Hierarchical clustering. More...

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

Inheritance diagram for bpp::HierarchicalClustering:

Collaboration diagram for bpp::HierarchicalClustering:

Public Member Functions
	HierarchicalClustering (const std::string &method, bool verbose=false)
	Builds a new clustering object. More...

	HierarchicalClustering (const std::string &method, const DistanceMatrix &matrix, bool verbose=false) throw (Exception)

virtual	~HierarchicalClustering ()

HierarchicalClustering *	clone () const

std::string	getName () const

TreeTemplate< Node > *	getTree () const
	Get the computed tree, if there is one. More...

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

virtual void	computeTree () throw (Exception)
	Compute the tree corresponding to the distance matrix. More...

void	setVerbose (bool yn)

bool	isVerbose () const

Static Public Attributes
static const std::string	COMPLETE = "Complete"

static const std::string	SINGLE = "Single"

static const std::string	AVERAGE = "Average"

static const std::string	MEDIAN = "Median"

static const std::string	WARD = "Ward"

static const std::string	CENTROID = "Centroid"

Protected Member Functions
std::vector< size_t >	getBestPair () throw (Exception)
	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
std::string	method_

DistanceMatrix	matrix_

Tree *	tree_

std::map< size_t, Node * >	currentNodes_

bool	verbose_

bool	rootTree_

Detailed Description

Hierarchical clustering.

This class implements the complete, single, average (= UPGMA), median, ward and centroid linkage methods.

Definition at line 64 of file HierarchicalClustering.h.

Constructor & Destructor Documentation

◆ HierarchicalClustering() [1/2]

bpp::HierarchicalClustering::HierarchicalClustering	(	const std::string &	method,
		bool	verbose = `false`
	)

inline

Builds a new clustering object.

Parameters

method	The linkage method to use. should be one of COMPLETE, SINGLE, AVERAGE, MEDIAN, WARD, CENTROID.
verbose	Tell if some progress information should be displayed.

Definition at line 85 of file HierarchicalClustering.h.

Referenced by clone().

◆ HierarchicalClustering() [2/2]

bpp::HierarchicalClustering::HierarchicalClustering	(	const std::string &	method,
		const DistanceMatrix &	matrix,
		bool	verbose = `false`
	)
throw	(	Exception
	)

inline

Definition at line 88 of file HierarchicalClustering.h.

References bpp::AbstractAgglomerativeDistanceMethod::computeTree().

◆ ~HierarchicalClustering()

virtual bpp::HierarchicalClustering::~HierarchicalClustering ( )

inlinevirtual

Definition at line 95 of file HierarchicalClustering.h.

Member Function Documentation

◆ clone()

HierarchicalClustering* bpp::HierarchicalClustering::clone ( ) const

inline

Definition at line 97 of file HierarchicalClustering.h.

References HierarchicalClustering().

◆ computeBranchLengthsForPair()

vector< double > HierarchicalClustering::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 104 of file HierarchicalClustering.cpp.

◆ computeDistancesFromPair()

double HierarchicalClustering::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 113 of file HierarchicalClustering.cpp.

◆ computeTree()

void AbstractAgglomerativeDistanceMethod::computeTree	(		)
throw	(	Exception
	)

virtualinherited

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::DistanceMethod.

Reimplemented in bpp::BioNJ.

Definition at line 62 of file AbstractAgglomerativeDistanceMethod.cpp.

References bpp::Node::setDistanceToFather().

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