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
  15         AlignCalcWorkerI
  16 {
  17   public StrucConsensusThread(AlignViewportI alignViewport,
  18           AlignmentViewPanel alignPanel)
  19   {
  20     super(alignViewport, alignPanel);
  21   }
  22
  23   AlignmentAnnotation strucConsensus;
  24
  25   Hashtable[] hStrucConsensus;
  26
  27   @Override
  28   public void run()
  29   {
  30     try
  31     {
  32       calcMan.notifyStart(this);
  33       while (!calcMan.notifyWorking(this))
  34       {
  35         try
  36         {
  37           if (ap != null)
  38           {
  39             ap.paintAlignment(false);
  40           }
  41
  42           Thread.sleep(200);
  43         } catch (Exception ex)
  44         {
  45           ex.printStackTrace();
  46         }
  47       }
  48       if (alignViewport.isClosed())
  49       {
  50         abortAndDestroy();
  51       }
  52       AlignmentI alignment = alignViewport.getAlignment();
  53
  54       int aWidth = -1;
  55
  56       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  57       {
  58         calcMan.workerComplete(this);
  59         return;
  60       }
  61       strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
  62       hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
  63       strucConsensus.annotations = null;
  64       strucConsensus.annotations = new Annotation[aWidth];
  65
  66       hStrucConsensus = new Hashtable[aWidth];
  67
  68       AlignmentAnnotation[] aa = alignViewport.getAlignment()
  69               .getAlignmentAnnotation();
  70       AlignmentAnnotation rnaStruc = null;
  71       // select rna struct to use for calculation
  72       for (int i = 0; i < aa.length; i++)
  73       {
  74         if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
  75         {
  76           rnaStruc = aa[i];
  77           break;
  78         }
  79       }
  80       // check to see if its valid
  81
  82       if (rnaStruc == null || !rnaStruc.isValidStruc())
  83       {
  84         calcMan.workerComplete(this);
  85         return;
  86       }
  87
  88       jalview.analysis.StructureFrequency.calculate(
  89               alignment.getSequencesArray(), 0, alignment.getWidth(),
  90               hStrucConsensus, true, rnaStruc);
  91       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
  92       // TODO AlignmentAnnotation rnaStruc!!!
  93       updateResultAnnotation(true);
  94       if (alignViewport.getGlobalColourScheme() != null)
  95       {
  96         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
  97       }
  98
  99     } catch (OutOfMemoryError error)
 100     {
 101       calcMan.workerCannotRun(this);
 102
 103       // consensus = null;
 104       // hconsensus = null;
 105       ap.raiseOOMWarning("calculating RNA structure consensus", error);
 106     }
 107
 108     calcMan.workerComplete(this);
 109     if (ap != null)
 110     {
 111       ap.paintAlignment(true);
 112     }
 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     if (immediate || !calcMan.isWorking(this) && strucConsensus != null
 129             && hStrucConsensus != null)
 130     {
 131       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
 132               0, hStrucConsensus.length,
 133               alignViewport.getIgnoreGapsConsensus(),
 134               alignViewport.isShowSequenceLogo());
 135     }
 136   }
 137
 138 }