70 BioNJ(
bool rooted =
false,
bool positiveLengths =
false,
bool verbose =
true) :
83 BioNJ(
const DistanceMatrix& matrix,
bool rooted =
false,
bool positiveLengths =
false,
bool verbose =
true) throw (Exception) :
99 std::string
getName()
const {
return "BioNJ"; }
void computeTree()
Compute the tree corresponding to the distance matrix.
BioNJ(bool rooted=false, bool positiveLengths=false, bool verbose=true)
Create a new BioNJ object instance and compute a tree from a distance matrix.
virtual void outputPositiveLengths(bool yn)
The BioNJ distance method.
std::string getName() const
The neighbor joining distance method.
void setDistanceMatrix(const DistanceMatrix &matrix)
Set the distance matrix to use.
double computeDistancesFromPair(const std::vector< size_t > &pair, const std::vector< double > &branchLengths, size_t pos)
Actualizes the distance matrix according to a given pair and the corresponding branch lengths...
BioNJ(const DistanceMatrix &matrix, bool rooted=false, bool positiveLengths=false, bool verbose=true)
Create a new BioNJ object instance and compute a tree from a distance matrix.
virtual void setDistanceMatrix(const DistanceMatrix &matrix)
Set the distance matrix to use.