import java.util.List;
import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.CommandLineArguments;
Phylogeny p = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogeny_infile, true );
p = factory.create( phylogeny_infile, pp )[ 0 ];
}
catch ( final Exception e ) {
}
if ( int_node_name_is_support ) {
try {
- ForesterUtil.transferInternalNodeNamesToConfidence( p );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( p );
}
catch ( final Exception e ) {
ForesterUtil.unexpectedFatalError( nhx_too.PRG_NAME,