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[jalview.git] / forester / java / src / org / forester / archaeopteryx / Options.java
diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 594c9ab..862db49 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -27,6 +27,9 @@ package org.forester.archaeopteryx;
 
 import java.awt.Font;
 
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
 import org.forester.phylogeny.data.NodeVisualization;
 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
@@ -37,44 +40,47 @@ import org.forester.util.ForesterUtil;
  */
 final public class Options {
 
-    static final double                 MIN_CONFIDENCE_DEFAULT = 0.0;
-    private boolean                     _show_branch_length_values;
-    private boolean                     _internal_number_are_confidence_for_nh_parsing;
-    private boolean                     _show_scale;
-    private boolean                     _show_overview;
-    private boolean                     _antialias_screen;
-    private boolean                     _antialias_print;
-    private boolean                     _graphics_export_visible_only;
-    private int                         _print_size_x;
-    private int                         _print_size_y;
-    private double                      _min_confidence_value;
-    private boolean                     _print_black_and_white;
-    private boolean                     _print_using_actual_size;
-    private boolean                     _graphics_export_using_actual_size;
-    private PHYLOGENY_GRAPHICS_TYPE     _phylogeny_graphics_type;
-    private CLADOGRAM_TYPE              _cladogram_type;
-    private OVERVIEW_PLACEMENT_TYPE     _ov_placement;
-    private NODE_LABEL_DIRECTION        _node_label_direction;
-    private Font                        _base_font;
-    private boolean                     _match_whole_terms_only;
-    private boolean                     _search_case_sensitive;
-    private float                       _print_line_width;
-    private boolean                     _inverse_search_result;
-    private double                      _scale_bar_length;
-    private short                       _number_of_digits_after_comma_for_confidence_values;
-    private short                       _number_of_digits_after_comma_for_branch_length_values;
-    private boolean                     _nh_parsing_replace_underscores;
-    private boolean                     _nh_parsing_extract_pfam_taxonomy_codes;
-    private boolean                     _editable;
-    private boolean                     _background_color_gradient;
-    private boolean                     _show_domain_labels;
-    private boolean                     _color_labels_same_as_parent_branch;
-    private boolean                     _abbreviate_scientific_names;
-    private NodeVisualization.NodeShape _default_node_shape;
-    private NodeVisualization.NodeFill  _default_node_fill;
-    private short                       _default_node_shape_size;
-    private boolean                     _taxonomy_colorize_node_shapes;
-    private boolean                     _show_default_node_shapes;
+    static final double                       MIN_CONFIDENCE_DEFAULT = 0.0;
+    private boolean                           _show_branch_length_values;
+    private boolean                           _internal_number_are_confidence_for_nh_parsing;
+    private boolean                           _show_scale;
+    private boolean                           _show_overview;
+    private boolean                           _antialias_screen;
+    private boolean                           _antialias_print;
+    private boolean                           _graphics_export_visible_only;
+    private int                               _print_size_x;
+    private int                               _print_size_y;
+    private double                            _min_confidence_value;
+    private boolean                           _print_black_and_white;
+    private boolean                           _print_using_actual_size;
+    private boolean                           _graphics_export_using_actual_size;
+    private PHYLOGENY_GRAPHICS_TYPE           _phylogeny_graphics_type;
+    private CLADOGRAM_TYPE                    _cladogram_type;
+    private OVERVIEW_PLACEMENT_TYPE           _ov_placement;
+    private NODE_LABEL_DIRECTION              _node_label_direction;
+    private Font                              _base_font;
+    private boolean                           _match_whole_terms_only;
+    private boolean                           _search_case_sensitive;
+    private float                             _print_line_width;
+    private boolean                           _inverse_search_result;
+    private double                            _scale_bar_length;
+    private short                             _number_of_digits_after_comma_for_confidence_values;
+    private short                             _number_of_digits_after_comma_for_branch_length_values;
+    private boolean                           _nh_parsing_replace_underscores;
+    private boolean                           _nh_parsing_extract_pfam_taxonomy_codes;
+    private boolean                           _editable;
+    private boolean                           _background_color_gradient;
+    private boolean                           _show_domain_labels;
+    private boolean                           _color_labels_same_as_parent_branch;
+    private boolean                           _abbreviate_scientific_names;
+    private NodeVisualization.NodeShape       _default_node_shape;
+    private NodeVisualization.NodeFill        _default_node_fill;
+    private short                             _default_node_shape_size;
+    private boolean                           _taxonomy_colorize_node_shapes;
+    private boolean                           _show_default_node_shapes;
+    private boolean                           _show_confidence_stddev;
+    private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
+    private NODE_DATA                         _ext_desc_data_to_return;
 
     private Options() {
         init();
@@ -184,6 +190,25 @@ final public class Options {
         _show_domain_labels = true;
         setAbbreviateScientificTaxonNames( false );
         _color_labels_same_as_parent_branch = false;
+        _show_confidence_stddev = true;
+        _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
+        _ext_desc_data_to_return = NODE_DATA.NODE_NAME;
+    }
+
+    boolean isShowConfidenceStddev() {
+        return _show_confidence_stddev;
+    }
+
+    void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
+        _show_confidence_stddev = show_confidence_stddev;
+    }
+
+    NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
+        return _nh_conversion_support_value_style;
+    }
+
+    void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
+        _nh_conversion_support_value_style = nh_conversion_support_value_style;
     }
 
     final boolean isAbbreviateScientificTaxonNames() {
@@ -494,6 +519,9 @@ final public class Options {
             }
             instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
             instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
+            if ( configuration.getExtDescNodeDataToReturn() != null ) {
+                instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
+            }
         }
         return instance;
     }
@@ -531,4 +559,12 @@ final public class Options {
     public static enum PHYLOGENY_GRAPHICS_TYPE {
         RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
     }
+
+    public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+        return _ext_desc_data_to_return;
+    }
+
+    public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+        _ext_desc_data_to_return = ext_desc_data_to_return;
+    }
 }