");
+ webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
@@ -1760,10 +1959,6 @@ public class GAlignFrame extends JInternalFrame
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- calculateTree.add(averageDistanceTreeMenuItem);
- calculateTree.add(neighbourTreeMenuItem);
- calculateTree.add(avDistanceTreeBlosumMenuItem);
- calculateTree.add(njTreeBlosumMenuItem);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
@@ -1802,8 +1997,27 @@ public class GAlignFrame extends JInternalFrame
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
- selectMenu.add(deleteGroups);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ calculateMenu.add(expandAlignment);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ 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)
@@ -2104,6 +2318,19 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
@@ -2139,6 +2366,14 @@ public class GAlignFrame extends JInternalFrame
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
+
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
protected void copy_actionPerformed(ActionEvent e)
{
@@ -2187,6 +2422,33 @@ public class GAlignFrame extends JInternalFrame
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
+
+ }
+
+ /**
+ * Template method to handle the 'load T-Coffee scores' menu event.
+ *
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void loadScores_actionPerformed(ActionEvent event)
+ {
+
+ }
+
+ /**
+ * Template method to handle the 'Color T-Coffee scores' menu event.
+ *
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ {
+
}
protected void jpred_actionPerformed(ActionEvent e)
@@ -2256,6 +2518,11 @@ public class GAlignFrame extends JInternalFrame
}
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void associatedData_actionPerformed(ActionEvent e)
{
@@ -2266,6 +2533,11 @@ public class GAlignFrame extends JInternalFrame
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_actionPerformed(ActionEvent e)
{
@@ -2375,4 +2647,10 @@ public class GAlignFrame extends JInternalFrame
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
}