in progress (special coloring is still true)

[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 fb23501..dedc7ac 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -107,8 +107,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
-    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
-    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
@@ -154,7 +155,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _confcolor_item;\r
     JMenuItem                   _color_rank_jmi;\r
     JMenuItem                   _collapse_species_specific_subtrees;\r
-    JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
     JMenuItem                   _obtain_seq_information_jmi;\r
@@ -194,6 +194,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _choose_minimal_confidence_mi;\r
     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
+    JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
     JMenuItem                   _cycle_node_shape_mi;\r
     JMenuItem                   _cycle_node_fill_mi;\r
     JMenuItem                   _choose_node_size_mi;\r
@@ -344,7 +345,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             switchColors();\r
         }\r
         else if ( o == _display_basic_information_item ) {\r
-            displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+            if ( getCurrentTreePanel() != null ) {\r
+                displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+            }\r
         }\r
         else if ( o == _view_as_NH_item ) {\r
             viewAsNH();\r
@@ -428,6 +431,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
             updateOptions( getOptions() );\r
         }\r
+        else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
             updateOptions( getOptions() );\r
             showWhole();\r
@@ -1307,6 +1313,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
+        options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+                && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
         }\r