Compute WPGMA and UPGMA trees from a distance matrix. More...

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

Inheritance diagram for bpp::PGMA:

Collaboration diagram for bpp::PGMA:

Public Member Functions
	PGMA (bool weighted=true)

	PGMA (const DistanceMatrix &matrix, bool weighted=true, bool verbose=true)
	Create a (U/W)PGMA object instance. More...

virtual	~PGMA ()

PGMA *	clone () const

std::string	getName () const

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

void	setWeighted (bool weighted)

bool	isWeighted () const

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...

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
bool	weighted_

DistanceMatrix	matrix_

std::unique_ptr< Tree >	tree_

std::map< size_t, Node * >	currentNodes_

bool	verbose_

bool	rootTree_

Detailed Description

Compute WPGMA and UPGMA trees from a distance matrix.

WPGMA = Weighted pair group method using arithmetic averaging, is equivalent to the average linkage hierarchical clustering method. The distance between two taxa is the average distance between all individuals in each taxa. The unweighted version (named UPGMA), uses a weighted average, with the number of individuals in a group as a weight.

Definition at line 32 of file PGMA.h.

Constructor & Destructor Documentation

◆ PGMA() [1/2]

bpp::PGMA::PGMA ( bool weighted = true )

inline

Definition at line 39 of file PGMA.h.

Referenced by clone().

◆ PGMA() [2/2]

bpp::PGMA::PGMA	(	const DistanceMatrix &	matrix,
		bool	weighted = `true`,
		bool	verbose = `true`
	)

inline

Create a (U/W)PGMA object instance.

Parameters

matrix	Input distance matrix.
weighted	Tell if we should perform Weighted or Unweighted pair group method.
verbose	Allow to display extra information, like progress bars.

Definition at line 50 of file PGMA.h.

References bpp::AbstractAgglomerativeDistanceMethod::computeTree().

◆ ~PGMA()

virtual bpp::PGMA::~PGMA ( )

inlinevirtual

Definition at line 56 of file PGMA.h.

Member Function Documentation

◆ clone()

PGMA* bpp::PGMA::clone ( ) const

inlinevirtual

Implements bpp::AgglomerativeDistanceMethodInterface.

Definition at line 58 of file PGMA.h.

References PGMA().

◆ computeBranchLengthsForPair()

vector< double > PGMA::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 49 of file PGMA.cpp.

◆ computeDistancesFromPair()

double PGMA::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 58 of file PGMA.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(), bpp::NeighborJoining::NeighborJoining(), and PGMA().