src/jalview/hmmer/HMMAlignThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.Alignment;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.HiddenMarkovModel;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.AlignFrame;
   9 import jalview.gui.Desktop;
  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.HashMap;
  20 import java.util.Map;
  21
  22 public class HMMAlignThread implements Runnable
  23 {
  24   HMMERCommands cmds = new HMMERCommands();
  25
  26   AlignFrame af;
  27
  28   AlignmentI alignment;
  29
  30   HiddenMarkovModel hmm;
  31
  32   boolean newFrame;
  33
  34   long barID;
  35
  36   Map<Integer, SequenceI> hmmSeqs;
  37
  38   File hmmTemp = null;
  39
  40   File outTemp = null;
  41
  42   File inputTemp = null;
  43
  44   public HMMAlignThread(AlignFrame af, boolean createNewFrame)
  45   {
  46     this.af = af;
  47     alignment = af.getViewport().getAlignment();
  48     hmm = alignment.getSequenceAt(0).getHMM();
  49     newFrame = createNewFrame;
  50   }
  51
  52   @Override
  53   public void run()
  54   {
  55     barID = System.currentTimeMillis();
  56     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  57             barID);
  58     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  59     try
  60     {
  61       hmmTemp = File.createTempFile("hmm", ".hmm");
  62       hmmTemp.deleteOnExit();
  63       outTemp = File.createTempFile("output", ".sto");
  64       outTemp.deleteOnExit();
  65       inputTemp = File.createTempFile("input", ".sto");
  66       inputTemp.deleteOnExit();
  67     } catch (IOException e1)
  68     {
  69       // TODO Auto-generated catch block
  70       e1.printStackTrace();
  71     }
  72
  73     try
  74     {
  75       try
  76       {
  77         hmmSeqs = alignment.getHMMConsensusSequences(true);
  78         cmds.exportData(alignment, outTemp.getAbsoluteFile(), hmm,
  79                 hmmTemp.getAbsoluteFile());
  80       } catch (FileNotFoundException e)
  81       {
  82         // TODO Auto-generated catch block
  83         e.printStackTrace();
  84
  85       }
  86       try
  87       {
  88         runCommand();
  89       } catch (IOException | InterruptedException e)
  90       {
  91         // TODO Auto-generated catch block
  92         e.printStackTrace();
  93       }
  94       try
  95       {
  96         importData();
  97       } catch (IOException | InterruptedException e)
  98       {
  99         // TODO Auto-generated catch block
 100         e.printStackTrace();
 101       }
 102     } catch (Exception e)
 103     {
 104       e.printStackTrace();
 105     } finally
 106     {
 107       af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
 108               barID);
 109     }
 110   }
 111
 112   private void runCommand() throws IOException, InterruptedException
 113   {
 114     String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
 115     if (!hmm.getFileHeader().contains("HMMER3/f"))
 116     {
 117       command += cmds.ALLCOL;
 118     }
 119     command += cmds.TRIM + " -o" + inputTemp.getAbsolutePath() + cmds.SPACE
 120             + hmmTemp.getAbsolutePath() + cmds.SPACE
 121             + outTemp.getAbsolutePath();
 122     cmds.runCommand(command);
 123   }
 124
 125   private void importData() throws IOException, InterruptedException
 126   {
 127     if (newFrame)
 128     {
 129       FileLoader loader = new FileLoader();
 130       AlignFrame aFrame = new AlignFrame(new Alignment(new SequenceI[1]),
 131               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 132       Desktop.addInternalFrame(aFrame, aFrame.getTitle(),
 133               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 134       aFrame.setTitle(
 135               af.getName() + "Aligned to " + hmm.getName() + "'s HMM");
 136       af.getViewport().setAlignment(null);
 137
 138       aFrame.loadJalviewDataFile(inputTemp.getAbsolutePath(),
 139               DataSourceType.FILE, FileFormat.Stockholm, null);
 140
 141
 142
 143       Map<Integer, SequenceI> copy = new HashMap<>(
 144               hmmSeqs);
 145       addSeqs(aFrame, copy);
 146       SequenceI seq = aFrame.getViewport().getAlignment()
 147               .getSequenceAt(0);
 148       seq.getHMM().mapToReferenceAnnotation(aFrame, seq);
 149       addSeqs(af, hmmSeqs);
 150     }
 151     else
 152     {
 153       af.getViewport().getAlignment().getSequences().clear();
 154       af.setIsRecurring(true);
 155       af.loadJalviewDataFile(inputTemp.getAbsolutePath(),
 156               DataSourceType.FILE, FileFormat.Stockholm, null);
 157       af.setIsRecurring(false);
 158       addSeqs(af, hmmSeqs);
 159     }
 160     hmmTemp.delete();
 161     outTemp.delete();
 162     inputTemp.delete();
 163   }
 164
 165   private void addSeqs(AlignFrame alignFrame, Map<Integer, SequenceI> map)
 166   {
 167     for (Map.Entry<Integer, SequenceI> entry : map.entrySet())
 168     {
 169       SequenceI seq = entry.getValue();
 170       Integer pos = entry.getKey();
 171       cmds.addHMMConsensusSequence(alignFrame, seq, pos);
 172     }
 173   }
 174
 175   }
 176
 177