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 cc2c9eb..4e76d1f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -97,13 +97,14 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Display Branch Length Values";
+    static final String COLOR_BY_TAXONOMIC_GROUP = "Color by Taxonomic Group";
     static final String         DISPLAY_SCALE_LABEL                     = "Display Scale";
     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
-    static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
+    static final String         COLOR_LABELS_LABEL                      = "Color Labels Same as Parent Branch";
     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Show External Node Shapes";
     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Show Internal Node Shapes";
@@ -176,6 +177,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JRadioButtonMenuItem        _uniform_cladograms_rbmi;
     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
     JCheckBoxMenuItem           _show_branch_length_values_cbmi;
+    JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
+    
     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
     JCheckBoxMenuItem           _show_overview_cbmi;
     JCheckBoxMenuItem           _show_domain_labels;
@@ -437,6 +440,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_branch_length_values_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _color_by_taxonomic_group_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        
         else if ( o == _show_confidence_stddev_cbmi ) {
             updateOptions( getOptions() );
         }
@@ -1304,6 +1311,12 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
         }
+        
+        if ( ( _color_by_taxonomic_group_cbmi != null ) &&  _color_by_taxonomic_group_cbmi.isEnabled() ) {
+            options.setColorByTaxonomicGroup(  _color_by_taxonomic_group_cbmi.isSelected() );
+        }
+        
+        
         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
                 && ( _print_using_actual_size_cbmi.isSelected() ) );
         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )