+ // these should be extracted from the view model - style and settings for
+ // derived annotation
+ private void initGapCounts()
+ {
+ if (showOccupancy)
+ {
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ "Number of aligned positions", new Annotation[1], 0f,
+ alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ alignment.addAnnotation(gapcounts);
+ }
+ }
+