in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index a24176c..d190da0 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -117,6 +117,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem            _cycle_node_fill_mi;
     private JMenuItem            _choose_node_size_mi;
     private JCheckBoxMenuItem    _taxonomy_colorize_node_shapes_cbmi;
+    private JCheckBoxMenuItem    _show_confidence_stddev_cbmi;
 
     @Override
     public void actionPerformed( final ActionEvent e ) {
@@ -236,6 +237,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _show_branch_length_values_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _show_confidence_stddev_cbmi ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _label_direction_cbmi ) {
             updateOptions( getOptions() );
         }
@@ -442,7 +446,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
-        //
+        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
+        _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
+        _options_jmenu
+                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
+        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu
                 .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
         _options_jmenu
@@ -450,11 +458,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _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( MainFrame.DISPLAY_SCALE_LABEL ) );
-        _options_jmenu
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
         _options_jmenu
                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
@@ -506,6 +509,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+        customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
         _jmenubar.add( _options_jmenu );
     }
 
@@ -1018,6 +1022,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             }
         }
         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
+        options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
+                && _show_confidence_stddev_cbmi.isSelected() );
         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 0b8b7fc..c715858 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -122,7 +122,6 @@ public final class Configuration {
     final static int                        show_vector_data                                       = 23;
     final static int                        show_taxonomy_images                                   = 24;
     final static int                        show_properties                                        = 25;
-    final static int                        write_confidence_values_sd                             = 26;
     // ------------------
     // Click-to options
     // ------------------
@@ -162,8 +161,7 @@ public final class Configuration {
             { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
             { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
             { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
-            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" },
-            { "Confidence StdDev", "display", "no" }                                              };
+            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" }             };
     final static String                     clickto_options[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 8a15e5a..471ca78 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -87,7 +87,6 @@ final class ControlPanel extends JPanel implements ActionListener {
     private JCheckBox            _show_node_names;
     private JCheckBox            _show_taxo_code;
     private JCheckBox            _write_confidence;
-    private JCheckBox            _write_confidence_sd;
     private JCheckBox            _show_events;
     private JCheckBox            _color_acc_species;
     private JCheckBox            _color_branches_cb;
@@ -438,11 +437,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
                 add( ch_panel );
                 break;
-            case Configuration.write_confidence_values_sd:
-                _write_confidence_sd = new JCheckBox( title );
-                addJCheckBox( getWriteConfidenceSDCb(), ch_panel );
-                add( ch_panel );
-                break;
             case Configuration.write_events:
                 _show_events = new JCheckBox( title );
                 addJCheckBox( getShowEventsCb(), ch_panel );
@@ -762,10 +756,6 @@ final class ControlPanel extends JPanel implements ActionListener {
         return _write_confidence;
     }
 
-    public JCheckBox getWriteConfidenceSDCb() {
-        return _write_confidence_sd;
-    }
-
     private void init() {
         _draw_phylogram = new ArrayList<Boolean>();
         setSpeciesColors( new HashMap<String, Color>() );
@@ -824,10 +814,6 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
     }
 
-    boolean isShowConfidenceSDValues() {
-        return ( ( getWriteConfidenceSDCb() != null ) && getWriteConfidenceSDCb().isSelected() );
-    }
-
     boolean isShowDomainArchitectures() {
         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
     }
@@ -1054,11 +1040,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                     getWriteConfidenceCb().setSelected( state );
                 }
                 break;
-            case Configuration.write_confidence_values_sd:
-                if ( getWriteConfidenceSDCb() != null ) {
-                    getWriteConfidenceSDCb().setSelected( state );
-                }
-                break;
             case Configuration.write_events:
                 if ( getShowEventsCb() != null ) {
                     getShowEventsCb().setSelected( state );
@@ -1603,10 +1584,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                          _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
             setCheckbox( Configuration.write_confidence_values,
                          _configuration.doCheckOption( Configuration.write_confidence_values ) );
-            addCheckbox( Configuration.write_confidence_values_sd,
-                         _configuration.getDisplayTitle( Configuration.write_confidence_values_sd ) );
-            setCheckbox( Configuration.write_confidence_values_sd,
-                         _configuration.doCheckOption( Configuration.write_confidence_values_sd ) );
         }
         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 0410fed..89dd29b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -85,7 +85,7 @@ 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 Shapes";
+    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";
@@ -96,6 +96,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     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";
     JMenuBar                  _jmenubar;
     JMenu                     _file_jmenu;
     JMenu                     _tools_menu;
@@ -156,6 +158,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                 _cycle_node_fill_mi;
     JMenuItem                 _choose_node_size_mi;
     JCheckBoxMenuItem         _taxonomy_colorize_node_shapes_cbmi;
+    JCheckBoxMenuItem         _show_confidence_stddev_cbmi;
     // _  print
     JCheckBoxMenuItem         _graphics_export_visible_only_cbmi;
     JCheckBoxMenuItem         _antialias_print_cbmi;
@@ -168,6 +171,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JCheckBoxMenuItem         _internal_number_are_confidence_for_nh_parsing_cbmi;
     JCheckBoxMenuItem         _extract_pfam_style_tax_codes_cbmi;
     JCheckBoxMenuItem         _replace_underscores_cbmi;
+    JCheckBoxMenuItem         _use_brackets_for_conf_in_nh_export_cbmi;
     // _  search
     JCheckBoxMenuItem         _search_case_senstive_cbmi;
     JCheckBoxMenuItem         _search_whole_words_only_cbmi;
@@ -381,6 +385,12 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_branch_length_values_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _show_confidence_stddev_cbmi ) {
+            updateOptions( getOptions() );
+        }
+        else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _label_direction_cbmi ) {
             updateOptions( getOptions() );
         }
@@ -956,6 +966,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             }
         }
         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
+        options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
+                && _show_confidence_stddev_cbmi.isSelected() );
         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
         }
@@ -964,6 +976,8 @@ 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() );
         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 )

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index cf9a672..b056ac8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -180,16 +180,17 @@ public final class MainFrameApplet extends MainFrame {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
+        _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
+        _options_jmenu
+                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
+        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu.add( _show_default_node_shapes_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( MainFrame.DISPLAY_SCALE_LABEL ) );
-        _options_jmenu
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
@@ -239,6 +240,7 @@ public final class MainFrameApplet extends MainFrame {
                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+        customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
         _jmenubar.add( _options_jmenu );
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 5053d83..efbd7ae 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -784,16 +784,17 @@ 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_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_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 ) );
+        _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( _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 ) );
-        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
@@ -827,13 +828,15 @@ 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 Parsing:" ), getConfiguration() ) );
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input/Output:" ),
+                                                      getConfiguration() ) );
         _options_jmenu
                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Numbers 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( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
         customizeJMenuItem( _choose_font_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _switch_colors_mi );
@@ -875,6 +878,9 @@ public final class MainFrameApplication extends MainFrame {
         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
                 .isGraphicsExportUsingActualSize() );
+        customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+        customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
+                .isUseBracketsForConfInNhExport() );
         _jmenubar.add( _options_jmenu );
     }
 
@@ -2312,7 +2318,7 @@ 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, file );
+            writer.toNewHampshire( t, false, true, getOptions().isUseBracketsForConfInNhExport(), file );
         }
         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 594c9ab..80be186 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -75,6 +75,8 @@ final public class Options {
     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;
 
     private Options() {
         init();
@@ -184,6 +186,24 @@ final public class Options {
         _show_domain_labels = true;
         setAbbreviateScientificTaxonNames( false );
         _color_labels_same_as_parent_branch = false;
+        _show_confidence_stddev = true;
+        _use_brackets_for_conf_in_nh_export = false;
+    }
+
+    boolean isShowConfidenceStddev() {
+        return _show_confidence_stddev;
+    }
+
+    void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
+        _show_confidence_stddev = show_confidence_stddev;
+    }
+
+    boolean isUseBracketsForConfInNhExport() {
+        return _use_brackets_for_conf_in_nh_export;
+    }
+
+    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;
     }
 
     final boolean isAbbreviateScientificTaxonNames() {

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 0ca4955..c69971a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -2705,7 +2705,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                               final PhylogenyNode node,
                                               final boolean to_pdf,
                                               final boolean to_graphics_file ) {
-        String conf_str = "";
         final List<Confidence> confidences = node.getBranchData().getConfidences();
         //        if ( confidences.size() == 1 ) {
         //            final double value = node.getBranchData().getConfidence( 0 ).getValue();
@@ -2719,6 +2718,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         boolean not_first = false;
         Collections.sort( confidences );
         final StringBuilder sb = new StringBuilder();
+        String conf_str = "";
         for( final Confidence confidence : confidences ) {
             final double value = confidence.getValue();
             if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
@@ -2733,7 +2733,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
                 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
                         .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
-                if ( getControlPanel().isShowConfidenceSDValues() ) {
+                if ( getOptions().isShowConfidenceStddev() ) {
                     if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
                         sb.append( "(" );
                         sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),

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 8dba277..7725ee5 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -87,7 +87,7 @@ public final class NHXParser implements PhylogenyParser {
     public final static Pattern                              UC_LETTERS_NUMBERS_PATTERN        = Pattern
                                                                                                        .compile( "^[A-Z0-9]+$" );
     public final static Pattern                              NUMBERS_ONLY_PATTERN              = Pattern
-                                                                                                       .compile( "^[0-9]+$" );
+                                                                                                       .compile( "^[0-9\\.]+$" );
     public final static Pattern                              MB_PROB_PATTERN                   = Pattern
                                                                                                        .compile( "prob=([^,]+)" );
     public final static Pattern                              MB_PROB_SD_PATTERN                = Pattern

diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index c443842..be4c24e 100644 (file)
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -73,6 +73,7 @@ public final class PhylogenyWriter {
     private Stack<PostOrderStackObject> _stack;
     private boolean                     _simple_nh;
     private boolean                     _nh_write_distance_to_parent;
+    private boolean                     _write_conf_values_in_branckets_in_nh;
     private boolean                     _indent_phyloxml;
     private int                         _node_level;
     private int                         _phyloxml_level;
@@ -80,6 +81,7 @@ public final class PhylogenyWriter {
 
     public PhylogenyWriter() {
         setIndentPhyloxml( INDENT_PHYLOXML_DEAFULT );
+        setWriteConfidenceValuesInBracketsInNH( false );
     }
 
     private void appendPhylogenyLevelPhyloXml( final Writer writer, final Phylogeny tree ) throws IOException {
@@ -336,6 +338,17 @@ public final class PhylogenyWriter {
 
     public StringBuffer toNewHampshire( final Phylogeny tree,
                                         final boolean simple_nh,
+                                        final boolean nh_write_distance_to_parent,
+                                        final boolean write_conf_values_in_branckets_in_nh ) throws IOException {
+        setOutputFormt( FORMAT.NH );
+        setWriteConfidenceValuesInBracketsInNH( write_conf_values_in_branckets_in_nh );
+        setSimpleNH( simple_nh );
+        setWriteDistanceToParentInNH( nh_write_distance_to_parent );
+        return getOutput( tree );
+    }
+
+    public StringBuffer toNewHampshire( final Phylogeny tree,
+                                        final boolean simple_nh,
                                         final boolean nh_write_distance_to_parent ) throws IOException {
         setOutputFormt( FORMAT.NH );
         setSimpleNH( simple_nh );
@@ -350,6 +363,14 @@ public final class PhylogenyWriter {
         writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent ), out_file );
     }
 
+    public void toNewHampshire( final Phylogeny tree,
+                                final boolean simple_nh,
+                                final boolean write_distance_to_parent,
+                                final boolean use_brackets_for_confidence,
+                                final File out_file ) throws IOException {
+        writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent, use_brackets_for_confidence ), out_file );
+    }
+
     public void toNewHampshire( final Phylogeny[] trees,
                                 final boolean simple_nh,
                                 final boolean write_distance_to_parent,
@@ -556,10 +577,20 @@ public final class PhylogenyWriter {
             getBuffer().append( node.toNewHampshireX() );
         }
         else if ( getOutputFormt() == FORMAT.NH ) {
-            getBuffer().append( node.toNewHampshire( isSimpleNH(), isWriteDistanceToParentInNH() ) );
+            getBuffer().append( node.toNewHampshire( isSimpleNH(),
+                                                     isWriteDistanceToParentInNH(),
+                                                     isWriteConfidenceValuesInBracketsInNH() ) );
         }
     }
 
+    private boolean isWriteConfidenceValuesInBracketsInNH() {
+        return _write_conf_values_in_branckets_in_nh;
+    }
+
+    private void setWriteConfidenceValuesInBracketsInNH( final boolean write_conf_values_in_branckets_in_nh ) {
+        _write_conf_values_in_branckets_in_nh = write_conf_values_in_branckets_in_nh;
+    }
+
     private void writeOpenClade( final PhylogenyNode node ) throws IOException {
         if ( !isSawComma() ) {
             if ( !node.isRoot() && node.isFirstChildNode() ) {

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 58ac6c7..a65de7c 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -33,6 +33,7 @@ import java.util.List;
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.phylogeny.data.BranchData;
+import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
@@ -922,7 +923,9 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     // ---------------------------------------------------------
     // Writing of Nodes to Strings
     // ---------------------------------------------------------
-    final public String toNewHampshire( final boolean simple_nh, final boolean write_distance_to_parent ) {
+    final public String toNewHampshire( final boolean simple_nh,
+                                        final boolean write_distance_to_parent,
+                                        final boolean write_support_values_in_brackets ) {
         final StringBuilder sb = new StringBuilder();
         String data = "";
         if ( !ForesterUtil.isEmpty( getName() ) ) {
@@ -961,10 +964,16 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                 sb.append( data );
             }
         }
-        if ( ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) && write_distance_to_parent ) {
+        if ( write_distance_to_parent && ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
             sb.append( ":" );
             sb.append( getDistanceToParent() );
         }
+        if ( write_support_values_in_brackets && !isExternal()
+                && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+            sb.append( "[" );
+            sb.append( getBranchData().getConfidence( 0 ).getValue() );
+            sb.append( "]" );
+        }
         return sb.toString();
     }