}
obtainDetailedTaxonomicInformation();
}
+ else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ obtainDetailedTaxonomicInformationDelete();
+ }
else if ( o == _obtain_uniprot_seq_information_jmi ) {
obtainUniProtSequenceInformation();
}
_obtain_detailed_taxonomic_information_jmi
.setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
_tools_menu
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
+ 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_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
_obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
JOptionPane.ERROR_MESSAGE );
return;
}
- final Phylogeny phy = _mainpanel.getCurrentPhylogeny().copy();
final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
_mainpanel.getCurrentTreePanel(),
- phy );
+ _mainpanel.getCurrentPhylogeny()
+ .copy() );
new Thread( inferrer ).start();
}
}
}
+ private void obtainDetailedTaxonomicInformationDelete() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true );
+ new Thread( t ).start();
+ }
+ }
+ }
+
private void obtainUniProtSequenceInformation() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();