X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=da1bdc42c5dba51c36d81598f3cbc3f21d374397;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;hp=c4978d9571fedf7c2626762ded42afccfbd659e2;hpb=59c04a80132a551d4e10864764747df35759d2c6;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index c4978d9..da1bdc4 100644
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -238,6 +238,7 @@ public final class Configuration {
     private float                           _print_line_width                                      = Constants.PDF_LINE_WIDTH_DEFAULT;
     private boolean                         _show_annotation_ref_source                            = true;
     private boolean                         _show_default_node_shapes_external                     = false;
+    private boolean                         _show_default_node_shapes_for_marked_nodes             = false;
     private boolean                         _show_default_node_shapes_internal                     = false;
     private boolean                         _show_domain_labels                                    = true;
     private boolean                         _show_overview                                         = true;
@@ -746,6 +747,10 @@ public final class Configuration {
         return _show_default_node_shapes_external;
     }
 
+    public boolean isShowDefaultNodeShapesForMarkedNodes() {
+        return _show_default_node_shapes_for_marked_nodes;
+    }
+
     public boolean isShowDefaultNodeShapesInternal() {
         return _show_default_node_shapes_internal;
     }
@@ -1380,20 +1385,15 @@ public final class Configuration {
         else if ( key.equals( "gui_button_border_color" ) ) {
             _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
         }
-        else if ( key.equals( "show_default_node_shapes" ) ) {
-            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( "show_node_shapes_for_nodes_with_vis_data" ) ) {
+            setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+        }
         else if ( key.equals( "default_node_size" ) ) {
             final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
             setDefaultNodeShapeSize( i );
@@ -1761,6 +1761,10 @@ public final class Configuration {
         _show_default_node_shapes_external = show_default_node_shapes_external;
     }
 
+    public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
+        _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
+    }
+
     public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
         _show_default_node_shapes_internal = show_default_node_shapes_internal;
     }