X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=ffc9104ba10d8b4cd52fe10536238996f0174764;hb=0fd0a770a96b63d7aede3af5f1e47c29a85595c6;hp=0eead289ffae9f24c057b6276f5c0ce4391460cb;hpb=ebc019e52cc784faa96c1360f23e0d4b8c12ecf5;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 0eead28..ffc9104 100644
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -45,10 +45,11 @@ import java.util.TreeMap;
 
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
-import org.forester.archaeopteryx.Options.NodeFill;
-import org.forester.archaeopteryx.Options.NodeShape;
 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.phylogeny.data.NodeVisualization;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
 import org.forester.util.ForesterUtil;
 
 public final class Configuration {
@@ -155,13 +156,13 @@ public final class Configuration {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
             { "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" },
             { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
-            { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes" },
+            { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
             { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
-            { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "no" },
+            { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
             { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
             { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
             { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
-            { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "no" },
+            { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "yes" },
             { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" },
             { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" }            };
     final static String                     clickto_options[][]                                    = {
@@ -1073,13 +1074,13 @@ public final class Configuration {
         }
         else if ( key.equals( "default_node_fill" ) ) {
             final String fill_str = ( ( String ) st.nextElement() ).trim();
-            if ( fill_str.equalsIgnoreCase( Options.NodeFill.NONE.toString() ) ) {
+            if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
                 setDefaultNodeFill( NodeFill.NONE );
             }
-            else if ( fill_str.equalsIgnoreCase( Options.NodeFill.GRADIENT.toString() ) ) {
+            else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
                 setDefaultNodeFill( NodeFill.GRADIENT );
             }
-            else if ( fill_str.equalsIgnoreCase( Options.NodeFill.SOLID.toString() ) ) {
+            else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
                 setDefaultNodeFill( NodeFill.SOLID );
             }
             else {
@@ -1089,10 +1090,10 @@ public final class Configuration {
         }
         else if ( key.equals( "default_node_shape" ) ) {
             final String shape_str = ( ( String ) st.nextElement() ).trim();
-            if ( shape_str.equalsIgnoreCase( Options.NodeShape.CIRCLE.toString() ) ) {
+            if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
                 setDefaultNodeShape( NodeShape.CIRCLE );
             }
-            else if ( shape_str.equalsIgnoreCase( Options.NodeShape.RECTANGLE.toString() ) ) {
+            else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
                 setDefaultNodeShape( NodeShape.RECTANGLE );
             }
             else {