private JMenuItem _aptx_ref_item;
private JMenuItem _remove_branch_color_item;
private JCheckBoxMenuItem _show_domain_labels;
+ private JCheckBoxMenuItem _show_annotation_ref_source;
private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
private JCheckBoxMenuItem _abbreviate_scientific_names;
private JCheckBoxMenuItem _screen_antialias_cbmi;
private JCheckBoxMenuItem _background_gradient_cbmi;
+ private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
private JRadioButtonMenuItem _uniform_cladograms_rbmi;
private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _search_whole_words_only_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
+ else if ( o == _color_by_taxonomic_group_cbmi ) {
+ updateOptions( getOptions() );
+ }
repaint();
}
_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_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 ) );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
+ }
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
+ _options_jmenu
+ .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
_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( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
_options_jmenu
.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
_color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
_options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
_label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
_options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
_options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_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( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
+ /////
_options_jmenu.addSeparator();
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
getConfiguration() ) );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _overview_placment_mi );
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
customizeCheckBoxMenuItem( _label_direction_cbmi,
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
.isShowDefaultNodeShapesExternal() );
_view_jmenu
.add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_XML_item );
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
}
- showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
+ showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
}
}
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 )
else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
}
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
+ }
}
void updateTypeCheckboxes( final Options options, final Object o ) {
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
.getNhConversionSupportValueStyle() ),
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "New Hampshire";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny()
.toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
}