+
+ /*
+ * wait for Conservation thread to complete
+ */
+ AlignViewport viewport = af.getViewport();
+ synchronized (this)
+ {
+ while (viewport.getAlignmentConservationAnnotation() != null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ AlignmentAnnotation[] anns = viewport.getAlignment()