X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=c4b242517d48d55c2d4373f73900d5e55795ff3d;hb=83086d32cf5b8c98a5c8d045187e07e4fa9bb752;hp=bc565ac748cb980faf30b54e1511273a2bc44222;hpb=6062dfb954cafb6af22e01af89222888d9d5ba66;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index bc565ac..c4b2425 100644
--- 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";
@@ -111,6 +112,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
+    static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Show Seq Annotation Ref Sources";
     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
@@ -135,7 +137,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _gsdi_item;
     JMenuItem                   _gsdir_item;
     JMenuItem                   _lineage_inference;
-    JMenuItem                   _function_analysis;
     // file menu:
     JMenuItem                   _open_item;
     JMenuItem                   _open_url_item;
@@ -176,9 +177,11 @@ 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;
+    JCheckBoxMenuItem           _show_annotation_ref_source;
     JCheckBoxMenuItem           _abbreviate_scientific_names;
     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
     JMenuItem                   _overview_placment_mi;
@@ -388,6 +391,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_domain_labels ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _show_annotation_ref_source ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _abbreviate_scientific_names ) {
             updateOptions( getOptions() );
         }
@@ -433,6 +439,9 @@ 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() );
         }
@@ -1260,6 +1269,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
                 && _background_gradient_cbmi.isSelected() );
         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+        options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+                && _show_annotation_ref_source.isSelected() );
         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
                 && _abbreviate_scientific_names.isSelected() );
         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
@@ -1298,6 +1309,9 @@ 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 )