X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=84f42f8a24d77387872ee3b84a7db23f17e1b033;hb=008a04d03169e3fccd2d1580d1ed4a8fc5ff3aeb;hp=d0c6c92e64cb524f1053e2ee5ff702ecbc45350f;hpb=ccf4c584032d16ed0ed8d0678f01305887724f96;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index d0c6c92..84f42f8 100644
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2009 Christian M. Zmasek
 // Copyright (C) 2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -35,7 +35,7 @@ import org.forester.util.ForesterUtil;
 final public class Options {
 
     static final double             MIN_CONFIDENCE_DEFAULT = 0.0;
-    private boolean                 _show_node_boxes;
+    private NodeShape                 _default_node_shape;
     private boolean                 _show_branch_length_values;
     private boolean                 _internal_number_are_confidence_for_nh_parsing;
     private boolean                 _show_scale;
@@ -68,6 +68,14 @@ final public class Options {
     private boolean                 _show_domain_labels;
     private boolean                 _color_labels_same_as_parent_branch;
     private boolean                 _abbreviate_scientific_names;
+    
+    enum NodeShape {
+        NONE, 
+        CIRCLE_WITH_GRADIENT,
+        CIRCLE_SOLID,
+        RECTANGLE_WITH_GRADIENT,
+        RECTANGLE_SOLID;
+    }
 
     private Options() {
         init();
@@ -122,7 +130,7 @@ final public class Options {
     }
 
     final private void init() {
-        _show_node_boxes = false;
+        _default_node_shape = NodeShape.RECTANGLE_WITH_GRADIENT;
         _show_branch_length_values = false;
         _internal_number_are_confidence_for_nh_parsing = false;
         _show_scale = false;
@@ -231,8 +239,8 @@ final public class Options {
         return _show_branch_length_values;
     }
 
-    final boolean isShowNodeBoxes() {
-        return _show_node_boxes;
+    final NodeShape getDefaultNodeShape() {
+        return _default_node_shape;
     }
 
     final boolean isShowOverview() {
@@ -365,8 +373,8 @@ final public class Options {
         _show_branch_length_values = show_branch_length_values;
     }
 
-    final void setShowNodeBoxes( final boolean show_node_boxes ) {
-        _show_node_boxes = show_node_boxes;
+    final void setDefaultNodeShape( final NodeShape default_node_shape ) {
+        _default_node_shape = default_node_shape;
     }
 
     final void setShowOverview( final boolean show_overview ) {
@@ -475,7 +483,11 @@ final public class Options {
     }
 
     boolean isAllowMagnificationOfTaxonomyImages() {
-        // TODO Auto-generated method stub
         return true;
     }
+
+   int getDefaultNodeBoxSize() {
+        // TODO make variable ~~
+        return 8;
+    }
 }