special domain coloring

[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 2bf8471..387bba6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -77,7 +77,6 @@ final public class Options {
     private double                            _scale_bar_length;
     private boolean                           _search_case_sensitive;
     private boolean                           _show_annotation_ref_source;
-    private boolean                           _show_branch_length_values;
     private boolean                           _show_confidence_stddev;
     private boolean                           _show_default_node_shapes_external;
     private boolean                           _show_default_node_shapes_internal;
@@ -272,10 +271,6 @@ final public class Options {
         return _search_case_sensitive;
     }
 
-    final boolean isShowBranchLengthValues() {
-        return _show_branch_length_values;
-    }
-
     boolean isShowConfidenceStddev() {
         return _show_confidence_stddev;
     }
@@ -414,10 +409,6 @@ final public class Options {
         _search_case_sensitive = search_case_sensitive;
     }
 
-    final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
-        _show_branch_length_values = show_branch_length_values;
-    }
-
     void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
         _show_confidence_stddev = show_confidence_stddev;
     }
@@ -446,7 +437,6 @@ final public class Options {
         _default_node_shape = NodeShape.CIRCLE;
         _default_node_fill = NodeFill.GRADIENT;
         _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-        _show_branch_length_values = false;
         _internal_number_are_confidence_for_nh_parsing = false;
         _show_scale = false;
         _antialias_screen = true;
@@ -487,10 +477,10 @@ final public class Options {
         _show_annotation_ref_source = true;
         setAbbreviateScientificTaxonNames( false );
         _color_labels_same_as_parent_branch = false;
-        _show_confidence_stddev = true;
+        _show_confidence_stddev = false;
         _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
         _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
-        _line_up_renderable_node_data = false;
+        _line_up_renderable_node_data = true;
         _right_align_domains = false;
     }
 
@@ -507,7 +497,6 @@ final public class Options {
         if ( configuration != null ) {
             instance.setAntialiasScreen( configuration.isAntialiasScreen() );
             instance.setShowScale( configuration.isShowScale() );
-            instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
             instance.setShowOverview( configuration.isShowOverview() );
             instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
             instance.setCladogramType( configuration.getCladogramType() );