inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 5b091b4..9146fe8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -113,7 +113,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _collapse_species_specific_subtrees;
     private JMenuItem                   _overview_placment_mi;
     private ButtonGroup                 _radio_group_1;
-    private JCheckBoxMenuItem           _show_default_node_shapes_cbmi;
+    private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
+    private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
     private JMenuItem                   _cycle_node_shape_mi;
     private JMenuItem                   _cycle_node_fill_mi;
     private JMenuItem                   _choose_node_size_mi;
@@ -266,7 +267,10 @@ public class ArchaeopteryxE extends JApplet 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 ) {
@@ -620,7 +624,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 .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_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
+                .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( _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 ) );
@@ -659,7 +665,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
-        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+                .isShowDefaultNodeShapesExternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+                .isShowDefaultNodeShapesInternal() );
         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
@@ -1017,8 +1026,10 @@ public class ArchaeopteryxE extends JApplet 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() ) ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 7b440a8..8fe8076 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -95,7 +95,8 @@ public final class Configuration {
     private boolean                         _show_domain_labels                                    = true;
     private boolean                         _abbreviate_scientific_names                           = false;
     private boolean                         _color_labels_same_as_parent_branch                    = false;
-    private boolean                         _show_default_node_shapes                              = false;
+    private boolean                         _show_default_node_shapes_internal                     = false;
+    private boolean                         _show_default_node_shapes_external                     = false;
     private NodeShape                       _default_node_shape                                    = NodeShape.CIRCLE;
     private NodeFill                        _default_node_fill                                     = NodeFill.GRADIENT;
     private short                           _default_node_shape_size                               = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
@@ -661,8 +662,12 @@ public final class Configuration {
         return _show_branch_length_values;
     }
 
-    public boolean isShowDefaultNodeShapes() {
-        return _show_default_node_shapes;
+    public boolean isShowDefaultNodeShapesExternal() {
+        return _show_default_node_shapes_external;
+    }
+
+    public boolean isShowDefaultNodeShapesInternal() {
+        return _show_default_node_shapes_internal;
     }
 
     public boolean isShowDomainLabels() {
@@ -1292,7 +1297,18 @@ 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() ) );
+            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( "default_node_size" ) ) {
             final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
@@ -1636,8 +1652,12 @@ public final class Configuration {
         _show_branch_length_values = show_branch_length_values;
     }
 
-    public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
-        _show_default_node_shapes = show_default_node_shapes;
+    public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+        _show_default_node_shapes_internal = show_default_node_shapes_internal;
+    }
+
+    public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+        _show_default_node_shapes_external = show_default_node_shapes_external;
     }
 
     public void setShowDomainLabels( final boolean show_domain_labels ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 48f7447..258e926 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                                                       = "0.979";
-    final static String         PRG_DATE                                                      = "130104";
+    final static String         VERSION                                                       = "0.9800";
+    final static String         PRG_DATE                                                      = "130108";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
             "Arial", "Helvetica", "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 733c04a..36e691c 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() ) ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 871cbc6..1248fa5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -191,7 +191,10 @@ public final class MainFrameApplet extends MainFrame {
         _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_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+        _options_jmenu
+                .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 ) );
         _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 ) );
@@ -222,7 +225,10 @@ public final class MainFrameApplet extends MainFrame {
         customizeJMenuItem( _switch_colors_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _overview_placment_mi );
-        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+                .isShowDefaultNodeShapesInternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+                .isShowDefaultNodeShapesExternal() );
         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 3f3aa17..b50cbf2 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -962,7 +962,10 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu
                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( 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_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+        _options_jmenu
+                .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 ) );
         _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 ) );
@@ -1033,7 +1036,10 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _print_size_mi );
         customizeJMenuItem( _choose_pdf_width_mi );
         customizeJMenuItem( _overview_placment_mi );
-        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+                .isShowDefaultNodeShapesExternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+                .isShowDefaultNodeShapesInternal() );
         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 43b8fec..69bd5b8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -78,7 +78,8 @@ final public class Options {
     private NodeVisualization.NodeFill        _default_node_fill;
     private short                             _default_node_shape_size;
     private boolean                           _taxonomy_colorize_node_shapes;
-    private boolean                           _show_default_node_shapes;
+    private boolean                           _show_default_node_shapes_internal;
+    private boolean                           _show_default_node_shapes_external;
     private boolean                           _show_confidence_stddev;
     private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
     private NODE_DATA                         _ext_desc_data_to_return;
@@ -87,6 +88,30 @@ final public class Options {
         init();
     }
 
+    public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+        return _ext_desc_data_to_return;
+    }
+
+    public final boolean isShowDomainLabels() {
+        return _show_domain_labels;
+    }
+
+    public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+        _background_color_gradient = background_color_gradient;
+    }
+
+    public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+        _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+    }
+
+    public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+        _ext_desc_data_to_return = ext_desc_data_to_return;
+    }
+
+    public void setShowDomainLabels( final boolean show_domain_labels ) {
+        _show_domain_labels = show_domain_labels;
+    }
+
     final Font getBaseFont() {
         return _base_font;
     }
@@ -111,6 +136,10 @@ final public class Options {
         return _min_confidence_value;
     }
 
+    NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
+        return _nh_conversion_support_value_style;
+    }
+
     final NODE_LABEL_DIRECTION getNodeLabelDirection() {
         return _node_label_direction;
     }
@@ -147,69 +176,8 @@ final public class Options {
         return _scale_bar_length;
     }
 
-    final private void init() {
-        _default_node_shape = NodeShape.CIRCLE;
-        _default_node_fill = NodeFill.GRADIENT;
-        _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-        _taxonomy_colorize_node_shapes = false;
-        _show_branch_length_values = false;
-        _internal_number_are_confidence_for_nh_parsing = false;
-        _show_scale = false;
-        _antialias_screen = true;
-        _antialias_print = true;
-        _graphics_export_visible_only = false;
-        _editable = true;
-        _background_color_gradient = false;
-        _show_default_node_shapes = false;
-        if ( AptxUtil.isUsOrCanada() ) {
-            _print_size_x = Constants.US_LETTER_SIZE_X;
-            _print_size_y = Constants.US_LETTER_SIZE_Y;
-        }
-        else {
-            _print_size_x = Constants.A4_SIZE_X;
-            _print_size_y = Constants.A4_SIZE_Y;
-        }
-        _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
-        _print_black_and_white = false;
-        _print_using_actual_size = false;
-        _graphics_export_using_actual_size = true;
-        _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
-        _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
-        _match_whole_terms_only = false;
-        _search_case_sensitive = false;
-        _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
-        _show_overview = true;
-        _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
-        _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
-        _inverse_search_result = false;
-        _scale_bar_length = 0.0;
-        _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
-        _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
-        _nh_parsing_replace_underscores = false;
-        _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
-        _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
-        _show_domain_labels = true;
-        setAbbreviateScientificTaxonNames( false );
-        _color_labels_same_as_parent_branch = false;
-        _show_confidence_stddev = true;
-        _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
-        _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
-    }
-
-    boolean isShowConfidenceStddev() {
-        return _show_confidence_stddev;
-    }
-
-    void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
-        _show_confidence_stddev = show_confidence_stddev;
-    }
-
-    NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
-        return _nh_conversion_support_value_style;
-    }
-
-    void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
-        _nh_conversion_support_value_style = nh_conversion_support_value_style;
+    final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+        return _taxonomy_extraction;
     }
 
     final boolean isAbbreviateScientificTaxonNames() {
@@ -240,10 +208,6 @@ final public class Options {
         return _editable;
     }
 
-    final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
-        return _taxonomy_extraction;
-    }
-
     final boolean isGraphicsExportUsingActualSize() {
         return _graphics_export_using_actual_size;
     }
@@ -284,8 +248,16 @@ final public class Options {
         return _show_branch_length_values;
     }
 
-    public final boolean isShowDomainLabels() {
-        return _show_domain_labels;
+    boolean isShowConfidenceStddev() {
+        return _show_confidence_stddev;
+    }
+
+    boolean isShowDefaultNodeShapesExternal() {
+        return _show_default_node_shapes_external;
+    }
+
+    boolean isShowDefaultNodeShapesInternal() {
+        return _show_default_node_shapes_internal;
     }
 
     final boolean isShowOverview() {
@@ -312,10 +284,6 @@ final public class Options {
         _antialias_screen = antialias_screen;
     }
 
-    public void setBackgroundColorGradient( final boolean background_color_gradient ) {
-        _background_color_gradient = background_color_gradient;
-    }
-
     final void setBaseFont( final Font base_font ) {
         _base_font = base_font;
     }
@@ -324,10 +292,6 @@ final public class Options {
         _cladogram_type = cladogram_type;
     }
 
-    public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
-        _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
-    }
-
     final void setDefaultNodeFill( final NodeFill default_node_fill ) {
         _default_node_fill = default_node_fill;
     }
@@ -344,10 +308,6 @@ final public class Options {
         _editable = editable;
     }
 
-    final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
-        _taxonomy_extraction = taxonomy_extraction;
-    }
-
     final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
         _graphics_export_using_actual_size = graphics_export_using_actual_size;
         if ( !graphics_export_using_actual_size ) {
@@ -378,16 +338,12 @@ final public class Options {
         _min_confidence_value = min_confidence_value;
     }
 
-    final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
-        _node_label_direction = node_label_direction;
-    }
-
-    final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
-        _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+    void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
+        _nh_conversion_support_value_style = nh_conversion_support_value_style;
     }
 
-    final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
-        _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+    final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+        _node_label_direction = node_label_direction;
     }
 
     final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
@@ -434,8 +390,16 @@ final public class Options {
         _show_branch_length_values = show_branch_length_values;
     }
 
-    public void setShowDomainLabels( final boolean show_domain_labels ) {
-        _show_domain_labels = show_domain_labels;
+    void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
+        _show_confidence_stddev = show_confidence_stddev;
+    }
+
+    void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+        _show_default_node_shapes_external = show_default_node_shapes_external;
+    }
+
+    void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+        _show_default_node_shapes_internal = show_default_node_shapes_internal;
     }
 
     final void setShowOverview( final boolean show_overview ) {
@@ -450,16 +414,66 @@ final public class Options {
         _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
     }
 
-    final static Options createDefaultInstance() {
-        return new Options();
+    final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+        _taxonomy_extraction = taxonomy_extraction;
+    }
+
+    final private void init() {
+        _default_node_shape = NodeShape.CIRCLE;
+        _default_node_fill = NodeFill.GRADIENT;
+        _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+        _taxonomy_colorize_node_shapes = false;
+        _show_branch_length_values = false;
+        _internal_number_are_confidence_for_nh_parsing = false;
+        _show_scale = false;
+        _antialias_screen = true;
+        _antialias_print = true;
+        _graphics_export_visible_only = false;
+        _editable = true;
+        _background_color_gradient = false;
+        _show_default_node_shapes_internal = false;
+        _show_default_node_shapes_external = false;
+        if ( AptxUtil.isUsOrCanada() ) {
+            _print_size_x = Constants.US_LETTER_SIZE_X;
+            _print_size_y = Constants.US_LETTER_SIZE_Y;
+        }
+        else {
+            _print_size_x = Constants.A4_SIZE_X;
+            _print_size_y = Constants.A4_SIZE_Y;
+        }
+        _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
+        _print_black_and_white = false;
+        _print_using_actual_size = false;
+        _graphics_export_using_actual_size = true;
+        _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+        _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
+        _match_whole_terms_only = false;
+        _search_case_sensitive = false;
+        _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
+        _show_overview = true;
+        _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
+        _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
+        _inverse_search_result = false;
+        _scale_bar_length = 0.0;
+        _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
+        _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
+        _nh_parsing_replace_underscores = false;
+        _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
+        _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
+        _show_domain_labels = true;
+        setAbbreviateScientificTaxonNames( false );
+        _color_labels_same_as_parent_branch = false;
+        _show_confidence_stddev = true;
+        _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
+        _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
     }
 
-    boolean isShowDefaultNodeShapes() {
-        return _show_default_node_shapes;
+    final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
+        _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
     }
 
-    void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
-        _show_default_node_shapes = show_default_node_shapes;
+    final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+        _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
     }
 
     public final static Options createInstance( final Configuration configuration ) {
@@ -519,7 +533,8 @@ final public class Options {
                 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
             }
             instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
-            instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
+            instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
+            instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
             if ( configuration.getExtDescNodeDataToReturn() != null ) {
                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
             }
@@ -527,6 +542,10 @@ final public class Options {
         return instance;
     }
 
+    final static Options createDefaultInstance() {
+        return new Options();
+    }
+
     public static enum CLADOGRAM_TYPE {
         NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP;
     }
@@ -535,6 +554,10 @@ final public class Options {
         HORIZONTAL, RADIAL;
     }
 
+    public static enum PHYLOGENY_GRAPHICS_TYPE {
+        RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
+    }
+
     static enum OVERVIEW_PLACEMENT_TYPE {
         UPPER_LEFT( "upper left" ),
         UPPER_RIGHT( "upper right" ),
@@ -556,16 +579,4 @@ final public class Options {
             return toString().replaceAll( " ", "_" );
         }
     }
-
-    public static enum PHYLOGENY_GRAPHICS_TYPE {
-        RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
-    }
-
-    public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
-        return _ext_desc_data_to_return;
-    }
-
-    public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
-        _ext_desc_data_to_return = ext_desc_data_to_return;
-    }
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java b/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java
index 44fa9af..a3c136d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java
@@ -87,7 +87,7 @@ public final class TreeFontSet {
     }
 
     Font getLargeFont() {
-        return getLargeFontSystem();
+        return _large_font;
     }
 
     private Font getLargeFontSystem() {

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 6b26c29..4c1529f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -524,7 +524,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             initNodeData();
             if ( recalc_longest_ext_node_info ) {
                 calculateLongestExtNodeInfo();
-                while ( ( getLongestExtNodeInfo() > y / 2 ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+                while ( ( getLongestExtNodeInfo() > ( x * 0.67 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
                     getMainPanel().getTreeFontSet().decreaseFontSize();
                     calculateLongestExtNodeInfo();
                 }
@@ -1838,7 +1838,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         if ( getMainPanel().getOptions().isAntialiasScreen() ) {
             if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
-                    && !getMainPanel().getOptions().isShowDefaultNodeShapes()
+                    && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
+                    && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
                     && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
                 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
             }
@@ -3811,7 +3812,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             final int box_size = getOptions().getDefaultNodeShapeSize();
             final int half_box_size = box_size / 2;
-            if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+            if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
+                    || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+                    || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
                 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
                     if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
                         drawOvalGradient( x - half_box_size,

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index e8ba376..c717966 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.015";
-    public final static String  FORESTER_DATE               = "130104";
+    public final static String  FORESTER_VERSION            = "1.016";
+    public final static String  FORESTER_DATE               = "130108";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";