"failed to read phylogeny from [" + in + "]: " + e.getLocalizedMessage() );
}
final File outtree = new File( ForesterUtil.removeSuffix( in.toString() )
- + "_preprocessed_gene_tree.phylo.xml" );
+ + "_preprocessed_gene_tree.phylo.xml" );
final File removed_nodes = new File( ForesterUtil.removeSuffix( in.toString() ) + "_removed_nodes.txt" );
final File present_species = new File( ForesterUtil.removeSuffix( in.toString() ) + "_species_present.txt" );
checkForOutputFileWriteability( outtree );
checkForOutputFileWriteability( present_species );
if ( phy.getNumberOfExternalNodes() < 2 ) {
ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
- + " external node(s), aborting" );
+ + " external node(s), aborting" );
}
final SortedSet<String> not_found = SequenceDbWsTools.obtainSeqInformation( phy,
true,