruptedException e)
 103     {
 104       // TODO Auto-generated catch block
 105       e.printStackTrace();
 106     }
 107     try
 108     {
 109
 110       importData();
 111     } catch (IOException | InterruptedException e)
 112     {
 113       // TODO Auto-generated catch block
 114       e.printStackTrace();
 115     }
 116     } catch (Exception e)
 117     {
 118       e.printStackTrace();
 119     } finally
 120     {
 121       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
 122               barID);
 123     }
 124   }
 125
 126
 127
 128
 129   private void runCommand() throws IOException, InterruptedException
 130   {
 131     final String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
 132             + af.getName() + cmds.SPACE + hmmTemp.getAbsolutePath()
 133             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
 134     cmds.runCommand(command);
 135   }
 136
 137   private void importData() throws IOException, InterruptedException
 138   {
 139     cmds.addHMMConsensusSequences(af);
 140     af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
 141             FileFormat.HMMER3, null);
 142     hmmTemp.delete();
 143     stoTemp.delete();
 144   }
 145
 146   public boolean canRun()
 147   {
 148     return canRun;
 149   }
 150
 151
 152
 153 }