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       {
  93         jalview.analysis.StructureFrequency.calculate(
  94                 alignment.getSequencesArray(), 0, alignment.getWidth(),
  95                 hStrucConsensus, true, rnaStruc);
  96       } catch (ArrayIndexOutOfBoundsException x)
  97       {
  98         calcMan.workerComplete(this);
  99         return;
 100       }
 101       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
 102       // TODO AlignmentAnnotation rnaStruc!!!
 103       updateResultAnnotation(true);
 104       if (alignViewport.getGlobalColourScheme() != null)
 105       {
 106         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
 107       }
 108
 109     } catch (OutOfMemoryError error)
 110     {
 111       calcMan.workerCannotRun(this);
 112
 113       // consensus = null;
 114       // hconsensus = null;
 115       ap.raiseOOMWarning("calculating RNA structure consensus", error);
 116     } finally
 117     {
 118       calcMan.workerComplete(this);
 119       if (ap != null)
 120       {
 121         ap.paintAlignment(true);
 122       }
 123     }
 124
 125   }
 126
 127   /**
 128    * update the consensus annotation from the sequence profile data using
 129    * current visualization settings.
 130    */
 131   @Override
 132   public void updateAnnotation()
 133   {
 134     updateResultAnnotation(false);
 135   }
 136
 137   public void updateResultAnnotation(boolean immediate)
 138   {
 139     if (immediate || !calcMan.isWorking(this) && strucConsensus != null
 140             && hStrucConsensus != null)
 141     {
 142       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
 143               0, hStrucConsensus.length,
 144               alignViewport.getIgnoreGapsConsensus(),
 145               alignViewport.isShowSequenceLogo());
 146     }
 147   }
 148
 149 }