+ 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);
+
+ if (aaa.groupRef != null)
+ {
+ /*
+ * group consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ /*
+ * alignment consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ ap.av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ ap.av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ ap.av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowSequenceLogo(true);
+ ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }