cleanup

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplication.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index c146900..4b860a1 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -531,6 +531,9 @@ public final class MainFrameApplication extends MainFrame {
                 }
                 updateOptions( getOptions() );
             }
+            else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
+                updateOptions( getOptions() );
+            }
             else if ( o == _collapse_below_threshold ) {
                 if ( isSubtreeDisplayed() ) {
                     return;
@@ -899,8 +902,6 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
-        _options_jmenu
-                .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
@@ -939,6 +940,8 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu
                 .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( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
         //
         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
         _options_jmenu
@@ -976,7 +979,6 @@ public final class MainFrameApplication extends MainFrame {
                 .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 );
         customizeJMenuItem( _choose_node_size_mi );
@@ -1012,6 +1014,8 @@ public final class MainFrameApplication extends MainFrame {
         customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
+        customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
+                .isReplaceUnderscoresInNhParsing() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
@@ -2341,6 +2345,7 @@ public final class MainFrameApplication extends MainFrame {
     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
+        nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
     }
 
     private void writeAllToFile() {