in progress (special coloring is still true)

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 7ea1610..2796e00 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -122,6 +122,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private ButtonGroup                 _radio_group_1;
     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
+    private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
     private JMenuItem                   _cycle_node_shape_mi;
     private JMenuItem                   _cycle_node_fill_mi;
     private JMenuItem                   _choose_node_size_mi;
@@ -751,13 +752,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
-        /////
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
         _options_jmenu
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
@@ -782,7 +784,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
-        /////
         _options_jmenu.addSeparator();
         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
                                                                 getConfiguration() ) );
@@ -807,6 +808,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 .isShowDefaultNodeShapesExternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
                 .isShowDefaultNodeShapesInternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+                .isShowDefaultNodeShapesForMarkedNodes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
@@ -1309,6 +1312,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 && _show_default_node_shapes_internal_cbmi.isSelected() );
         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
                 && _show_default_node_shapes_external_cbmi.isSelected() );
+        options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+                && _show_default_node_shapes_for_marked_cbmi.isSelected() );
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index c4978d9..da1bdc4 100644 (file)
--- 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;
     }

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index b9c91cd..86ac819 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                                             // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9899 beta";
-    final static String         PRG_DATE                                                      = "140925";
+    final static String         VERSION                                                       = "0.9900 beta";
+    final static String         PRG_DATE                                                      = "141010";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 2411d9d..dedc7ac 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -107,8 +107,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
-    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
-    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
@@ -193,6 +194,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _choose_minimal_confidence_mi;\r
     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
+    JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
     JMenuItem                   _cycle_node_shape_mi;\r
     JMenuItem                   _cycle_node_fill_mi;\r
     JMenuItem                   _choose_node_size_mi;\r
@@ -429,6 +431,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
             updateOptions( getOptions() );\r
         }\r
+        else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
             updateOptions( getOptions() );\r
             showWhole();\r
@@ -1308,6 +1313,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
+        options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+                && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
         }\r

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 8314448..43fdc2e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -208,13 +208,14 @@ public final class MainFrameApplet extends MainFrame {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
-        ////////////
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
         _options_jmenu
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
@@ -239,7 +240,6 @@ public final class MainFrameApplet extends MainFrame {
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
-        //////
         _options_jmenu.addSeparator();
         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
                                                                 getConfiguration() ) );
@@ -255,6 +255,8 @@ public final class MainFrameApplet extends MainFrame {
                 .isShowDefaultNodeShapesInternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
                 .isShowDefaultNodeShapesExternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+                .isShowDefaultNodeShapesForMarkedNodes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 125471d..e0d7990 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -901,13 +901,14 @@ public final class MainFrameApplication extends MainFrame {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
         _radio_group_1.add( _uniform_cladograms_rbmi );\r
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
-        ///////\r
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
         _options_jmenu\r
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
         _options_jmenu\r
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+        _options_jmenu\r
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
@@ -930,7 +931,6 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
-        ///////\r
         _options_jmenu.addSeparator();\r
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
@@ -956,7 +956,6 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
         _options_jmenu\r
                 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
-        //\r
         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
         _options_jmenu\r
                 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
@@ -975,7 +974,6 @@ public final class MainFrameApplication extends MainFrame {
         _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
         _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
         _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
-        // \r
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
         _options_jmenu\r
                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
@@ -993,6 +991,8 @@ public final class MainFrameApplication extends MainFrame {
                 .isShowDefaultNodeShapesExternal() );\r
         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
                 .isShowDefaultNodeShapesInternal() );\r
+        customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+                .isShowDefaultNodeShapesForMarkedNodes() );\r
         customizeJMenuItem( _cycle_node_shape_mi );\r
         customizeJMenuItem( _cycle_node_fill_mi );\r
         customizeJMenuItem( _choose_node_size_mi );\r

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 387bba6..36d0224 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -78,6 +78,7 @@ final public class Options {
     private boolean                           _search_case_sensitive;
     private boolean                           _show_annotation_ref_source;
     private boolean                           _show_confidence_stddev;
+    private boolean                           _show_default_node_shapes_for_marked_nodes;
     private boolean                           _show_default_node_shapes_external;
     private boolean                           _show_default_node_shapes_internal;
     private boolean                           _show_domain_labels;
@@ -279,6 +280,10 @@ final public class Options {
         return _show_default_node_shapes_external;
     }
 
+    boolean isShowDefaultNodeShapesForMarkedNodes() {
+        return _show_default_node_shapes_for_marked_nodes;
+    }
+
     boolean isShowDefaultNodeShapesInternal() {
         return _show_default_node_shapes_internal;
     }
@@ -421,6 +426,10 @@ final public class Options {
         _show_default_node_shapes_internal = show_default_node_shapes_internal;
     }
 
+    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;
+    }
+
     final void setShowOverview( final boolean show_overview ) {
         _show_overview = show_overview;
     }
@@ -446,6 +455,7 @@ final public class Options {
         _background_color_gradient = false;
         _show_default_node_shapes_internal = false;
         _show_default_node_shapes_external = false;
+        _show_default_node_shapes_for_marked_nodes = false;
         if ( AptxUtil.isUsOrCanada() ) {
             _print_size_x = Constants.US_LETTER_SIZE_X;
             _print_size_y = Constants.US_LETTER_SIZE_Y;
@@ -551,6 +561,7 @@ final public class Options {
             }
             instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
             instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+            instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
             if ( configuration.getExtDescNodeDataToReturn() != null ) {
                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index df7306b..bb31d7e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -136,6 +136,7 @@ import org.forester.util.TaxonomyUtil;
 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 
+    public final static boolean          SPECIAL_DOMAIN_COLORING                            = true;
     final static Cursor                  ARROW_CURSOR                                       = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
     final static Cursor                  CUT_CURSOR                                         = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
     final static Cursor                  HAND_CURSOR                                        = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
@@ -173,7 +174,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private static final BasicStroke     STROKE_2                                           = new BasicStroke( 2f );
     private static final double          TWO_PI                                             = 2 * Math.PI;
     private final static int             WIGGLE                                             = 2;
-    private static final String          SHOW_ONLY_THIS_CONF_TYPE                           = null;                                                     //TODO remove me
+    private static final String          SHOW_ONLY_THIS_CONF_TYPE                           = "posterior probability";                                  //TODO remove me
     HashMap<Long, Short>                 _nodeid_dist_to_leaf                               = new HashMap<Long, Short>();
     final private Arc2D                  _arc                                               = new Arc2D.Double();
     private AffineTransform              _at;
@@ -255,7 +256,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private float                        _y_distance                                        = 0.0f;
     private int                          _length_of_longest_text;
     private int                          _longest_domain;
-    public final static boolean          SPECIAL_DOMAIN_COLORING                            = true;
     //  private Image                           offscreenImage;
     //  private Graphics                        offscreenGraphics;
     //  private Dimension                       offscreenDimension;
@@ -4166,6 +4166,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
                 || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
                 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+                || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
+                        && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
+                        .getNodeVisualData().isEmpty() ) )
                 || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
                         .getNodeData().getNodeVisualData().getNodeColor() != null )
                         || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )