- while (av.isCalcInProgress())
- {
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
-
- }
- }
-
- av.showAllHiddenColumns();
- av.showAllHiddenSeqs();
- av.setSelectionGroup(null);
- // o/w hidden seqs retain selection group, causes problems later when hiding
- // sequences
-
- // wait for conservation calc to complete again
- while (av.isCalcInProgress())
- {
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
-
- }
- }
-
- viewHeight = av.getEndSeq() - av.getStartSeq() + 1;
- viewWidth = av.getEndRes() - av.getStartRes() + 1;
-
- // wait for gui to get set up
- // this does actually appear to be necessary
- while (viewHeight != 18 || viewWidth != 63)
- {
- try
- {
- Thread.sleep(50);
- av.getAlignPanel().setScrollValues(0, 1);
- av.getAlignPanel().setScrollValues(1, 0);
- viewHeight = av.getEndSeq() - av.getStartSeq() + 1;
- viewWidth = av.getEndRes() - av.getStartRes() + 1;
- } catch (InterruptedException e)
- {
-
- }
- }
-
- od = new OverviewDimensions(av.getPosProps(), true);