in progress...

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 342fcdb..162ac79 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -93,10 +93,11 @@ public final class Configuration {
     private boolean                         _abbreviate_scientific_names                           = false;
     private boolean                         _color_labels_same_as_parent_branch                    = false;
     private int                             _default_bootstrap_samples                             = -1;
+    private boolean                         _show_default_node_shapes                              = false;
     private NodeShape                       _default_node_shape                                    = NodeShape.NONE;
     private NodeFill                        _default_node_fill                                     = NodeFill.GRADIENT;
     private short                           _default_node_shape_size                               = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-    private boolean                         _taxonomy_colorize_node_shapes_instead_of_labels       = false;
+    private boolean                         _taxonomy_colorize_node_shapes       = false;
     final static int                        display_as_phylogram                                   = 0;
     final static int                        show_node_names                                        = 1;
     final static int                        show_tax_code                                          = 2;
@@ -106,22 +107,23 @@ public final class Configuration {
     final static int                        color_according_to_species                             = 6;
     final static int                        color_branches                                         = 7;
     final static int                        width_branches                                         = 8;
-    final static int                        show_domain_architectures                              = 9;
-    final static int                        show_binary_characters                                 = 10;
-    final static int                        show_binary_character_counts                           = 11;
-    final static int                        show_gene_names                                        = 12;
-    final static int                        show_sequence_acc                                      = 13;
-    final static int                        display_internal_data                                  = 14;
-    final static int                        dynamically_hide_data                                  = 15;
-    final static int                        show_taxonomy_scientific_names                         = 16;
-    final static int                        show_taxonomy_common_names                             = 17;
-    final static int                        color_according_to_annotation                          = 18;
-    final static int                        show_property                                          = 19;
-    final static int                        show_gene_symbols                                      = 20;
-    final static int                        node_data_popup                                        = 21;
-    final static int                        show_relation_confidence                               = 22;
-    final static int                        show_vector_data                                       = 23;
-    final static int                        show_taxonomy_images                                   = 24;
+    final static int                        show_custom_node_shapes                                = 9;
+    final static int                        show_domain_architectures                              = 10;
+    final static int                        show_binary_characters                                 = 11;
+    final static int                        show_binary_character_counts                           = 12;
+    final static int                        show_gene_names                                        = 13;
+    final static int                        show_sequence_acc                                      = 14;
+    final static int                        display_internal_data                                  = 15;
+    final static int                        dynamically_hide_data                                  = 16;
+    final static int                        show_taxonomy_scientific_names                         = 17;
+    final static int                        show_taxonomy_common_names                             = 18;
+    final static int                        color_according_to_annotation                          = 19;
+    final static int                        show_property                                          = 20;
+    final static int                        show_gene_symbols                                      = 21;
+    final static int                        node_data_popup                                        = 22;
+    final static int                        show_relation_confidence                               = 23;
+    final static int                        show_vector_data                                       = 24;
+    final static int                        show_taxonomy_images                                   = 25;
     // ------------------
     // Click-to options
     // ------------------
@@ -153,7 +155,7 @@ public final class Configuration {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
             { "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" },
             { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
-            { "Use Branch-Width", "nodisplay", "no" }, { "Domains", "nodisplay", "no" },
+            { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes"}, { "Domains", "nodisplay", "no" },
             { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
             { "Prot/Gene Name", "display", "no" }, { "Prot/Gene Acc", "display", "no" },
             { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
@@ -364,6 +366,7 @@ public final class Configuration {
         return _cladogram_type;
     }
 
+    
     private int getClickToIndex( final String name ) {
         int index = -1;
         if ( name.equals( "edit_info" ) ) {
@@ -1063,6 +1066,9 @@ public final class Configuration {
             _domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
         }
         //
+        else if ( key.equals( "show_default_node_shapes" ) ) {
+            setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+        }
         else if ( key.equals( "default_node_size" ) ) {
             final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
             setDefaultNodeShapeSize( i );
@@ -1100,7 +1106,7 @@ public final class Configuration {
             }
         }
         else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
-            setTaxonomyColorizeNodeShapesInsteadOfLabels( parseBoolean( ( String ) st.nextElement() ) );
+            setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
         }
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
@@ -1232,6 +1238,9 @@ public final class Configuration {
             else if ( key.equals( "show_relation_confidence" ) ) {
                 key_index = Configuration.show_relation_confidence;
             }
+            else if ( key.equals( "show_custom_node_shapes" ) ) {
+                key_index = Configuration.show_custom_node_shapes;
+            }
             // If we've found the key, set the values
             if ( key_index >= 0 ) {
                 display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
@@ -1408,11 +1417,19 @@ public final class Configuration {
         return _default_node_shape_size;
     }
 
-    private void setTaxonomyColorizeNodeShapesInsteadOfLabels( final boolean taxonomy_colorize_node_shapes_instead_of_labels ) {
-        _taxonomy_colorize_node_shapes_instead_of_labels = taxonomy_colorize_node_shapes_instead_of_labels;
+    private void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
+        _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
     }
 
-    public boolean isTaxonomyColorizeNodeShapesInsteadOfLabels() {
-        return _taxonomy_colorize_node_shapes_instead_of_labels;
+    public boolean isTaxonomyColorizeNodeShapes() {
+        return _taxonomy_colorize_node_shapes;
     }
+    
+    public boolean isShowDefaultNodeShapes() {
+        return _show_default_node_shapes;   
+    }    
+    private void setShowDefaultNodeShapes(boolean show_default_node_shapes) {
+         _show_default_node_shapes =show_default_node_shapes;   
+    } 
+    
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 1fab617..0b5433b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -33,6 +33,7 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 
+import javax.swing.Icon;
 import javax.swing.JApplet;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JFrame;
@@ -82,13 +83,17 @@ 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           = "Display Node Boxes";
+    static final String       DISPLAY_NODE_BOXES_LABEL           = "Display 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";
     static final String       SHOW_DOMAIN_LABELS_LABEL           = "Show Domain Labels";
     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";
     JMenuBar                  _jmenubar;
     JMenu                     _file_jmenu;
     JMenu                     _tools_menu;
@@ -131,7 +136,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     // _  screen display
     JCheckBoxMenuItem         _screen_antialias_cbmi;
     JCheckBoxMenuItem         _background_gradient_cbmi;
-    JCheckBoxMenuItem         _show_node_boxes_cbmi;
+   
     JRadioButtonMenuItem      _non_lined_up_cladograms_rbmi;
     JRadioButtonMenuItem      _uniform_cladograms_rbmi;
     JRadioButtonMenuItem      _ext_node_dependent_cladogram_rbmi;
@@ -143,6 +148,12 @@ 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;
+    JMenuItem                 _cycle_node_shape_mi;
+    JMenuItem                 _cycle_node_fill_mi;
+    JMenuItem                 _choose_node_size_mi;
+    JCheckBoxMenuItem                 _taxonomy_colorize_node_shapes_cbmi;
     // _  print
     JCheckBoxMenuItem         _graphics_export_visible_only_cbmi;
     JCheckBoxMenuItem         _antialias_print_cbmi;
@@ -320,9 +331,13 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _color_labels_same_as_parent_branch ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _show_node_boxes_cbmi ) {
+        else if ( o == _show_default_node_shapes_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        
         else if ( o == _non_lined_up_cladograms_rbmi ) {
             updateOptions( getOptions() );
             showWhole();
@@ -851,7 +866,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
                 && _color_labels_same_as_parent_branch.isSelected() );
         //TODO FIXME ~~
-        //options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.isSelected() );
+        options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) && _show_default_node_shapes_cbmi.isSelected() );
+        options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
+        
         //TODO FIXME ~~
         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/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 6a63002..ec01faf 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -178,7 +178,7 @@ 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_node_boxes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
+        _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_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 ) );
@@ -208,7 +208,7 @@ public final class MainFrameApplet extends MainFrame {
         customizeJMenuItem( _switch_colors_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _overview_placment_mi );
-        customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().getDefaultNodeShape() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().getDefaultNodeShape() );
         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 186a567..4ef0472 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -44,6 +44,7 @@ import java.util.List;
 import java.util.Set;
 
 import javax.swing.ButtonGroup;
+import javax.swing.Icon;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JFileChooser;
 import javax.swing.JMenu;
@@ -187,6 +188,7 @@ public final class MainFrameApplication extends MainFrame {
     private final static SequencesFileFilter seqsfilter                      = new SequencesFileFilter();
     private final static DefaultFilter       defaultfilter                   = new DefaultFilter();
     private static final long                serialVersionUID                = -799735726778865234L;
+  
     private final JFileChooser               _values_filechooser;
     private final JFileChooser               _open_filechooser;
     private final JFileChooser               _msa_filechooser;
@@ -711,7 +713,17 @@ 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_node_boxes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+        
+        //
+        _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+        
+        
+        _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( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
         _options_jmenu
                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
@@ -763,7 +775,11 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _choose_pdf_width_mi );
         customizeJMenuItem( _overview_placment_mi );
         //TODO FIXME ~~
-        //customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().getDefaultNodeShape() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+        customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
+        customizeJMenuItem( _cycle_node_shape_mi );
+        customizeJMenuItem( _cycle_node_fill_mi );
+        customizeJMenuItem( _choose_node_size_mi );
         //TODO FIXME ~~
         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 31c9873..294afdc 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -70,7 +70,8 @@ final public class Options {
     private NodeShape               _default_node_shape;
     private NodeFill                _default_node_fill;
     private short                   _default_node_shape_size;
-    private boolean                 _taxonomy_colorize_node_shapes_instead_of_labels;
+    private boolean                 _taxonomy_colorize_node_shapes;
+    private boolean                  _show_default_node_shapes;
 
     private Options() {
         init();
@@ -84,11 +85,6 @@ final public class Options {
         return _cladogram_type;
     }
 
-    int getDefaultNodeBoxSize() {
-        // TODO make variable ~~
-        return 8;
-    }
-
     final NodeFill getDefaultNodeFill() {
         return _default_node_fill;
     }
@@ -145,7 +141,7 @@ final public class Options {
         _default_node_shape = NodeShape.NONE;
         _default_node_fill = NodeFill.GRADIENT;
         _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-        _taxonomy_colorize_node_shapes_instead_of_labels = false;
+        _taxonomy_colorize_node_shapes = false;
         _show_branch_length_values = false;
         _internal_number_are_confidence_for_nh_parsing = false;
         _show_scale = false;
@@ -154,6 +150,7 @@ final public class Options {
         _graphics_export_visible_only = false;
         _editable = true;
         _background_color_gradient = false;
+        _show_default_node_shapes = false;
         if ( Util.isUsOrCanada() ) {
             _print_size_x = Constants.US_LETTER_SIZE_X;
             _print_size_y = Constants.US_LETTER_SIZE_Y;
@@ -270,8 +267,8 @@ final public class Options {
         return _show_scale;
     }
 
-    boolean isTaxonomyColorizeNodeShapesInsteadOfLabels() {
-        return _taxonomy_colorize_node_shapes_instead_of_labels;
+    boolean isTaxonomyColorizeNodeShapes() {
+        return _taxonomy_colorize_node_shapes;
     }
 
     final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
@@ -420,14 +417,20 @@ final public class Options {
         _show_scale = show_scale;
     }
 
-    void setTaxonomyColorizeNodeShapesInsteadOfLabels( final boolean taxonomy_colorize_node_shapes_instead_of_labels ) {
-        _taxonomy_colorize_node_shapes_instead_of_labels = taxonomy_colorize_node_shapes_instead_of_labels;
+    void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
+        _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
     }
 
     final static Options createDefaultInstance() {
         return new Options();
     }
 
+     boolean isShowDefaultNodeShapes() {
+        return                  _show_default_node_shapes;   
+    }    
+     void setShowDefaultNodeShapes(boolean show_default_node_shapes) {
+         _show_default_node_shapes = show_default_node_shapes;
+    }
     final static Options createInstance( final Configuration configuration ) {
         final Options instance = createDefaultInstance();
         if ( configuration != null ) {
@@ -484,8 +487,9 @@ final public class Options {
             if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
                 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
             }
-            instance.setTaxonomyColorizeNodeShapesInsteadOfLabels( configuration
-                    .isTaxonomyColorizeNodeShapesInsteadOfLabels() );
+            instance.setTaxonomyColorizeNodeShapes( configuration
+                    .isTaxonomyColorizeNodeShapes() );
+            instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
         }
         return instance;
     }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index a37c5dc..8e94a08 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -268,8 +268,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _configuration = configuration;
         _phylogeny = t;
         _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
-        _box_size = tjp.getOptions().getDefaultNodeBoxSize();
-        _half_box_size = tjp.getOptions().getDefaultNodeBoxSize() / 2;
+        _box_size = tjp.getOptions().getDefaultNodeShapeSize();
+        _half_box_size = tjp.getOptions().getDefaultNodeShapeSize() / 2;
         _half_box_size_plus_wiggle = _half_box_size + WIGGLE;
         init();
         // if ( !_phylogeny.isEmpty() ) {