+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
+ selectMenu.add(selectHighlighted);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /**
+ * Generate the reverse sequence (or reverse complement if the flag is true)
+ * and add it to the alignment
+ *
+ * @param complement
+ */
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ }
+
+ /**
+ * Try to run script in a Groovy console, having first ensured that this
+ * alignframe is set as currentAlignFrame in Desktop
+ */
+ protected void runGroovy_actionPerformed()
+ {
+
+ }
+
+ /**
+ * Adds the given action listener and key accelerator to the given menu item.
+ * Also saves in a lookup table to support lookup of action by key stroke.
+ *
+ * @param keyStroke
+ * @param menuItem
+ * @param actionListener
+ */
+ protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+ JMenuItem menuItem, ActionListener actionListener)
+ {
+ menuItem.setAccelerator(keyStroke);
+ accelerators.put(keyStroke, menuItem);
+ menuItem.addActionListener(actionListener);
+ }
+
+ /**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(true, forSequences, forAlignment);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(false, forSequences, forAlignment);
+ }
+
+ /**
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
+
+ }
+
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+