import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Annotation;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.sdi.GSDI;
import org.forester.sdi.GSDIR;
import org.forester.sdi.SDIException;
JMenuItem _lineage_inference;
// file menu:
JMenuItem _open_item;
- JMenuItem _open_url_item;
JMenuItem _save_item;
JMenuItem _save_all_item;
JMenuItem _close_item;
JMenuItem _cycle_node_shape_mi;
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;
JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
// _ search
applet = getCurrentTreePanel().obtainApplet();
}
}
- if ( o == _open_url_item ) {
- readPhylogeniesFromURL();
- }
- else if ( o == _exit_item ) {
+ if ( o == _exit_item ) {
close();
}
else if ( o == _gsdi_item ) {
else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
- updateOptions( getOptions() );
- }
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
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() );
void buildFileMenu() {
_file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
- _file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _open_url_item );
customizeJMenuItem( _exit_item );
_jmenubar.add( _file_jmenu );
}
}
}
- abstract void readPhylogeniesFromURL();
-
void readPhylogeniesFromWebservice( final int i ) {
final UrlTreeReader reader = new UrlTreeReader( this, i );
new Thread( reader ).start();
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
- options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
- && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
}
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
private void annotateSequences() {
if ( getCurrentTreePanel() != null ) {
- final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,