src/jalview/workers/StrucConsensusThread.java

   1 package jalview.workers;
   2
   3 import java.util.Hashtable;
   4
   5 import jalview.analysis.StructureFrequency;
   6 import jalview.api.AlignCalcWorkerI;
   7 import jalview.api.AlignViewportI;
   8 import jalview.api.AlignmentViewPanel;
   9 import jalview.datamodel.AlignmentAnnotation;
  10 import jalview.datamodel.AlignmentI;
  11 import jalview.datamodel.Annotation;
  12
  13 public class StrucConsensusThread extends AlignCalcWorker implements
  14         AlignCalcWorkerI
  15 {
  16   public StrucConsensusThread(AlignViewportI alignViewport,
  17           AlignmentViewPanel alignPanel)
  18   {
  19     super(alignViewport, alignPanel);
  20   }
  21
  22   AlignmentAnnotation strucConsensus;
  23
  24   Hashtable[] hStrucConsensus;
  25
  26   @Override
  27   public void run()
  28   {
  29     try
  30     {
  31       if (calcMan.isPending(this))
  32       {
  33         return;
  34       }
  35       calcMan.notifyStart(this);
  36       while (!calcMan.notifyWorking(this))
  37       {
  38         try
  39         {
  40           if (ap != null)
  41           {
  42             // ap.paintAlignment(false);
  43           }
  44
  45           Thread.sleep(200);
  46         } catch (Exception ex)
  47         {
  48           ex.printStackTrace();
  49         }
  50       }
  51       if (alignViewport.isClosed())
  52       {
  53         abortAndDestroy();
  54       }
  55       AlignmentI alignment = alignViewport.getAlignment();
  56
  57       int aWidth = -1;
  58
  59       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  60       {
  61         calcMan.workerComplete(this);
  62         return;
  63       }
  64       strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
  65       hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
  66       strucConsensus.annotations = null;
  67       strucConsensus.annotations = new Annotation[aWidth];
  68
  69       hStrucConsensus = new Hashtable[aWidth];
  70
  71       AlignmentAnnotation[] aa = alignViewport.getAlignment()
  72               .getAlignmentAnnotation();
  73       AlignmentAnnotation rnaStruc = null;
  74       // select rna struct to use for calculation
  75       for (int i = 0; i < aa.length; i++)
  76       {
  77         if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
  78         {
  79           rnaStruc = aa[i];
  80           break;
  81         }
  82       }
  83       // check to see if its valid
  84
  85       if (rnaStruc == null || !rnaStruc.isValidStruc())
  86       {
  87         calcMan.workerComplete(this);
  88         return;
  89       }
  90
  91       try {
  92               jalview.analysis.StructureFrequency.calculate(
  93               alignment.getSequencesArray(), 0, alignment.getWidth(),
  94               hStrucConsensus, true, rnaStruc);
  95       } catch (ArrayIndexOutOfBoundsException x)
  96       {
  97         calcMan.workerComplete(this);
  98         return;
  99       }
 100       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
 101       // TODO AlignmentAnnotation rnaStruc!!!
 102       updateResultAnnotation(true);
 103       if (alignViewport.getGlobalColourScheme() != null)
 104       {
 105         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
 106       }
 107
 108     } catch (OutOfMemoryError error)
 109     {
 110       calcMan.workerCannotRun(this);
 111
 112       // consensus = null;
 113       // hconsensus = null;
 114       ap.raiseOOMWarning("calculating RNA structure consensus", error);
 115     } finally
 116     {
 117       calcMan.workerComplete(this);
 118       if (ap != null)
 119       {
 120         ap.paintAlignment(true);
 121       }
 122     }
 123
 124   }
 125
 126   /**
 127    * update the consensus annotation from the sequence profile data using
 128    * current visualization settings.
 129    */
 130   @Override
 131   public void updateAnnotation()
 132   {
 133     updateResultAnnotation(false);
 134   }
 135
 136   public void updateResultAnnotation(boolean immediate)
 137   {
 138     if (immediate || !calcMan.isWorking(this) && strucConsensus != null
 139             && hStrucConsensus != null)
 140     {
 141       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
 142               0, hStrucConsensus.length,
 143               alignViewport.getIgnoreGapsConsensus(),
 144               alignViewport.isShowSequenceLogo());
 145     }
 146   }
 147
 148 }