+ boolean searchSelection = viewport.getSelectionGroup() != null
+ && !extendCurrent;
+ SequenceCollectionI sqcol = searchSelection ? viewport
+ .getSelectionGroup() : viewport.getAlignment();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ String key = searchSelection ? "label.no_feature_found_selection"
+ : "label.no_feature_of_type_found";
+ avcg.setStatus(MessageManager.formatMessage(key,
+ new String[] { featureType }));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(false, false);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes a visible feature of the specified feature type.
+ * Returns the number of sequences which have the feature visible in the
+ * selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ FeatureRenderer fr = alignPanel == null ? null : alignPanel
+ .getFeatureRenderer();
+
+ final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+ final int endColumn = sqcol.getEndRes() + 1;