inprogress

[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 7cefee5..8fe8076 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -95,7 +95,8 @@ public final class Configuration {
     private boolean                         _show_domain_labels                                    = true;
     private boolean                         _abbreviate_scientific_names                           = false;
     private boolean                         _color_labels_same_as_parent_branch                    = false;
-    private boolean                         _show_default_node_shapes                              = false;
+    private boolean                         _show_default_node_shapes_internal                     = false;
+    private boolean                         _show_default_node_shapes_external                     = false;
     private NodeShape                       _default_node_shape                                    = NodeShape.CIRCLE;
     private NodeFill                        _default_node_fill                                     = NodeFill.GRADIENT;
     private short                           _default_node_shape_size                               = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
@@ -163,17 +164,18 @@ public final class Configuration {
     String                                  default_config_filename                                = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
     final static String                     display_options[][]                                    = {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
-            { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Node Events", "display", "?" },
-            { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
-            { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
-            { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
-            { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" },
-            { "Seq Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
-            { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
-            { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
-            { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
-            { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" },
-            { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" }             };
+            { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
+            { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
+            { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
+            { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
+            { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
+            { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
+            { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
+            { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+            { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
+            { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+            { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+            { "Properties", "nodisplay", "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" },
@@ -660,8 +662,12 @@ public final class Configuration {
         return _show_branch_length_values;
     }
 
-    public boolean isShowDefaultNodeShapes() {
-        return _show_default_node_shapes;
+    public boolean isShowDefaultNodeShapesExternal() {
+        return _show_default_node_shapes_external;
+    }
+
+    public boolean isShowDefaultNodeShapesInternal() {
+        return _show_default_node_shapes_internal;
     }
 
     public boolean isShowDomainLabels() {
@@ -1291,7 +1297,18 @@ public final class Configuration {
             _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
         }
         else if ( key.equals( "show_default_node_shapes" ) ) {
-            setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+            ForesterUtil
+                    .printWarningMessage( Constants.PRG_NAME,
+                                          "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
+            final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
+            setShowDefaultNodeShapesInternal( b );
+            setShowDefaultNodeShapesExternal( b );
+        }
+        else if ( key.equals( "show_default_node_shapes_internal" ) ) {
+            setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+        }
+        else if ( key.equals( "show_default_node_shapes_external" ) ) {
+            setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
         }
         else if ( key.equals( "default_node_size" ) ) {
             final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
@@ -1635,8 +1652,12 @@ public final class Configuration {
         _show_branch_length_values = show_branch_length_values;
     }
 
-    public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
-        _show_default_node_shapes = show_default_node_shapes;
+    public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+        _show_default_node_shapes_internal = show_default_node_shapes_internal;
+    }
+
+    public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+        _show_default_node_shapes_external = show_default_node_shapes_external;
     }
 
     public void setShowDomainLabels( final boolean show_domain_labels ) {