@Override
public void run()
{
+ boolean annotationAdded = false;
try
{
calcMan.notifyStart(this);
{
try
{
- computeAnnotations();
+ annotationAdded = computeAnnotations();
} catch (IndexOutOfBoundsException x)
{
// probable race condition. just finish and return without any fuss.
if (ap != null)
{
- ap.adjustAnnotationHeight();
+ if (annotationAdded)
+ {
+ ap.adjustAnnotationHeight();
+ }
ap.paintAlignment(true);
}
/**
* Scan each column of the alignment to calculate a count by feature type. Set
* the count as the value of the alignment annotation for that feature type.
+ *
+ * @return
*/
- void computeAnnotations()
+ boolean computeAnnotations()
{
FeatureRenderer fr = new FeatureRenderer(alignViewport);
// TODO use the commented out code once JAL-2075 is fixed
max[crow] = Math.max(count[crow], max[crow]);
}
}
+
+ boolean annotationAdded = false;
+
for (int anrow = 0; anrow < rows; anrow++)
{
Annotation[] anns = new Annotation[width];
* construct or update the annotation
*/
String description = counter.getDescriptions()[anrow];
- AlignmentAnnotation ann = alignViewport.getAlignment()
- .findOrCreateAnnotation(counter.getNames()[anrow],
- description, false, null, null);
+ if (!alignment.findAnnotation(description).iterator().hasNext())
+ {
+ annotationAdded = true;
+ }
+ AlignmentAnnotation ann = alignment.findOrCreateAnnotation(
+ counter.getNames()[anrow], description, false, null, null);
ann.description = description;
ann.showAllColLabels = true;
ann.scaleColLabel = true;
ourAnnots.add(ann);
}
}
+ return annotationAdded;
}
/**