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();
- nj.setVerbose( verbose );
+ final NeighborJoining nj = NeighborJoining.createInstance( verbose );
final long start_time = new Date().getTime();
for( final DistanceMatrix matrix : matrices ) {
- ps.add( nj.execute( matrix ) );
+ ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
}
final long end_time = new Date().getTime();
final PhylogenyWriter w = new PhylogenyWriter();