import java.util.List;
import org.forester.evoinference.distance.NeighborJoining;
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.evoinference.matrix.distance.DistanceMatrix;
import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
import org.forester.io.writers.PhylogenyWriter;
+ matrices[ 0 ].getSize() );
}
final List<Phylogeny> ps = new ArrayList<Phylogeny>();
- final NeighborJoining nj = NeighborJoining.createInstance( verbose );
+ final NeighborJoining nj = NeighborJoining.createInstance( verbose, 6 );
final long start_time = new Date().getTime();
for( final DistanceMatrix matrix : matrices ) {
- ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
+ ps.add( nj.execute( ( DistanceMatrix ) matrix ) );
}
final long end_time = new Date().getTime();
final PhylogenyWriter w = new PhylogenyWriter();
System.out.println( "Usage:" );
System.out.println();
System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME
- + " [options] <pairwise distances infile> <out file>" );
+ + " [options] <pairwise distances infile> <out file>" );
System.out.println();
System.out.println( " Options: " );
System.out.println( VERBOSE_OPTION + ": verbose on" );