- 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();
- }
- 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;