inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 42e7ab1..d26127a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -397,9 +397,23 @@ public final class AptxUtil {
         return iter.hasNext();
     }
 
-    final static String createBasicInformation( final Phylogeny phy ) {
+    final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
         final StringBuilder desc = new StringBuilder();
         if ( ( phy != null ) && !phy.isEmpty() ) {
+            String f = null;
+            if ( treefile != null ) {
+                try {
+                    f = treefile.getCanonicalPath();
+                }
+                catch ( final IOException e ) {
+                    //Not important, ignore.
+                }
+                if ( !ForesterUtil.isEmpty( f ) ) {
+                    desc.append( "Path: " );
+                    desc.append( f );
+                    desc.append( "\n" );
+                }
+            }
             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
                 desc.append( "Name: " );
                 desc.append( phy.getName() );
@@ -488,10 +502,10 @@ public final class AptxUtil {
                 desc.append( "\n" );
                 desc.append( "Descendants per node statistics: " );
                 desc.append( "\n" );
-                desc.append( "    Median: " + ForesterUtil.round( ds.median(), 2 ) );
+                desc.append( "    Median: " + ForesterUtil.round( ds.median(), 6 ) );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (stdev: "
-                        + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) + ")" );
+                desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
+                        + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
                 desc.append( "\n" );
@@ -530,9 +544,9 @@ public final class AptxUtil {
                             desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
                         }
                         desc.append( "\n" );
-                        desc.append( "    Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+                        desc.append( "    Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
                         desc.append( "\n" );
-                        desc.append( "    Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+                        desc.append( "    Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
                         desc.append( "\n" );
                     }
                 }

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 286bf47..da77e22 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -102,6 +102,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JCheckBoxMenuItem           _abbreviate_scientific_names;
     private JCheckBoxMenuItem           _screen_antialias_cbmi;
     private JCheckBoxMenuItem           _background_gradient_cbmi;
+    private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
@@ -337,6 +338,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
             }
         }
+        else if ( o == _color_by_taxonomic_group_cbmi ) {
+            updateOptions( getOptions() );
+        }
         repaint();
     }
 
@@ -700,35 +704,40 @@ 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_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_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 ) );
+        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
+        }
+        _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
+        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
+        _options_jmenu
+                .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
         _options_jmenu
                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
-        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
-        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
-        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
         _options_jmenu
                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
+        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
-        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
-            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
-        }
+        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
         _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() ) );
@@ -741,6 +750,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _switch_colors_mi );
         customizeJMenuItem( _overview_placment_mi );
+        customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
         customizeCheckBoxMenuItem( _label_direction_cbmi,
                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
@@ -820,9 +830,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _view_jmenu
                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
         _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_nexus_item = new JMenuItem( "View as Nexus" ) );
+        _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+        _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+        _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
         customizeJMenuItem( _display_basic_information_item );
         customizeJMenuItem( _view_as_NH_item );
         customizeJMenuItem( _view_as_XML_item );
@@ -875,9 +885,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
             String title = "Basic Information";
             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
-                title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+                title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
             }
-            showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
+            showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
         }
     }
 
@@ -1350,6 +1360,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
         }
+        if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
+            options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
+        }
     }
 
     void updateTypeCheckboxes( final Options options, final Object o ) {
@@ -1361,7 +1374,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
             String title = "Nexus";
             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
-                title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
                                    .getNhConversionSupportValueStyle() ),
@@ -1373,7 +1386,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
             String title = "New Hampshire";
             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
-                title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
             showTextFrame( getMainPanel().getCurrentPhylogeny()
                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
@@ -1385,7 +1398,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
             String title = "phyloXML";
             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
-                title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index c4b2425..0f7fd20 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -30,6 +30,7 @@ import java.awt.Container;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.File;
 import java.io.IOException;
 import java.util.LinkedList;
 import java.util.List;
@@ -96,33 +97,33 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";
     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
-    static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Display Branch Length Values";
-    static final String         COLOR_BY_TAXONOMIC_GROUP                = "Color by Taxonomic Group";
-    static final String         DISPLAY_SCALE_LABEL                     = "Display Scale";
+    static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";
+    static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";
+    static final String         DISPLAY_SCALE_LABEL                     = "Scale";
     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
-    static final String         COLOR_LABELS_LABEL                      = "Color Labels Same as Parent Branch";
+    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_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         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";
+    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";
+    static final String         SHOW_OVERVIEW_LABEL                     = "Overview";
     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
-    static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
-    static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Show Seq Annotation Ref Sources";
+    static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";
+    static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";
     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
-    static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
+    static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";
     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
-    static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Show Basic Tree Information";
+    static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";
     JMenuBar                    _jmenubar;
     JMenu                       _file_jmenu;
     JMenu                       _tools_menu;
@@ -322,7 +323,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             switchColors();
         }
         else if ( o == _display_basic_information_item ) {
-            displayBasicInformation();
+            displayBasicInformation( getCurrentTreePanel().getTreeFile() );
         }
         else if ( o == _view_as_NH_item ) {
             viewAsNH();
@@ -664,9 +665,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _view_jmenu = createMenu( "View", getConfiguration() );
         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
         _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_nexus_item = new JMenuItem( "View as Nexus" ) );
+        _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+        _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+        _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
         customizeJMenuItem( _display_basic_information_item );
         customizeJMenuItem( _view_as_NH_item );
         customizeJMenuItem( _view_as_XML_item );
@@ -761,13 +762,13 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
-    void displayBasicInformation() {
+    void displayBasicInformation( final File treefile ) {
         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
             String title = "Basic Information";
             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+                title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
             }
-            showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
+            showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
         }
     }
 
@@ -1395,7 +1396,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
             String title = "Nexus";
             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
                            title );
@@ -1406,7 +1407,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
             String title = "New Hampshire";
             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
             showTextFrame( _mainpanel.getCurrentPhylogeny()
                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
@@ -1418,7 +1419,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
             String title = "phyloXML";
             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 7580196..a5cd07d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -208,35 +208,40 @@ 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_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu
-                .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+                .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( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+                .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
+        }
+        _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
+        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
+        _options_jmenu
+                .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
         _options_jmenu
                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
-        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
-        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
-        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
-        _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
-        _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
+        _options_jmenu
+                .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
+        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
+        _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
-        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
-            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
-        }
-        _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
+        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
         _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() ) );
@@ -256,6 +261,7 @@ public final class MainFrameApplet extends MainFrame {
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
+        customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 5d13def..c146900 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -884,6 +884,7 @@ public final class MainFrameApplication 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( SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
         _options_jmenu
@@ -892,28 +893,29 @@ public final class MainFrameApplication extends MainFrame {
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
+        }
+        _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
+        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
         _options_jmenu
                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
-        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
-        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
-        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
-        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
-        _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
+        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
+        _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
-        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
-            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
-        }
-        _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
+        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
         _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( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );