bpp::BioNJ Member List

This is the complete list of members for bpp::BioNJ, including all inherited members.

AbstractAgglomerativeDistanceMethod(bool verbose=true, bool rootTree=false)	bpp::AbstractAgglomerativeDistanceMethod	inline
AbstractAgglomerativeDistanceMethod(const DistanceMatrix &matrix, bool verbose=true, bool rootTree=false)	bpp::AbstractAgglomerativeDistanceMethod	inline
AbstractAgglomerativeDistanceMethod(const AbstractAgglomerativeDistanceMethod &a)	bpp::AbstractAgglomerativeDistanceMethod	inline
AgglomerativeDistanceMethod()	bpp::AgglomerativeDistanceMethod	inline
BioNJ(bool rooted=false, bool positiveLengths=false, bool verbose=true)	bpp::BioNJ	inline
BioNJ(const DistanceMatrix &matrix, bool rooted=false, bool positiveLengths=false, bool verbose=true)	bpp::BioNJ	inline
clone() const	bpp::BioNJ	inline
computeBranchLengthsForPair(const std::vector< size_t > &pair)	bpp::NeighborJoining	protectedvirtual
computeDistancesFromPair(const std::vector< size_t > &pair, const std::vector< double > &branchLengths, size_t pos)	bpp::BioNJ	virtual
computeTree()	bpp::BioNJ	virtual
currentNodes_	bpp::AbstractAgglomerativeDistanceMethod	protected
DistanceMethod()	bpp::DistanceMethod	inline
finalStep(int idRoot)	bpp::NeighborJoining	protectedvirtual
getBestPair()	bpp::NeighborJoining	protectedvirtual
getLeafNode(int id, const std::string &name)	bpp::AbstractAgglomerativeDistanceMethod	protectedvirtual
getName() const	bpp::BioNJ	inlinevirtual
getParentNode(int id, Node *son1, Node *son2)	bpp::AbstractAgglomerativeDistanceMethod	protectedvirtual
getTree() const	bpp::AbstractAgglomerativeDistanceMethod	inlinevirtual
isVerbose() const	bpp::AbstractAgglomerativeDistanceMethod	inlinevirtual
lambda_	bpp::BioNJ	private
matrix_	bpp::AbstractAgglomerativeDistanceMethod	protected
NeighborJoining(bool rooted=false, bool positiveLengths=false, bool verbose=true)	bpp::NeighborJoining	inline
NeighborJoining(const DistanceMatrix &matrix, bool rooted=false, bool positiveLengths=false, bool verbose=true)	bpp::NeighborJoining	inline
operator=(const AbstractAgglomerativeDistanceMethod &a)	bpp::AbstractAgglomerativeDistanceMethod	inline
outputPositiveLengths(bool yn)	bpp::NeighborJoining	inlinevirtual
positiveLengths_	bpp::NeighborJoining	protected
rootTree_	bpp::AbstractAgglomerativeDistanceMethod	protected
setDistanceMatrix(const DistanceMatrix &matrix)	bpp::BioNJ	inlinevirtual
setVerbose(bool yn)	bpp::AbstractAgglomerativeDistanceMethod	inlinevirtual
sumDist_	bpp::NeighborJoining	protected
tree_	bpp::AbstractAgglomerativeDistanceMethod	protected
variance_	bpp::BioNJ	private
verbose_	bpp::AbstractAgglomerativeDistanceMethod	protected
~AbstractAgglomerativeDistanceMethod()	bpp::AbstractAgglomerativeDistanceMethod	inlinevirtual
~AgglomerativeDistanceMethod()	bpp::AgglomerativeDistanceMethod	inlinevirtual
~BioNJ()	bpp::BioNJ	inlinevirtual
~DistanceMethod()	bpp::DistanceMethod	inlinevirtual
~NeighborJoining()	bpp::NeighborJoining	inlinevirtual