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