import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
-import org.forester.archaeopteryx.tools.GoAnnotation;
import org.forester.archaeopteryx.tools.InferenceManager;
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
}
executeLineageInference();
}
- else if ( o == _function_analysis ) {
- executeFunctionAnalysis();
- }
else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
if ( isSubtreeDisplayed() ) {
return;
customizeJMenuItem( _move_node_names_to_seq_names_jmi );
_move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
_tools_menu.addSeparator();
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
+ customizeJMenuItem( _obtain_seq_information_jmi );
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu
.add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
.setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
- _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
- customizeJMenuItem( _obtain_seq_information_jmi );
- _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu.addSeparator();
- if ( !Constants.__RELEASE ) {
- _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
- customizeJMenuItem( _function_analysis );
- _function_analysis
- .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" );
- _tools_menu.addSeparator();
- }
_tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
customizeJMenuItem( _read_values_jmi );
_read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
exit();
}
- void executeFunctionAnalysis() {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
- return;
- }
- final GoAnnotation a = new GoAnnotation( this,
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getCurrentPhylogeny() );
- new Thread( a ).start();
- }
-
void executeLineageInference() {
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;
nodes = phy.getNodesViaSequenceSymbol( seq_name );
}
if ( nodes.isEmpty() ) {
+ nodes = phy.getNodesViaGeneName( seq_name );
+ }
+ if ( nodes.isEmpty() ) {
nodes = phy.getNodes( seq_name );
}
if ( nodes.size() > 1 ) {