- final PAEContactMatrix cm = (PAEContactMatrix) av
- .getContactMatrix(aa[selectedRow]);
- if (cm.getNewick()!=null && cm.getNewick().length()>0)
+ addContactMatrixOptions(ap,aa[selectedRow],pop);
+ // Set/adjust threshold for grouping ?
+ // colour alignment by this [type]
+ // select/hide columns by this row
+
+ }
+ }
+
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ static void addColourOrFilterByOptions(final AlignmentPanel ap,
+ final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ {
+ JMenuItem item;
+ item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+ };
+ });
+ pop.add(item);
+ if (alignmentAnnotation.sequenceRef!=null)
+ {
+ item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)