src/jalview/workers/StrucConsensusThread.java

   1 package jalview.workers;
   2
   3 import java.util.Hashtable;
   4
   5 import jalview.analysis.StructureFrequency;
   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       if (calcMan.isPending(this))
  33       {
  34         return;
  35       }
  36       calcMan.notifyStart(this);
  37       while (!calcMan.notifyWorking(this))
  38       {
  39         try
  40         {
  41           if (ap != null)
  42           {
  43             // ap.paintAlignment(false);
  44           }
  45
  46           Thread.sleep(200);
  47         } catch (Exception ex)
  48         {
  49           ex.printStackTrace();
  50         }
  51       }
  52       if (alignViewport.isClosed())
  53       {
  54         abortAndDestroy();
  55       }
  56       AlignmentI alignment = alignViewport.getAlignment();
  57
  58       int aWidth = -1;
  59
  60       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  61       {
  62         calcMan.workerComplete(this);
  63         return;
  64       }
  65       strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
  66       hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
  67       strucConsensus.annotations = null;
  68       strucConsensus.annotations = new Annotation[aWidth];
  69
  70       hStrucConsensus = new Hashtable[aWidth];
  71
  72       AlignmentAnnotation[] aa = alignViewport.getAlignment()
  73               .getAlignmentAnnotation();
  74       AlignmentAnnotation rnaStruc = null;
  75       // select rna struct to use for calculation
  76       for (int i = 0; i < aa.length; i++)
  77       {
  78         if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
  79         {
  80           rnaStruc = aa[i];
  81           break;
  82         }
  83       }
  84       // check to see if its valid
  85
  86       if (rnaStruc == null || !rnaStruc.isValidStruc())
  87       {
  88         calcMan.workerComplete(this);
  89         return;
  90       }
  91
  92       try {
  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 }