}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
+ gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
}
catch ( final IOException e ) {
fatalError( "error",
final long start_time = new Date().getTime();
try {
if ( base_algorithm == ALGORITHM.GSDI ) {
- System.out.println( "Algorithm : GSDI" );
- log_writer.println( "Algorithm : GSDI" );
+ System.out.println( "Algorithm : GSDI" );
+ log_writer.println( "Algorithm : GSDI" );
}
else if ( base_algorithm == ALGORITHM.GSDIR ) {
- System.out.println( "Algorithm : GSDIR" );
- log_writer.println( "Algorithm : GSDIR" );
+ System.out.println( "Algorithm : GSDIR" );
+ log_writer.println( "Algorithm : GSDIR" );
}
System.out.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );