src/jalview/workers/StrucConsensusThread.java

   1 package jalview.workers;
   2
   3 import java.util.Hashtable;
   4
   5 import jalview.analysis.AAFrequency;
   6 import jalview.analysis.StructureFrequency;
   7 import jalview.api.AlignCalcWorkerI;
   8 import jalview.api.AlignViewportI;
   9 import jalview.api.AlignmentViewPanel;
  10 import jalview.datamodel.AlignmentAnnotation;
  11 import jalview.datamodel.AlignmentI;
  12 import jalview.datamodel.Annotation;
  13
  14 public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
  15 {
  16   public StrucConsensusThread(AlignViewportI alignViewport,
  17           AlignmentViewPanel alignPanel)
  18   {
  19     super(alignViewport, alignPanel);
  20   }
  21   public void run()
  22   {
  23     try
  24     {
  25       calcMan.notifyStart(this);
  26       while (!calcMan.notifyWorking(this))
  27       {
  28         try
  29         {
  30           if (ap != null)
  31           {
  32             ap.paintAlignment(false);
  33           }
  34
  35           Thread.sleep(200);
  36         } catch (Exception ex)
  37         {
  38           ex.printStackTrace();
  39         }
  40       }
  41       if (alignViewport.isClosed())
  42       {
  43         abortAndDestroy();
  44       }
  45       AlignmentI alignment = alignViewport.getAlignment();
  46
  47       int aWidth = -1;
  48
  49       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  50       {
  51         calcMan.workerComplete(this);
  52         return;
  53       }
  54       AlignmentAnnotation strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
  55       Hashtable[] hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
  56       strucConsensus.annotations = null;
  57       strucConsensus.annotations = new Annotation[aWidth];
  58
  59       hStrucConsensus = new Hashtable[aWidth];
  60
  61       AlignmentAnnotation[] aa = alignViewport.getAlignment()
  62               .getAlignmentAnnotation();
  63       AlignmentAnnotation rnaStruc = null;
  64       for (int i = 0; i < aa.length; i++)
  65       {
  66         if (aa[i].getRNAStruc() != null)
  67         {
  68           rnaStruc = aa[i];
  69           break;
  70         }
  71       }
  72
  73       jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
  74               alignment.getWidth(), hStrucConsensus, true, rnaStruc);
  75       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
  76       // TODO AlignmentAnnotation rnaStruc!!!
  77       updateResultAnnotation(true);
  78       if (alignViewport.getGlobalColourScheme()!= null)
  79       {
  80         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
  81       }
  82
  83     } catch (OutOfMemoryError error)
  84     {
  85       calcMan.workerCannotRun(this);
  86
  87       // consensus = null;
  88       // hconsensus = null;
  89       ap.raiseOOMWarning("calculating RNA structure consensus", error);
  90     }
  91
  92     calcMan.workerComplete(this);
  93     if (ap != null)
  94     {
  95       ap.paintAlignment(true);
  96     }
  97
  98   }
  99   /**
 100    * update the consensus annotation from the sequence profile data using
 101    * current visualization settings.
 102    */
 103   public void updateAnnotation()
 104   {
 105     updateResultAnnotation(false);
 106   }
 107
 108   public void updateResultAnnotation(boolean immediate)
 109   {
 110     AlignmentAnnotation strucConsensus = alignViewport
 111             .getAlignmentStrucConsensusAnnotation();
 112     Hashtable[] hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
 113     if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
 114     {
 115       StructureFrequency.completeConsensus(strucConsensus,
 116               hStrucConsensus, 0, hStrucConsensus.length,
 117               alignViewport.getIgnoreGapsConsensus(),
 118             alignViewport.isShowSequenceLogo());
 119     }
 120   }
 121
 122 }