import org.forester.tools.ConfidenceAssessor;
import org.forester.util.ForesterUtil;
-public class PhylogeneticInferrer implements Runnable {
+public class PhylogeneticInferrer extends RunnableProcess {
private Msa _msa;
private final MainFrameApplication _mf;
if ( ( _msa == null ) && ( _seqs == null ) ) {
throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
}
+ start( _mf, "phylogenetic inference" );
if ( _msa == null ) {
Msa msa = null;
try {
msa = inferMsa();
}
catch ( final IOException e ) {
+ end( _mf );
JOptionPane.showMessageDialog( _mf,
"Could not create multiple sequence alignment with \""
+ _options.getMsaPrg() + "\" and the following parameters:\n\""
return;
}
catch ( final Exception e ) {
+ end( _mf );
JOptionPane.showMessageDialog( _mf,
"Could not create multiple sequence alignment with \""
+ _options.getMsaPrg() + "\" and the following parameters:\n\""
return;
}
if ( msa == null ) {
+ end( _mf );
JOptionPane.showMessageDialog( _mf,
"Could not create multiple sequence alignment with "
+ _options.getMsaPrg() + "\nand the following parameters:\n\""
_options.getMsaProcessingMinAllowedLength(),
msa );
if ( msa == null ) {
+ end( _mf );
JOptionPane.showMessageDialog( _mf,
"Less than two sequences longer than "
+ _options.getMsaProcessingMinAllowedLength()
ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
}
_mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
- _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+ // _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
+ end( _mf );
JOptionPane.showMessageDialog( _mf,
"Inference successfully completed",
"Inference Completed",