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   AlignmentAnnotation strucConsensus;
  22   Hashtable[] hStrucConsensus;
  23
  24   public void run()
  25   {
  26     try
  27     {
  28       calcMan.notifyStart(this);
  29       while (!calcMan.notifyWorking(this))
  30       {
  31         try
  32         {
  33           if (ap != null)
  34           {
  35             ap.paintAlignment(false);
  36           }
  37
  38           Thread.sleep(200);
  39         } catch (Exception ex)
  40         {
  41           ex.printStackTrace();
  42         }
  43       }
  44       if (alignViewport.isClosed())
  45       {
  46         abortAndDestroy();
  47       }
  48       AlignmentI alignment = alignViewport.getAlignment();
  49
  50       int aWidth = -1;
  51
  52       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  53       {
  54         calcMan.workerComplete(this);
  55         return;
  56       }
  57       strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
  58       hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
  59       strucConsensus.annotations = null;
  60       strucConsensus.annotations = new Annotation[aWidth];
  61
  62       hStrucConsensus = new Hashtable[aWidth];
  63
  64       AlignmentAnnotation[] aa = alignViewport.getAlignment()
  65               .getAlignmentAnnotation();
  66       AlignmentAnnotation rnaStruc = null;
  67       // select rna struct to use for calculation
  68       for (int i = 0; i < aa.length; i++)
  69       {
  70         if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
  71         {
  72           rnaStruc = aa[i];
  73           break;
  74         }
  75       }
  76       // check to see if its valid
  77
  78       if (rnaStruc==null || !rnaStruc.isValidStruc())
  79       {
  80         calcMan.workerComplete(this);
  81         return;
  82       }
  83
  84       jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
  85               alignment.getWidth(), hStrucConsensus, true, rnaStruc);
  86       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
  87       // TODO AlignmentAnnotation rnaStruc!!!
  88       updateResultAnnotation(true);
  89       if (alignViewport.getGlobalColourScheme()!= null)
  90       {
  91         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
  92       }
  93
  94     } catch (OutOfMemoryError error)
  95     {
  96       calcMan.workerCannotRun(this);
  97
  98       // consensus = null;
  99       // hconsensus = null;
 100       ap.raiseOOMWarning("calculating RNA structure consensus", error);
 101     }
 102
 103     calcMan.workerComplete(this);
 104     if (ap != null)
 105     {
 106       ap.paintAlignment(true);
 107     }
 108
 109   }
 110   /**
 111    * update the consensus annotation from the sequence profile data using
 112    * current visualization settings.
 113    */
 114   public void updateAnnotation()
 115   {
 116     updateResultAnnotation(false);
 117   }
 118
 119   public void updateResultAnnotation(boolean immediate)
 120   {
 121     if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
 122     {
 123       StructureFrequency.completeConsensus(strucConsensus,
 124               hStrucConsensus, 0, hStrucConsensus.length,
 125               alignViewport.getIgnoreGapsConsensus(),
 126             alignViewport.isShowSequenceLogo());
 127     }
 128   }
 129
 130 }