messed up at the moment

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 72f2e27..ec2e600 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -20,7 +20,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -101,7 +101,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
-    static final String         DISPLAY_NODE_BOXES_LABEL                = "Show Node Shapes";
+    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Show External Node Shapes";
+    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Show Internal Node Shapes";
     static final String         SHOW_OVERVIEW_LABEL                     = "Show Overview";
     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
@@ -170,7 +171,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
     JMenuItem                   _overview_placment_mi;
     JMenuItem                   _choose_minimal_confidence_mi;
-    JCheckBoxMenuItem           _show_default_node_shapes_cbmi;
+    JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
+    JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
     JMenuItem                   _cycle_node_shape_mi;
     JMenuItem                   _cycle_node_fill_mi;
     JMenuItem                   _choose_node_size_mi;
@@ -208,7 +210,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JCheckBoxMenuItem           _circular_type_cbmi;
     // view as text menu:
     JMenuItem                   _view_as_NH_item;
-    JMenuItem                   _view_as_NHX_item;
     JMenuItem                   _view_as_XML_item;
     JMenuItem                   _view_as_nexus_item;
     JMenuItem                   _display_basic_information_item;
@@ -297,9 +298,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _view_as_NH_item ) {
             viewAsNH();
         }
-        else if ( o == _view_as_NHX_item ) {
-            viewAsNHX();
-        }
         else if ( o == _view_as_XML_item ) {
             viewAsXML();
         }
@@ -370,7 +368,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _color_labels_same_as_parent_branch ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _show_default_node_shapes_cbmi ) {
+        else if ( o == _show_default_node_shapes_internal_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        else if ( o == _show_default_node_shapes_external_cbmi ) {
             updateOptions( getOptions() );
         }
         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
@@ -630,11 +631,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _view_jmenu.addSeparator();
         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
-        _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
         customizeJMenuItem( _display_basic_information_item );
         customizeJMenuItem( _view_as_NH_item );
-        customizeJMenuItem( _view_as_NHX_item );
         customizeJMenuItem( _view_as_XML_item );
         customizeJMenuItem( _view_as_nexus_item );
         _jmenubar.add( _view_jmenu );
@@ -889,7 +888,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
         sb.append( "\n" );
-        sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
+        sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
         TextFrame.instantiate( sb.toString(), "Help", _textframes );
     }
@@ -1067,8 +1066,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _abbreviate_scientific_names.isSelected() );
         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
                 && _color_labels_same_as_parent_branch.isSelected() );
-        options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
-                && _show_default_node_shapes_cbmi.isSelected() );
+        options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+                && _show_default_node_shapes_internal_cbmi.isSelected() );
+        options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+                && _show_default_node_shapes_external_cbmi.isSelected() );
         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
@@ -1198,16 +1199,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
-    void viewAsNHX() {
-        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
-            String title = "NHX";
-            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
-            }
-            showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
-        }
-    }
-
     void viewAsXML() {
         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
             String title = "phyloXML";
@@ -1369,7 +1360,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
      */
     static void about() {
         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
-        about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
+        about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
         about.append( "All Rights Reserved\n" );
         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );