if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
{
- al.addAnnotation(
+ jalview.datamodel.AlignmentAnnotation jda =
(jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
- getId())
- );
+ getId());
+ if (an[i].hasVisible())
+ jda.visible = an[i].getVisible();
+
+ al.addAnnotation(jda);
continue;
}