+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ // display formatting settings for this row.
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+ aa[selectedRow].scaleColLabel);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ }
+ else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ "Ignore Gaps In Consensus",
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .getIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addActionListener(new ActionListener()
+ {
+ 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.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)