in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 6d96616..7ba34f4 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -333,7 +333,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             case NHX:
                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
             case NEXUS:
-                return getMainPanel().getCurrentPhylogeny().toNexus( false );
+                return getMainPanel().getCurrentPhylogeny().toNexus();
             case PHYLOXML:
                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
             default:
@@ -1068,7 +1068,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
             return;
         }
-        _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus( false ) );
+        _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() );
     }
 
     void viewAsNH() {
@@ -1077,7 +1077,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
             return;
         }
-        _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false, false ) );
+        _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire() );
     }
 
     void viewAsNHX() {

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index da8bf0c..00511a7 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -41,8 +41,8 @@ public final class Constants {
     public final static boolean __SNAPSHOT_RELEASE                                            = true;                                                     // TODO remove me
     public final static boolean __SYNTH_LF                                                    = false;                                                    // TODO remove me
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.966 beta T2P";
-    final static String         PRG_DATE                                                      = "2011.12.15";
+    final static String         VERSION                                                       = "0.967 beta T2P";
+    final static String         PRG_DATE                                                      = "2011.12.20";
     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 2aaf8fc..6b4c096 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -47,6 +47,7 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
 import org.forester.util.ForesterConstants;
@@ -54,50 +55,51 @@ import org.forester.util.ForesterUtil;
 
 public abstract class MainFrame extends JFrame implements ActionListener {
 
-    static final String       USE_MOUSEWHEEL_SHIFT_TO_ROTATE      = "In this display type, use mousewheel + Shift to rotate [or A and S]";
-    static final String       PHYLOXML_REF_TOOL_TIP               = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
-    static final String       APTX_REF_TOOL_TIP                   = Constants.APTX_REFERENCE;
-    private static final long serialVersionUID                    = 3655000897845508358L;
-    final static Font         menu_font                           = new Font( Configuration.getDefaultFontFamilyName(),
-                                                                              Font.PLAIN,
-                                                                              10 );
-    static final String       TYPE_MENU_HEADER                    = "Type";
-    static final String       RECTANGULAR_TYPE_CBMI_LABEL         = "Rectangular";
-    static final String       EURO_TYPE_CBMI_LABEL                = "Euro Type";
-    static final String       CURVED_TYPE_CBMI_LABEL              = "Curved";
-    static final String       TRIANGULAR_TYPE_CBMI_LABEL          = "Triangular";
-    static final String       CONVEX_TYPE_CBMI_LABEL              = "Convex";
-    static final String       ROUNDED_TYPE_CBMI_LABEL             = "Rounded";
-    static final String       UNROOTED_TYPE_CBMI_LABEL            = "Unrooted (alpha)";                                                                                                                                                 //TODO
-    static final String       CIRCULAR_TYPE_CBMI_LABEL            = "Circular (alpha)";                                                                                                                                                 //TODO
-    static final String       OPTIONS_HEADER                      = "Options";
-    static final String       SEARCH_SUBHEADER                    = "Search:";
-    static final String       DISPLAY_SUBHEADER                   = "Display:";
-    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       DISPLAY_SCALE_LABEL                 = "Display 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                  = "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       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";
-    static final String       SHOW_CONF_STDDEV_LABEL              = "Show Confidence Standard Deviations";
-    static final String       USE_BRACKETS_FOR_CONF_IN_NH_LABEL   = "Brackets for Confidences in NH/Nexus Output";
+    static final String       USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";
+    static final String       PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
+    static final String       APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;
+    private static final long serialVersionUID                        = 3655000897845508358L;
+    final static Font         menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),
+                                                                                  Font.PLAIN,
+                                                                                  10 );
+    static final String       TYPE_MENU_HEADER                        = "Type";
+    static final String       RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";
+    static final String       EURO_TYPE_CBMI_LABEL                    = "Euro Type";
+    static final String       CURVED_TYPE_CBMI_LABEL                  = "Curved";
+    static final String       TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";
+    static final String       CONVEX_TYPE_CBMI_LABEL                  = "Convex";
+    static final String       ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";
+    static final String       UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO
+    static final String       CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO
+    static final String       OPTIONS_HEADER                          = "Options";
+    static final String       SEARCH_SUBHEADER                        = "Search:";
+    static final String       DISPLAY_SUBHEADER                       = "Display:";
+    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       DISPLAY_SCALE_LABEL                     = "Display 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                      = "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       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";
+    static final String       SHOW_CONF_STDDEV_LABEL                  = "Show 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";
     JMenuBar                  _jmenubar;
     JMenu                     _file_jmenu;
     JMenu                     _tools_menu;
@@ -121,7 +123,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                 _color_rank_jmi;
     JMenuItem                 _infer_common_sn_names_item;
     JMenuItem                 _collapse_species_specific_subtrees;
-    JMenuItem                 _collapse_below_threshold;                                                                                                                                                                                //TODO implememt me
+    JMenuItem                 _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
     JMenuItem                 _obtain_detailed_taxonomic_information_jmi;
     JMenuItem                 _obtain_detailed_taxonomic_information_deleting_jmi;
     JMenuItem                 _obtain_uniprot_seq_information_jmi;
@@ -146,7 +148,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JRadioButtonMenuItem      _uniform_cladograms_rbmi;
     JRadioButtonMenuItem      _ext_node_dependent_cladogram_rbmi;
     JCheckBoxMenuItem         _show_branch_length_values_cbmi;
-    JCheckBoxMenuItem         _show_scale_cbmi;                                                                                                                                                                                         //TODO fix me
+    JCheckBoxMenuItem         _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
     JCheckBoxMenuItem         _show_overview_cbmi;
     JCheckBoxMenuItem         _show_domain_labels;
     JCheckBoxMenuItem         _abbreviate_scientific_names;
@@ -172,6 +174,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JCheckBoxMenuItem         _extract_pfam_style_tax_codes_cbmi;
     JCheckBoxMenuItem         _replace_underscores_cbmi;
     JCheckBoxMenuItem         _use_brackets_for_conf_in_nh_export_cbmi;
+    JCheckBoxMenuItem         _use_internal_names_for_conf_in_nh_export_cbmi;
     // _  search
     JCheckBoxMenuItem         _search_case_senstive_cbmi;
     JCheckBoxMenuItem         _search_whole_words_only_cbmi;
@@ -389,6 +392,15 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             updateOptions( getOptions() );
         }
         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
+            if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+                _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
+            }
+            updateOptions( getOptions() );
+        }
+        else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
+            if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+                _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
+            }
             updateOptions( getOptions() );
         }
         else if ( o == _label_direction_cbmi ) {
@@ -976,8 +988,17 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
-        options.setUseBracketsForConfInNhExport( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
-                && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() );
+        if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
+                && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
+            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+        }
+        else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
+                && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
+            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+        }
+        else {
+            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+        }
         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
                 && _print_black_and_white_cbmi.isSelected() );
         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
@@ -1045,7 +1066,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             return;
         }
         _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions()
-                .isUseBracketsForConfInNhExport() ) );
+                .getNhConversionSupportValueStyle() ) );
     }
 
     void viewAsNH() {
@@ -1055,7 +1076,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             return;
         }
         _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny()
-                .toNewHampshire( false, getOptions().isUseBracketsForConfInNhExport() ) );
+                .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) );
     }
 
     void viewAsNHX() {

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 10d1a56..20c775d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -88,6 +88,7 @@ import org.forester.msa.MsaFormatException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
@@ -828,15 +829,19 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
         _options_jmenu.addSeparator();
-        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input/Output:" ),
-                                                      getConfiguration() ) );
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
         _options_jmenu
-                .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Numbers Are Confidence Values" ) );
+                .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
         _options_jmenu
                 .add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
         _options_jmenu
                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
+        _use_brackets_for_conf_in_nh_export_cbmi
+                .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
+        _options_jmenu
+                .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
         customizeJMenuItem( _choose_font_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _switch_colors_mi );
@@ -880,7 +885,9 @@ public final class MainFrameApplication extends MainFrame {
                 .isGraphicsExportUsingActualSize() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
-                .isUseBracketsForConfInNhExport() );
+                .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+        customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
+                .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
         _jmenubar.add( _options_jmenu );
     }
 
@@ -2318,7 +2325,7 @@ public final class MainFrameApplication extends MainFrame {
     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toNewHampshire( t, false, true, getOptions().isUseBracketsForConfInNhExport(), file );
+            writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
         }
         catch ( final Exception e ) {
             exception = true;
@@ -2330,7 +2337,7 @@ public final class MainFrameApplication extends MainFrame {
     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toNexus( file, t, getOptions().isUseBracketsForConfInNhExport() );
+            writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
         }
         catch ( final Exception e ) {
             exception = true;

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 80be186..4ba2ded 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -27,6 +27,7 @@ package org.forester.archaeopteryx;
 
 import java.awt.Font;
 
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.NodeVisualization;
 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
@@ -37,46 +38,46 @@ import org.forester.util.ForesterUtil;
  */
 final public class Options {
 
-    static final double                 MIN_CONFIDENCE_DEFAULT = 0.0;
-    private boolean                     _show_branch_length_values;
-    private boolean                     _internal_number_are_confidence_for_nh_parsing;
-    private boolean                     _show_scale;
-    private boolean                     _show_overview;
-    private boolean                     _antialias_screen;
-    private boolean                     _antialias_print;
-    private boolean                     _graphics_export_visible_only;
-    private int                         _print_size_x;
-    private int                         _print_size_y;
-    private double                      _min_confidence_value;
-    private boolean                     _print_black_and_white;
-    private boolean                     _print_using_actual_size;
-    private boolean                     _graphics_export_using_actual_size;
-    private PHYLOGENY_GRAPHICS_TYPE     _phylogeny_graphics_type;
-    private CLADOGRAM_TYPE              _cladogram_type;
-    private OVERVIEW_PLACEMENT_TYPE     _ov_placement;
-    private NODE_LABEL_DIRECTION        _node_label_direction;
-    private Font                        _base_font;
-    private boolean                     _match_whole_terms_only;
-    private boolean                     _search_case_sensitive;
-    private float                       _print_line_width;
-    private boolean                     _inverse_search_result;
-    private double                      _scale_bar_length;
-    private short                       _number_of_digits_after_comma_for_confidence_values;
-    private short                       _number_of_digits_after_comma_for_branch_length_values;
-    private boolean                     _nh_parsing_replace_underscores;
-    private boolean                     _nh_parsing_extract_pfam_taxonomy_codes;
-    private boolean                     _editable;
-    private boolean                     _background_color_gradient;
-    private boolean                     _show_domain_labels;
-    private boolean                     _color_labels_same_as_parent_branch;
-    private boolean                     _abbreviate_scientific_names;
-    private NodeVisualization.NodeShape _default_node_shape;
-    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_confidence_stddev;
-    private boolean                     _use_brackets_for_conf_in_nh_export;
+    static final double                       MIN_CONFIDENCE_DEFAULT = 0.0;
+    private boolean                           _show_branch_length_values;
+    private boolean                           _internal_number_are_confidence_for_nh_parsing;
+    private boolean                           _show_scale;
+    private boolean                           _show_overview;
+    private boolean                           _antialias_screen;
+    private boolean                           _antialias_print;
+    private boolean                           _graphics_export_visible_only;
+    private int                               _print_size_x;
+    private int                               _print_size_y;
+    private double                            _min_confidence_value;
+    private boolean                           _print_black_and_white;
+    private boolean                           _print_using_actual_size;
+    private boolean                           _graphics_export_using_actual_size;
+    private PHYLOGENY_GRAPHICS_TYPE           _phylogeny_graphics_type;
+    private CLADOGRAM_TYPE                    _cladogram_type;
+    private OVERVIEW_PLACEMENT_TYPE           _ov_placement;
+    private NODE_LABEL_DIRECTION              _node_label_direction;
+    private Font                              _base_font;
+    private boolean                           _match_whole_terms_only;
+    private boolean                           _search_case_sensitive;
+    private float                             _print_line_width;
+    private boolean                           _inverse_search_result;
+    private double                            _scale_bar_length;
+    private short                             _number_of_digits_after_comma_for_confidence_values;
+    private short                             _number_of_digits_after_comma_for_branch_length_values;
+    private boolean                           _nh_parsing_replace_underscores;
+    private boolean                           _nh_parsing_extract_pfam_taxonomy_codes;
+    private boolean                           _editable;
+    private boolean                           _background_color_gradient;
+    private boolean                           _show_domain_labels;
+    private boolean                           _color_labels_same_as_parent_branch;
+    private boolean                           _abbreviate_scientific_names;
+    private NodeVisualization.NodeShape       _default_node_shape;
+    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_confidence_stddev;
+    private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
 
     private Options() {
         init();
@@ -187,7 +188,7 @@ final public class Options {
         setAbbreviateScientificTaxonNames( false );
         _color_labels_same_as_parent_branch = false;
         _show_confidence_stddev = true;
-        _use_brackets_for_conf_in_nh_export = false;
+        _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
     }
 
     boolean isShowConfidenceStddev() {
@@ -198,12 +199,12 @@ final public class Options {
         _show_confidence_stddev = show_confidence_stddev;
     }
 
-    boolean isUseBracketsForConfInNhExport() {
-        return _use_brackets_for_conf_in_nh_export;
+    NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
+        return _nh_conversion_support_value_style;
     }
 
-    void setUseBracketsForConfInNhExport( final boolean use_brackets_for_conf_in_nh_export ) {
-        _use_brackets_for_conf_in_nh_export = use_brackets_for_conf_in_nh_export;
+    void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
+        _nh_conversion_support_value_style = nh_conversion_support_value_style;
     }
 
     final boolean isAbbreviateScientificTaxonNames() {

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
index 39f677a..600f00f 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -128,7 +128,7 @@ public final class NHXParser implements PhylogenyParser {
                       isReplaceUnderscores() );
             if ( NHXParser.GUESS_IF_SUPPORT_VALUES ) {
                 if ( NHXParser.isBranchLengthsLikeBootstrapValues( getCurrentPhylogeny() ) ) {
-                    NHXParser.moveBranchLengthsToBootstrapValues( getCurrentPhylogeny() );
+                    NHXParser.moveBranchLengthsToConfidenceValues( getCurrentPhylogeny() );
                 }
             }
             if ( isGuessRootedness() ) {
@@ -631,7 +631,7 @@ public final class NHXParser implements PhylogenyParser {
         return true;
     }
 
-    private static void moveBranchLengthsToBootstrapValues( final Phylogeny p ) {
+    private static void moveBranchLengthsToConfidenceValues( final Phylogeny p ) {
         final PhylogenyNodeIterator it = p.iteratorPostorder();
         while ( it.hasNext() ) {
             final PhylogenyNode n = it.next();

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 91f714d..f61a79a 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -1311,6 +1311,10 @@ public class Phylogeny {
         }
     }
 
+    public String toNexus() {
+        return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+    }
+
     public String toPhyloXML( final int phyloxml_level ) {
         try {
             return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index cbf2885..9ca9086 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -193,7 +193,7 @@ public class PhylogenyMethods {
         final PhylogenyNodeIterator it = phy.iteratorPostorder();
         while ( it.hasNext() ) {
             final PhylogenyNode n = it.next();
-            if ( !n.isRoot() && !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
+            if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
                 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
                     double d = -1.0;
                     try {