}
catch ( final Exception e ) {
ForesterUtil
- .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
- + "]" );
+ .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
+ + "]" );
}
try {
obtainSeqInformation( phy );
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
}
- try {
- inferTaxonomyFromDescendents( phy );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- catch ( final AncestralTaxonomyInferenceException e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
+ // try {
+ // inferTaxonomyFromDescendents( phy );
+ // }
+ // catch ( final IOException e ) {
+ // ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ // }
+ // catch ( final AncestralTaxonomyInferenceException e ) {
+ // ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ // }
+ //phy.setRerootable( false );
try {
final PhylogenyWriter w = new PhylogenyWriter();
w.toPhyloXML( phy, 0, outfile );
}
private static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
- AncestralTaxonomyInferenceException {
+ AncestralTaxonomyInferenceException {
AncestralTaxonomyInference.inferTaxonomyFromDescendents( phy );
}