bpp::AgglomerativeDistanceMethodInterface Class Reference

Interface for agglomerative distance methods. More...

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

Inheritance diagram for bpp::AgglomerativeDistanceMethodInterface:

Collaboration diagram for bpp::AgglomerativeDistanceMethodInterface:

Public Member Functions
	AgglomerativeDistanceMethodInterface ()
virtual	~AgglomerativeDistanceMethodInterface ()
virtual AgglomerativeDistanceMethodInterface *	clone () const override=0
virtual void	setDistanceMatrix (const DistanceMatrix &matrix)=0
	Set the distance matrix to use. More...
virtual void	computeTree ()=0
	Perform the clustering. More...
virtual bool	hasTree () const =0
virtual const Tree &	tree () const =0
virtual std::string	getName () const =0
virtual void	setVerbose (bool yn)=0
virtual bool	isVerbose () const =0

Detailed Description

Interface for agglomerative distance methods.

This interface does not contain any specific method and is there only for "ontology" purposes. Specific methods might be added later.

Definition at line 81 of file DistanceMethod.h.

Constructor & Destructor Documentation

AgglomerativeDistanceMethodInterface()

bpp::AgglomerativeDistanceMethodInterface::AgglomerativeDistanceMethodInterface ( )

inline

Definition at line 85 of file DistanceMethod.h.

~AgglomerativeDistanceMethodInterface()

virtual bpp::AgglomerativeDistanceMethodInterface::~AgglomerativeDistanceMethodInterface ( )

inlinevirtual

Definition at line 86 of file DistanceMethod.h.

Member Function Documentation

clone()

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

overridepure virtual

Implements bpp::DistanceMethodInterface.

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

computeTree()

virtual void bpp::DistanceMethodInterface::computeTree ( )

pure virtualinherited

Perform the clustering.

Implemented in bpp::AbstractAgglomerativeDistanceMethod, and bpp::BioNJ.

Referenced by bpp::OptimizationTools::buildDistanceTree().

getName()

virtual std::string bpp::DistanceMethodInterface::getName ( ) const

pure virtualinherited

Returns

The name of the distance method.

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

hasTree()

virtual bool bpp::DistanceMethodInterface::hasTree ( ) const

pure virtualinherited

Returns

True if a tree has been computed.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

isVerbose()

virtual bool bpp::DistanceMethodInterface::isVerbose ( ) const

pure virtualinherited

Returns

True if verbose mode is enabled.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

setDistanceMatrix()

virtual void bpp::DistanceMethodInterface::setDistanceMatrix ( const DistanceMatrix &  matrix )

pure virtualinherited

Set the distance matrix to use.

Parameters

matrix

The matrix to use.

Exceptions

Exception

In case an incorrect matrix is provided (eg smaller than 3).

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

Referenced by bpp::OptimizationTools::buildDistanceTree().

setVerbose()

virtual void bpp::DistanceMethodInterface::setVerbose ( bool  yn )

pure virtualinherited

Parameters

yn	Enable/Disable verbose mode.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

tree()

virtual const Tree& bpp::DistanceMethodInterface::tree ( ) const

pure virtualinherited

Returns

A reference toward the computed tree. Throws an exception if no tree was computed.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

Referenced by bpp::OptimizationTools::buildDistanceTree().

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The documentation for this class was generated from the following file:

• Bpp/Phyl/Distance/DistanceMethod.h