X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=80f0861edbc70c95b5ea370b26e36488c29c15fc;hb=a32f4076b5b309b4dcc0852d6283a2bd18785f28;hp=dd3a6bcb7f39072beeb125fb7460427d06fe5068;hpb=3ce13fed094f2f10da69eb4f22ee6136af51c133;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index dd3a6bc..80f0861 100644
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -29,8 +29,7 @@ import java.awt.Font;
 
 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
-import org.forester.phylogeny.data.NodeData;
-import org.forester.phylogeny.data.NodeData.NODE_DATA;
+import org.forester.phylogeny.data.NodeDataField;
 import org.forester.phylogeny.data.NodeVisualData;
 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
@@ -55,7 +54,7 @@ final public class Options {
     private NodeVisualData.NodeShape          _default_node_shape;
     private short                             _default_node_shape_size;
     private boolean                           _editable;
-    private NODE_DATA                         _ext_desc_data_to_return;
+    private NodeDataField                         _ext_desc_data_to_return;
     private boolean                           _graphics_export_using_actual_size;
     private boolean                           _graphics_export_visible_only;
     private boolean                           _internal_number_are_confidence_for_nh_parsing;
@@ -93,12 +92,8 @@ final public class Options {
         init();
     }
 
-    public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
-        return NodeData.NODE_DATA.DOMAINS_ALL;
-        // TODO fix me
-        // FIXME remove me
-        // ~~~~~~
-        //return _ext_desc_data_to_return;
+    public NodeDataField getExtDescNodeDataToReturn() {
+        return _ext_desc_data_to_return;
     }
 
     public boolean isAllowErrorsInDistanceToParent() {
@@ -125,7 +120,7 @@ final public class Options {
         _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
     }
 
-    public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+    public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
         _ext_desc_data_to_return = ext_desc_data_to_return;
     }
 
@@ -481,7 +476,7 @@ final public class Options {
         _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
         _match_whole_terms_only = false;
         _search_with_regex = false;
-        _search_case_sensitive = true;
+        _search_case_sensitive = false;
         _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
         _show_overview = true;
         _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
@@ -499,7 +494,7 @@ final public class Options {
         _color_labels_same_as_parent_branch = false;
         _show_confidence_stddev = false;
         _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
-        _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+        _ext_desc_data_to_return = NodeDataField.UNKNOWN;
         _line_up_renderable_node_data = true;
         _right_align_domains = false;
     }