src/jalview/workers/ConsensusThread.java

   1 package jalview.workers;
   2
   3 import jalview.analysis.AAFrequency;
   4 import jalview.api.AlignCalcWorkerI;
   5 import jalview.api.AlignViewportI;
   6 import jalview.api.AlignmentViewPanel;
   7 import jalview.datamodel.AlignmentAnnotation;
   8 import jalview.datamodel.AlignmentI;
   9 import jalview.datamodel.Annotation;
  10 import jalview.schemes.ColourSchemeI;
  11
  12 import java.util.Hashtable;
  13
  14 public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
  15 {
  16   public ConsensusThread(AlignViewportI alignViewport,
  17           AlignmentViewPanel alignPanel)
  18   {
  19     super(alignViewport, alignPanel);
  20   }
  21
  22   public void run()
  23   {
  24     try
  25     {
  26       AlignmentAnnotation consensus = alignViewport.getAlignmentConsensusAnnotation();
  27       if (consensus==null) { return;
  28       }
  29       calcMan.notifyStart(this);
  30       while (!calcMan.notifyWorking(this))
  31       {
  32         try
  33         {
  34           if (ap != null)
  35           {
  36             ap.paintAlignment(false);
  37           }
  38
  39           Thread.sleep(200);
  40         } catch (Exception ex)
  41         {
  42           ex.printStackTrace();
  43         }
  44       }
  45       calcMan.notifyWorking(this);
  46       if (alignViewport.isClosed())
  47       {
  48         abortAndDestroy();
  49       }
  50       AlignmentI alignment = alignViewport.getAlignment();
  51
  52       int aWidth = -1;
  53
  54       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  55       {
  56         calcMan.workerComplete(this);
  57         // .updatingConservation = false;
  58         // AlignViewport.UPDATING_CONSERVATION = false;
  59
  60         return;
  61       }
  62       consensus = alignViewport
  63               .getAlignmentConsensusAnnotation();
  64
  65       consensus.annotations = null;
  66       consensus.annotations = new Annotation[aWidth];
  67       Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
  68       hconsensus = new Hashtable[aWidth];
  69       AAFrequency.calculate(alignment.getSequencesArray(), 0,
  70               alignment.getWidth(), hconsensus, true);
  71       alignViewport.setSequenceConsensusHash(hconsensus);
  72       updateResultAnnotation(true);
  73       ColourSchemeI globalColourScheme = alignViewport
  74               .getGlobalColourScheme();
  75       if (globalColourScheme != null)
  76       {
  77         globalColourScheme.setConsensus(hconsensus);
  78       }
  79
  80     } catch (OutOfMemoryError error)
  81     {
  82       calcMan.workerCannotRun(this);
  83
  84       // consensus = null;
  85       // hconsensus = null;
  86       ap.raiseOOMWarning("calculating consensus", error);
  87     }
  88
  89     calcMan.workerComplete(this);
  90     if (ap != null)
  91     {
  92       ap.paintAlignment(true);
  93     }
  94   }
  95
  96   /**
  97    * update the consensus annotation from the sequence profile data using
  98    * current visualization settings.
  99    */
 100   public void updateAnnotation()
 101   {
 102     updateResultAnnotation(false);
 103   }
 104
 105   public void updateResultAnnotation(boolean immediate)
 106   {
 107     AlignmentAnnotation consensus = alignViewport
 108             .getAlignmentConsensusAnnotation();
 109     Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
 110     if (immediate || !calcMan.isWorking(this) && consensus!=null && hconsensus!=null)
 111     {
 112       AAFrequency.completeConsensus(consensus, hconsensus, 0,
 113             hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
 114             alignViewport.isShowSequenceLogo());
 115     }
 116   }
 117 }