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