Partial implementation of the AgglomerativeDistanceMethod interface. More...

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

Inheritance diagram for bpp::AbstractAgglomerativeDistanceMethod:

Collaboration diagram for bpp::AbstractAgglomerativeDistanceMethod:

Public Member Functions
	AbstractAgglomerativeDistanceMethod (bool verbose=true, bool rootTree=false)

	AbstractAgglomerativeDistanceMethod (const DistanceMatrix &matrix, bool verbose=true, bool rootTree=false)

virtual	~AbstractAgglomerativeDistanceMethod ()

	AbstractAgglomerativeDistanceMethod (const AbstractAgglomerativeDistanceMethod &a)

AbstractAgglomerativeDistanceMethod &	operator= (const AbstractAgglomerativeDistanceMethod &a)

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

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

virtual AgglomerativeDistanceMethodInterface *	clone () const override=0

virtual std::string	getName () const =0

Protected Member Functions
Specific methods.
virtual std::vector< size_t >	getBestPair ()=0
	Get the best pair of nodes to agglomerate. More...

virtual std::vector< double >	computeBranchLengthsForPair (const std::vector< size_t > &pair)=0
	Compute the branch lengths for two nodes to agglomerate. More...

virtual double	computeDistancesFromPair (const std::vector< size_t > &pair, const std::vector< double > &branchLengths, size_t pos)=0
	Actualizes the distance matrix according to a given pair and the corresponding branch lengths. More...

virtual void	finalStep (int idRoot)=0
	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
DistanceMatrix	matrix_

std::unique_ptr< Tree >	tree_

std::map< size_t, Node * >	currentNodes_

bool	verbose_

bool	rootTree_

Detailed Description

Partial implementation of the AgglomerativeDistanceMethod interface.

This class provides a DistanceMatrix object for computations, and a map with pivot indices and a pointer toward the corresponding subtree.

Several methods, commons to several algorithm are provided.

Definition at line 26 of file AbstractAgglomerativeDistanceMethod.h.

Constructor & Destructor Documentation

◆ AbstractAgglomerativeDistanceMethod() [1/3]

bpp::AbstractAgglomerativeDistanceMethod::AbstractAgglomerativeDistanceMethod	(	bool	verbose = `true`,
		bool	rootTree = `false`
	)

inline

Definition at line 38 of file AbstractAgglomerativeDistanceMethod.h.

◆ AbstractAgglomerativeDistanceMethod() [2/3]

bpp::AbstractAgglomerativeDistanceMethod::AbstractAgglomerativeDistanceMethod	(	const DistanceMatrix &	matrix,
		bool	verbose = `true`,
		bool	rootTree = `false`
	)

inline

Definition at line 47 of file AbstractAgglomerativeDistanceMethod.h.

References setDistanceMatrix().

◆ ~AbstractAgglomerativeDistanceMethod()

virtual bpp::AbstractAgglomerativeDistanceMethod::~AbstractAgglomerativeDistanceMethod ( )

inlinevirtual

Definition at line 60 of file AbstractAgglomerativeDistanceMethod.h.

◆ AbstractAgglomerativeDistanceMethod() [3/3]

bpp::AbstractAgglomerativeDistanceMethod::AbstractAgglomerativeDistanceMethod ( const AbstractAgglomerativeDistanceMethod & a )

inline

Definition at line 62 of file AbstractAgglomerativeDistanceMethod.h.

References tree_.

Member Function Documentation

◆ clone()

virtual AgglomerativeDistanceMethodInterface* bpp::AgglomerativeDistanceMethodInterface::clone ( ) const

overridepure virtualinherited

Implements bpp::DistanceMethodInterface.

Implemented in bpp::PGMA, bpp::NeighborJoining, bpp::HierarchicalClustering, and bpp::BioNJ.

◆ computeBranchLengthsForPair()

virtual std::vector<double> bpp::AbstractAgglomerativeDistanceMethod::computeBranchLengthsForPair ( const std::vector< size_t > & pair )

protectedpure virtual

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.

Implemented in bpp::PGMA, bpp::NeighborJoining, and bpp::HierarchicalClustering.

◆ computeDistancesFromPair()

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

protectedpure virtual

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.

Implemented in bpp::PGMA, bpp::NeighborJoining, bpp::HierarchicalClustering, and bpp::BioNJ.

◆ computeTree()

void AbstractAgglomerativeDistanceMethod::computeTree ( )

overridevirtual

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 bpp::PGMA::PGMA().