import java.util.TreeSet;
import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
}
}
- Phylogeny pi( String matrix ) {
+ Phylogeny pi( final String matrix ) {
final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix );
final int seed = 15;
final int n = 100;
return master_phy;
}
- private Phylogeny inferNJphylogeny( PWD_DISTANCE_METHOD pwd_distance_method,
+ private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
final Msa msa,
- boolean write_matrix,
- String matrix_name ) {
+ final boolean write_matrix,
+ final String matrix_name ) {
BasicSymmetricalDistanceMatrix m = null;
switch ( pwd_distance_method ) {
case KIMURA_DISTANCE:
try {
m.write( ForesterUtil.createBufferedWriter( matrix_name ) );
}
- catch ( IOException e ) {
+ catch ( final IOException e ) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
- final NeighborJoining nj = NeighborJoining.createInstance();
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
final Phylogeny phy = nj.execute( m );
return phy;
}