src/jalview/hmmer/HMMAlignThread.java

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