+ userDefinedColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed(e);
+ }
+ });
+ BLOSUM62Colour
+ .setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed(e);
+ }
+ });
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
+ * });
+ */
+
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ annotationPanelMenuItem.setActionCommand("");
+ annotationPanelMenuItem.setText(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
+ true));
+ annotationPanelMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ showAllAlAnnotations.setText(MessageManager
+ .getString("label.show_all_al_annotations"));
+ final boolean isAnnotationPanelShown = annotationPanelMenuItem
+ .getState();
+ showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllAlAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllAnnotations_actionPerformed(false, true);
+ }
+ });
+ hideAllAlAnnotations.setText(MessageManager
+ .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllAlAnnotations.addActionListener(new ActionListener()