+ @Override
+ public void run()
+ {
+ final long progBar;
+ ap.alignFrame.setProgressBar(
+ MessageManager.formatMessage(
+ "action.clustering_matrix_for",
+ cm.getAnnotDescr(), 5f),
+ progBar = System.currentTimeMillis());
+ cm.setGroupSet(GroupSet.makeGroups(cm, true));
+ cm.randomlyReColourGroups();
+ cm.transferGroupColorsTo(alignmentAnnotation);
+ ap.alignmentChanged();
+ ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
+ ap.alignFrame.setProgressBar(null, progBar);
+ }
+ }).start();
+ }
+ });
+ pop.add(item);
+ }
+ }
+ }
+
+ /**
+ * A helper method that adds menu options for calculation and visualisation of
+ * group and/or alignment consensus annotation to a popup menu. This is
+ * designed to be reusable for either unwrapped mode (popup menu is shown on
+ * component AnnotationLabels), or wrapped mode (popup menu is shown on
+ * IdPanel when the mouse is over an annotation label).
+ *
+ * @param ap
+ * @param ann
+ * @param pop
+ */
+ static void addConsensusMenuOptions(AlignmentPanel ap,
+ AlignmentAnnotation ann, JPopupMenu pop)
+ {
+ pop.addSeparator();
+
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = ann;
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);