The neighbor joining distance method. More...

#include <Bpp/Phyl/Distance/NeighborJoining.h>

Inheritance diagram for bpp::NeighborJoining:

Collaboration diagram for bpp::NeighborJoining:

Public Member Functions
	NeighborJoining (bool rooted=false, bool positiveLengths=false, bool verbose=true)
	Create a new NeighborJoining object instance, without performing any computation. More...

	NeighborJoining (const DistanceMatrix &matrix, bool rooted=false, bool positiveLengths=false, bool verbose=true)
	Create a new NeighborJoining object instance and compute a tree from a distance matrix. More...

virtual	~NeighborJoining ()

NeighborJoining *	clone () const

std::string	getName () const

virtual void	setDistanceMatrix (const DistanceMatrix &matrix)
	Set the distance matrix to use. More...

virtual void	outputPositiveLengths (bool yn)

bool	hasTree () const override

const Tree &	tree () const override

void	computeTree () override
	Compute the tree corresponding to the distance matrix. More...

void	setVerbose (bool yn) override

bool	isVerbose () const override

Protected Member Functions
std::vector< size_t >	getBestPair ()
	Get the best pair of nodes to agglomerate. More...

std::vector< double >	computeBranchLengthsForPair (const std::vector< size_t > &pair)
	Compute the branch lengths for two nodes to agglomerate. More...

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. More...

void	finalStep (int idRoot)
	Method called when there ar eonly three remaining node to agglomerate, and creates the root node of the tree. More...

Specific methods.
virtual Node *	getLeafNode (int id, const std::string &name)
	Get a leaf node. More...

virtual Node *	getParentNode (int id, Node son1, Node son2)
	Get an inner node. More...

Protected Attributes
std::vector< double >	sumDist_

bool	positiveLengths_

DistanceMatrix	matrix_

std::unique_ptr< Tree >	tree_

std::map< size_t, Node * >	currentNodes_

bool	verbose_

bool	rootTree_

Detailed Description

The neighbor joining distance method.

Reference: N Saitou and M Nei (1987), Molecular Biology and Evolution 4(4) 406-25.

Definition at line 19 of file NeighborJoining.h.

Constructor & Destructor Documentation

◆ NeighborJoining() [1/2]

bpp::NeighborJoining::NeighborJoining	(	bool	rooted = `false`,
		bool	positiveLengths = `false`,
		bool	verbose = `true`
	)

inline

Create a new NeighborJoining object instance, without performing any computation.

Parameters

rooted	Tell if the output tree should be rooted.
positiveLengths	Tell if negative lengths should be avoided.
verbose	Allow to display extra information, like progress bars.

Definition at line 34 of file NeighborJoining.h.

Referenced by clone().

◆ NeighborJoining() [2/2]

bpp::NeighborJoining::NeighborJoining	(	const DistanceMatrix &	matrix,
		bool	rooted = `false`,
		bool	positiveLengths = `false`,
		bool	verbose = `true`
	)

inline

Create a new NeighborJoining object instance and compute a tree from a distance matrix.

Parameters

matrix	Input distance matrix.
rooted	Tell if the output tree should be rooted.
positiveLengths	Tell if negative lengths should be avoided.
verbose	Allow to display extra information, like progress bars.

Definition at line 48 of file NeighborJoining.h.

References bpp::AbstractAgglomerativeDistanceMethod::computeTree(), bpp::DistanceMatrix::size(), and sumDist_.

◆ ~NeighborJoining()

virtual bpp::NeighborJoining::~NeighborJoining ( )

inlinevirtual

Definition at line 57 of file NeighborJoining.h.

Member Function Documentation

◆ clone()

NeighborJoining* bpp::NeighborJoining::clone ( ) const

inlinevirtual

Implements bpp::AgglomerativeDistanceMethodInterface.

Definition at line 59 of file NeighborJoining.h.

References NeighborJoining().

◆ computeBranchLengthsForPair()

std::vector< double > NeighborJoining::computeBranchLengthsForPair ( const std::vector< size_t > & pair )

protectedvirtual

Compute the branch lengths for two nodes to agglomerate.

+---l1-----N1
|
+---l2-----N2

This method compute l1 and l2 given N1 and N2.

Parameters

pair	The indices of the nodes to be agglomerated.

Returns: A size 2 vector with branch lengths.

Implements bpp::AbstractAgglomerativeDistanceMethod.

Definition at line 56 of file NeighborJoining.cpp.

◆ computeDistancesFromPair()

double NeighborJoining::computeDistancesFromPair	(	const std::vector< size_t > &	pair,
		const std::vector< double > &	branchLengths,
		size_t	pos
	)

protectedvirtual

Actualizes the distance matrix according to a given pair and the corresponding branch lengths.

Parameters

pair	The indices of the nodes to be agglomerated.
branchLengths	The corresponding branch lengths.
pos	The index of the node whose distance ust be updated.

Returns: The distance between the 'pos' node and the agglomerated pair.

Implements bpp::AbstractAgglomerativeDistanceMethod.

Definition at line 73 of file NeighborJoining.cpp.

◆ computeTree()

void AbstractAgglomerativeDistanceMethod::computeTree ( )

overridevirtualinherited

Compute the tree corresponding to the distance matrix.

This method implements the following algorithm: 1) Build all leaf nodes (getLeafNode method) 2) Get the best pair to agglomerate (getBestPair method) 3) Compute the branch lengths for this pair (computeBranchLengthsForPair method) 4) Build the parent node of the pair (getParentNode method) 5) For each remaining node, update distances from the pair (computeDistancesFromPair method) 6) Return to step 2 while there are more than 3 remaining nodes. 7) Perform the final step, and send a rooted or unrooted tree.

Implements bpp::DistanceMethodInterface.

Reimplemented in bpp::BioNJ.

Definition at line 26 of file AbstractAgglomerativeDistanceMethod.cpp.

References bpp::ApplicationTools::displayGauge(), and bpp::Node::setDistanceToFather().

Referenced by bpp::HierarchicalClustering::HierarchicalClustering(), NeighborJoining(), and bpp::PGMA::PGMA().