import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.Util.GraphicsExportType;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
+import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
+import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
+import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
+import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
+import org.forester.archaeopteryx.tools.UniProtSequenceObtainer;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.FastaParser;
}
obtainDetailedTaxonomicInformation();
}
+ else if ( o == _obtain_uniprot_seq_information_jmi ) {
+ obtainUniProtSequenceInformation();
+ }
else if ( o == _read_values_jmi ) {
if ( isSubtreeDisplayed() ) {
return;
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
.setToolTipText( "To add additional taxonomic information (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)" );
_tools_menu.addSeparator();
if ( !Constants.__RELEASE ) {
_tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;
}
- final MainPanelEdit a = new MainPanelEdit( this,
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getCurrentPhylogeny() );
+ final GoAnnotation a = new GoAnnotation( this,
+ _mainpanel.getCurrentTreePanel(),
+ _mainpanel.getCurrentPhylogeny() );
new Thread( a ).start();
}
}
@Override
- MainPanel getMainPanel() {
+ public MainPanel getMainPanel() {
return _mainpanel;
}
}
}
+ private void obtainUniProtSequenceInformation() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final UniProtSequenceObtainer u = new UniProtSequenceObtainer( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy() );
+ new Thread( u ).start();
+ }
+ }
+ }
+
private void print() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
|| getCurrentTreePanel().getPhylogeny().isEmpty() ) {
System.gc();
}
- void readSeqsFromFile() {
+ public void readSeqsFromFile() {
// Set an initial directory if none set yet
final File my_dir = getCurrentDir();
_seqs_filechooser.setMultiSelectionEnabled( false );
}
}
- void readMsaFromFile() {
+ public void readMsaFromFile() {
// Set an initial directory if none set yet
final File my_dir = getCurrentDir();
_msa_filechooser.setMultiSelectionEnabled( false );
return _phylogenetic_inference_options;
}
- Msa getMsa() {
+ public Msa getMsa() {
return _msa;
}
_msa_file = msa_file;
}
- File getMsaFile() {
+ public File getMsaFile() {
return _msa_file;
}
- List<Sequence> getSeqs() {
+ public List<Sequence> getSeqs() {
return _seqs;
}
_seqs_file = seqs_file;
}
- File getSeqsFile() {
+ public File getSeqsFile() {
return _seqs_file;
}
} // MainFrameApplication.