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 SHOW_ANN_REF_SOURCE_LABEL = "Show Seq Annotation Ref Sources";
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";
JMenuItem _gsdi_item;
JMenuItem _gsdir_item;
JMenuItem _lineage_inference;
- JMenuItem _function_analysis;
// file menu:
JMenuItem _open_item;
JMenuItem _open_url_item;
JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
JCheckBoxMenuItem _show_overview_cbmi;
JCheckBoxMenuItem _show_domain_labels;
+ JCheckBoxMenuItem _show_annotation_ref_source;
JCheckBoxMenuItem _abbreviate_scientific_names;
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
// _ parsing
JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_yes_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
else if ( o == _show_domain_labels ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_annotation_ref_source ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _abbreviate_scientific_names ) {
updateOptions( getOptions() );
}
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
&& _background_gradient_cbmi.isSelected() );
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+ && _show_annotation_ref_source.isSelected() );
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _print_black_and_white_cbmi.isSelected() );
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
- if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
}
- else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
}
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );