Apple Macintosh graphics are slow, turn off anti-alias.

[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 733c04a..37f84e4 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -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;
@@ -366,7 +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 ) {
@@ -1061,8 +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() ) ) {
@@ -1114,10 +1121,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
         if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.YES );
+            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
         }
         else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
         }
         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
@@ -1204,7 +1211,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     private void annotateSequences() {
         if ( getCurrentTreePanel() != null ) {
-            final Set<Integer> nodes = getCurrentTreePanel().getFoundNodes();
+            final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
             if ( ( nodes == null ) || nodes.isEmpty() ) {
                 JOptionPane
                         .showMessageDialog( this,
@@ -1253,7 +1260,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                         desc = desc.replaceAll( "\\s+", " " );
                     }
                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
-                        for( final Integer id : nodes ) {
+                        for( final Long id : nodes ) {
                             final PhylogenyNode n = phy.getNode( id );
                             ForesterUtil.ensurePresenceOfSequence( n );
                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
@@ -1353,7 +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" );