src/jalview/hmmer/HMMAlignThread.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.AlignmentOrder;
   6 import jalview.datamodel.HiddenMarkovModel;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.AlignFrame;
   9 import jalview.gui.Preferences;
  10 import jalview.io.DataSourceType;
  11 import jalview.io.FileFormat;
  12 import jalview.io.FileLoader;
  13 import jalview.util.MessageManager;
  14
  15 import java.io.FileNotFoundException;
  16 import java.io.IOException;
  17 import java.util.HashMap;
  18 import java.util.Map;
  19
  20 public class HMMAlignThread implements Runnable
  21 {
  22
  23   AlignFrame af;
  24
  25   AlignmentI alignment;
  26
  27   HiddenMarkovModel hmm;
  28
  29   boolean newFrame;
  30
  31   long barID;
  32
  33   Map<Integer, SequenceI> hmmSeqs;
  34
  35   public HMMAlignThread(AlignFrame af, boolean createNewFrame)
  36   {
  37     this.af = af;
  38     alignment = af.getViewport().getAlignment();
  39     hmm = alignment.getSequenceAt(0).getHMM();
  40     newFrame = createNewFrame;
  41   }
  42
  43   @Override
  44   public void run()
  45   {
  46     barID = System.currentTimeMillis();
  47     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
  48             barID);
  49     HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
  50     try
  51     {
  52       try
  53       {
  54         hmmSeqs = alignment.getHMMConsensusSequences(true);
  55         HMMERCommands.exportData(alignment, true, true, hmm);
  56       } catch (FileNotFoundException e)
  57       {
  58         // TODO Auto-generated catch block
  59         e.printStackTrace();
  60
  61       }
  62       try
  63       {
  64         runCommand();
  65       } catch (IOException | InterruptedException e)
  66       {
  67         // TODO Auto-generated catch block
  68         e.printStackTrace();
  69       }
  70       try
  71       {
  72         importData();
  73       } catch (IOException | InterruptedException e)
  74       {
  75         // TODO Auto-generated catch block
  76         e.printStackTrace();
  77       }
  78     } catch (Exception e)
  79     {
  80       e.printStackTrace();
  81     } finally
  82     {
  83       af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
  84               barID);
  85     }
  86   }
  87
  88   private void runCommand() throws IOException, InterruptedException
  89   {
  90     String command = HMMERCommands.HMMERFOLDER + HMMERCommands.HMMALIGN;
  91     if (!hmm.getFileHeader().contains("HMMER3/f"))
  92     {
  93       command += HMMERCommands.ALLCOL;
  94     }
  95     command += HMMERCommands.TRIM + HMMERCommands.OUTPUTALIGNMENT
  96             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
  97             + HMMERCommands.JALVIEWDIRECTORY
  98             + HMMERCommands.ALIGNMENTBUFFER;
  99     HMMERCommands.runCommand(command);
 100   }
 101
 102   private void importData() throws IOException, InterruptedException
 103   {
 104     if (newFrame)
 105     {
 106       FileLoader loader = new FileLoader();
 107       AlignmentOrder order = new AlignmentOrder(alignment);
 108       AlignFrame newAFrame = loader.LoadFileWaitTillLoaded(
 109               HMMERCommands.ALIGNMENTINPUT, DataSourceType.FILE);
 110       Map<Integer, SequenceI> copy = new HashMap<>(
 111               hmmSeqs);
 112       addSeqs(newAFrame, copy);
 113       SequenceI seq = newAFrame.getViewport().getAlignment()
 114               .getSequenceAt(0);
 115       hmm.mapToReferenceAnnotation(newAFrame, seq);
 116       addSeqs(af, hmmSeqs);
 117     }
 118     else
 119     {
 120       af.getViewport().getAlignment().getSequences().clear();
 121       af.setIsRecurring(true);
 122       af.loadJalviewDataFile(HMMERCommands.ALIGNMENTBUFFER,
 123               DataSourceType.FILE, FileFormat.Stockholm, null);
 124       af.setIsRecurring(false);
 125       addSeqs(af, hmmSeqs);
 126     }
 127   }
 128
 129   private void addSeqs(AlignFrame alignFrame, Map<Integer, SequenceI> map)
 130   {
 131     for (Map.Entry<Integer, SequenceI> entry : map.entrySet())
 132     {
 133       SequenceI seq = entry.getValue();
 134       Integer pos = entry.getKey();
 135       HMMERCommands.addHMMConsensusSequence(alignFrame, seq, pos);
 136     }
 137   }
 138
 139   }
 140
 141