- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus("Marked "
- + (invert ? alw - bs.cardinality() : bs.cardinality())
- + " columns containing features of type " + featureType
- + " across " + nseq);
- return true;
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ (toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked")),
+ (invert ? (Integer.valueOf((alw - alStart)
+ - bs.cardinality()).toString()) : (Integer
+ .valueOf(bs.cardinality()).toString())),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.no_feature_of_type_found",
+ new String[] { featureType }));
+ if (!extendCurrent && cs != null)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public void sortAlignmentByFeatureDensity(List<String> typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ protected void sortBy(List<String> typ, String methodText,
+ final String method)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ if (typ == null && fr != null)
+ {
+ typ = fr.getDisplayedFeatureTypes();
+ }
+ List<String> gps = null;
+ if (fr != null)
+ {
+ gps = fr.getDisplayedFeatureGroups();
+ }
+ AlignmentI al = viewport.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();