- aa[selectedRow].scaleColLabel);
- item.addActionListener(this);
- pop.add(item);
- }
- }
- else if (label.indexOf("Consensus") > -1)
- {
- pop.addSeparator();
- // av and sequencegroup need to implement same interface for
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null)
- ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
- : ap.av.isIgnoreGapsConsensus());
- final AlignmentAnnotation aaa = aa[selectedRow];
- cbmi.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (aaa.groupRef != null)
- {
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel()
- .paint(ap.getAnnotationPanel().getGraphics());
- }
- else
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
- }
- ap.alignmentChanged();
- }
- });
- pop.add(cbmi);
- // av and sequencegroup need to implement same interface for
- if (aaa.groupRef != null)
- {
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
- aa[selectedRow].groupRef.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setShowConsensusHistogram(chist.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
- aa[selectedRow].groupRef.isShowSequenceLogo());
- cprofl.addActionListener(new ActionListener()