@Override
public void run()
{
- try
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
{
- calcMan.notifyStart(this); // updatingConservation = true;
-
- while (!calcMan.notifyWorking(this))
- {
- try
- {
- if (ap != null)
- {
- // ap.paintAlignment(false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return;
- }
- List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
- AlignmentI alignment = alignViewport.getAlignment();
- conservation = alignViewport.getAlignmentConservationAnnotation();
- quality = alignViewport.getAlignmentQualityAnnot();
- ourAnnot.add(conservation);
- ourAnnot.add(quality);
- ourAnnots = ourAnnot;
- ConsPercGaps = alignViewport.getConsPercGaps();
- // AlignViewport.UPDATING_CONSERVATION = true;
-
- if (alignment == null || (alWidth = alignment.getWidth()) < 0)
- {
- calcMan.workerComplete(this);
- // .updatingConservation = false;
- // AlignViewport.UPDATING_CONSERVATION = false;
+ abortAndDestroy();
+ return;
+ }
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+ AlignmentI alignment = alignViewport.getAlignment();
+ conservation = alignViewport.getAlignmentConservationAnnotation();
+ quality = alignViewport.getAlignmentQualityAnnot();
+ ourAnnot.add(conservation);
+ ourAnnot.add(quality);
+ ourAnnots = ourAnnot;
+ ConsPercGaps = alignViewport.getConsPercGaps();
+ // AlignViewport.UPDATING_CONSERVATION = true;
- return;
- }
- try
- {
- cons = Conservation.calculateConservation("All",
- alignment.getSequences(), 0, alWidth - 1, false,
- ConsPercGaps, quality != null);
- } catch (IndexOutOfBoundsException x)
- {
- // probable race condition. just finish and return without any fuss.
- calcMan.workerComplete(this);
- return;
- }
- updateResultAnnotation(true);
- } catch (OutOfMemoryError error)
+ if (alignment == null || (alWidth = alignment.getWidth()) < 0)
{
- ap.raiseOOMWarning("calculating conservation", error);
- calcMan.disableWorker(this);
- // alignViewport.conservation = null;
- // this.alignViewport.quality = null;
-
+ // .updatingConservation = false;
+ // AlignViewport.UPDATING_CONSERVATION = false;
+ return;
}
- calcMan.workerComplete(this);
+ try
+ {
+ cons = Conservation.calculateConservation("All",
+ alignment.getSequences(), 0, alWidth - 1, false,
+ ConsPercGaps, quality != null);
+ } catch (IndexOutOfBoundsException x)
+ {
+ // probable race condition. just finish and return without any fuss.
+ return;
+ }
+ updateResultAnnotation(true);
+ if ((alignViewport == null) || (calcMan == null)
+ || (alignViewport.isClosed()))
+ {
+ abortAndDestroy();
+ return;
+ }
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}