in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / Configuration.java

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 0eead28..32cec55 100644 (file)
--- 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 {
@@ -155,21 +156,21 @@ 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[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
-            { "Open Sequence Web", "nodisplay" }, { "Open Taxonomy Web", "nodisplay" }, { "Cut Subtree", "display" },
+            { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" },
             { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
-            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } };
+            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" } };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------
@@ -217,7 +218,7 @@ public final class Configuration {
         }
     }
 
-    Configuration( final String cf, final boolean is_url, final boolean is_applet ) {
+    public Configuration( final String cf, final boolean is_url, final boolean is_applet ) {
         if ( ForesterUtil.isEmpty( cf ) ) {
             config_filename = default_config_filename;
         }
@@ -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 {