bpp::DistanceMethod Class Reference

General interface for distance-based phylogenetic reconstruction methods. More...

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

Inheritance diagram for bpp::DistanceMethod:

Collaboration diagram for bpp::DistanceMethod:

Public Member Functions
	DistanceMethod ()
virtual	~DistanceMethod ()
virtual void	setDistanceMatrix (const DistanceMatrix &matrix)=0 throw (Exception)
	Set the distance matrix to use. More...
virtual void	computeTree ()=0
	Perform the clustering. More...
virtual Tree *	getTree () const =0
virtual std::string	getName () const =0
virtual void	setVerbose (bool yn)=0
virtual bool	isVerbose () const =0

Detailed Description

General interface for distance-based phylogenetic reconstruction methods.

Definition at line 61 of file DistanceMethod.h.

Constructor & Destructor Documentation

DistanceMethod()

bpp::DistanceMethod::DistanceMethod ( )

inline

Definition at line 65 of file DistanceMethod.h.

~DistanceMethod()

virtual bpp::DistanceMethod::~DistanceMethod ( )

inlinevirtual

Definition at line 66 of file DistanceMethod.h.

Member Function Documentation

computeTree()

virtual void bpp::DistanceMethod::computeTree ( )

pure virtual

Perform the clustering.

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

getName()

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

pure virtual

Returns

The name of the distance method.

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

getTree()

virtual Tree* bpp::DistanceMethod::getTree ( ) const

pure virtual

Returns

The computed tree.

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

isVerbose()

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

pure virtual

Returns

True if verbose mode is enabled.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

setDistanceMatrix()

virtual void bpp::DistanceMethod::setDistanceMatrix ( const DistanceMatrix &  matrix ) throw ( Exception )

pure virtual

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::BioNJ, bpp::NeighborJoining, and bpp::PGMA.

setVerbose()

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

pure virtual

Parameters

yn	Enable/Disable verbose mode.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

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

• Bpp/Phyl/Distance/DistanceMethod.h