+ @Override
+ public void initInformation()
+ {
+ for (SequenceI seq : alignment.getHMMConsensusSequences(false))
+ {
+ if (!seq.hasHMMAnnotation())
+ {
+ AlignmentAnnotation information;
+ information = new AlignmentAnnotation(seq.getName(),
+ MessageManager.getString("label.information_description"),
+ new Annotation[1], 0f, 6.52f,
+ AlignmentAnnotation.BAR_GRAPH);
+ information.hasText = true;
+ information.autoCalculated = true;
+ information.hasText = true;
+ information.autoCalculated = false;
+ information.sequenceRef = seq;
+ information.setCalcId("HMM annotation");
+ this.information.add(information);
+ hinformation.add(new Profiles(new ProfileI[1]));
+ alignment.addAnnotation(information);
+ seq.updateHMMMapping();
+ seq.setHasInfo(true);
+ seq.addAlignmentAnnotation(information);
+ }
+ }
+
+ }
+
+ // these should be extracted from the view model - style and settings for
+ // derived annotation
+ private void initGapCounts()
+ {
+ if (showOccupancy)
+ {
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ MessageManager.getString("label.occupancy_descr"),
+ 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);
+ }
+ }
+