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
  15         AlignCalcWorkerI
  16 {
  17   public ConsensusThread(AlignViewportI alignViewport,
  18           AlignmentViewPanel alignPanel)
  19   {
  20     super(alignViewport, alignPanel);
  21   }
  22
  23   @Override
  24   public void run()
  25   {
  26     if (calcMan.isPending(this))
  27     {
  28       return;
  29     }
  30     calcMan.notifyStart(this);
  31     long started = System.currentTimeMillis();
  32     try
  33     {
  34       AlignmentAnnotation consensus = alignViewport
  35               .getAlignmentConsensusAnnotation();
  36       if (consensus == null || calcMan.isPending(this))
  37       {
  38         calcMan.workerComplete(this);
  39         return;
  40       }
  41       while (!calcMan.notifyWorking(this))
  42       {
  43         // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
  44         try
  45         {
  46           if (ap != null)
  47           {
  48             ap.paintAlignment(false);
  49           }
  50           Thread.sleep(200);
  51         } catch (Exception ex)
  52         {
  53           ex.printStackTrace();
  54         }
  55       }
  56       if (alignViewport.isClosed())
  57       {
  58         abortAndDestroy();
  59       }
  60       AlignmentI alignment = alignViewport.getAlignment();
  61
  62       int aWidth = -1;
  63
  64       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  65       {
  66         calcMan.workerComplete(this);
  67         // .updatingConservation = false;
  68         // AlignViewport.UPDATING_CONSERVATION = false;
  69
  70         return;
  71       }
  72       consensus = alignViewport.getAlignmentConsensusAnnotation();
  73
  74       consensus.annotations = null;
  75       consensus.annotations = new Annotation[aWidth];
  76       Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
  77       hconsensus = new Hashtable[aWidth];
  78       try
  79       {
  80         AAFrequency.calculate(alignment.getSequencesArray(), 0,
  81                 alignment.getWidth(), hconsensus, true);
  82       } catch (ArrayIndexOutOfBoundsException x)
  83       {
  84         // this happens due to a race condition -
  85         // alignment was edited at same time as calculation was running
  86         //
  87         // calcMan.workerCannotRun(this);
  88         calcMan.workerComplete(this);
  89         return;
  90       }
  91       alignViewport.setSequenceConsensusHash(hconsensus);
  92       updateResultAnnotation(true);
  93       ColourSchemeI globalColourScheme = alignViewport
  94               .getGlobalColourScheme();
  95       if (globalColourScheme != null)
  96       {
  97         globalColourScheme.setConsensus(hconsensus);
  98       }
  99
 100     } catch (OutOfMemoryError error)
 101     {
 102       calcMan.workerCannotRun(this);
 103
 104       // consensus = null;
 105       // hconsensus = null;
 106       ap.raiseOOMWarning("calculating consensus", error);
 107     }
 108
 109     calcMan.workerComplete(this);
 110     if (ap != null)
 111     {
 112       ap.paintAlignment(true);
 113     }
 114   }
 115
 116   /**
 117    * update the consensus annotation from the sequence profile data using
 118    * current visualization settings.
 119    */
 120   @Override
 121   public void updateAnnotation()
 122   {
 123     updateResultAnnotation(false);
 124   }
 125
 126   public void updateResultAnnotation(boolean immediate)
 127   {
 128     AlignmentAnnotation consensus = alignViewport
 129             .getAlignmentConsensusAnnotation();
 130     Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
 131     if (immediate || !calcMan.isWorking(this) && consensus != null
 132             && hconsensus != null)
 133     {
 134       AAFrequency.completeConsensus(consensus, hconsensus, 0,
 135               hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
 136               alignViewport.isShowSequenceLogo());
 137     }
 138   }
 139 }