AnnotationProviderI counter)
{
super(viewport, panel);
- ourAnnots = new ArrayList<AlignmentAnnotation>();
+ ourAnnots = new ArrayList<>();
this.counter = counter;
calcMan.registerWorker(this);
}
for (AlignmentAnnotation ann : anns)
{
AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
- ann.label, ann.description, false, null, null);
+ ann.label, ann.getCalcId(), ann.autoCalculated,
+ ann.sequenceRef,
+ ann.groupRef);
+ if (ann.description!=null) {
+ theAnn.description = ann.description;
+ }
theAnn.showAllColLabels = true;
theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
theAnn.scaleColLabel = true;
if (ap != null)
{
ap.adjustAnnotationHeight();
- ap.paintAlignment(true);
+ // TODO: only need to update colour and geometry if panel height changes
+ // and view is coloured by annotation, and the annotation is actually
+ // changed!
+ ap.paintAlignment(true, true);
}
}