in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 4127698..d1ad9b4 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -113,6 +113,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                 _collapse_species_specific_subtrees;
     JMenuItem                 _collapse_below_threshold;                                                                                                                                                                               //TODO implememt me
     JMenuItem                 _obtain_detailed_taxonomic_information_jmi;
+    JMenuItem                 _obtain_uniprot_seq_information_jmi;
     JMenuItem                 _move_node_names_to_tax_sn_jmi;
     JMenuItem                 _move_node_names_to_seq_names_jmi;
     JMenuItem                 _extract_tax_code_from_node_names_jmi;
@@ -417,13 +418,15 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     }
 
     boolean isSubtreeDisplayed() {
-        if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
-            JOptionPane
-                    .showMessageDialog( this,
-                                        "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
-                                        "Operation can not be exectuted on a sub-tree",
-                                        JOptionPane.WARNING_MESSAGE );
-            return true;
+        if ( getCurrentTreePanel() != null ) {
+            if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+                JOptionPane
+                        .showMessageDialog( this,
+                                            "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+                                            "Operation can not be exectuted on a sub-tree",
+                                            JOptionPane.WARNING_MESSAGE );
+                return true;
+            }
         }
         return false;
     }
@@ -508,11 +511,12 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     void buildViewMenu() {
         _view_jmenu = createMenu( "View", getConfiguration() );
+        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+        _view_jmenu.addSeparator();
         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
-        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
         customizeJMenuItem( _display_basic_information_item );
         customizeJMenuItem( _view_as_NH_item );
         customizeJMenuItem( _view_as_NHX_item );
@@ -655,7 +659,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
-    Configuration getConfiguration() {
+    public Configuration getConfiguration() {
         return _configuration;
     }
 
@@ -790,7 +794,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _circular_type_cbmi.setSelected( false );
     }
 
-    void showWhole() {
+    public void showWhole() {
         _mainpanel.getControlPanel().showWhole();
     }
 
@@ -846,7 +850,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _abbreviate_scientific_names.isSelected() );
         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
                 && _color_labels_same_as_parent_branch.isSelected() );
-        options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.isSelected() );
+        //TODO FIXME ~~
+        //options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.isSelected() );
+      //TODO FIXME ~~
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
         }