bpp::DistanceMethodInterface Class Reference

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

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

Inheritance diagram for bpp::DistanceMethodInterface:

Collaboration diagram for bpp::DistanceMethodInterface:

Public Member Functions
	DistanceMethodInterface ()
virtual	~DistanceMethodInterface ()
virtual DistanceMethodInterface *	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

General interface for distance-based phylogenetic reconstruction methods.

Definition at line 25 of file DistanceMethod.h.

Constructor & Destructor Documentation

DistanceMethodInterface()

bpp::DistanceMethodInterface::DistanceMethodInterface ( )

inline

Definition at line 29 of file DistanceMethod.h.

~DistanceMethodInterface()

virtual bpp::DistanceMethodInterface::~DistanceMethodInterface ( )

inlinevirtual

Definition at line 30 of file DistanceMethod.h.

Member Function Documentation

clone()

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

overridepure virtual

Implements bpp::Clonable.

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

computeTree()

virtual void bpp::DistanceMethodInterface::computeTree ( )

pure virtual

Perform the clustering.

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

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

getName()

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

pure virtual

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 virtual

Returns

True if a tree has been computed.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

isVerbose()

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

pure virtual

Returns

True if verbose mode is enabled.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

setDistanceMatrix()

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

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

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

setVerbose()

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

pure virtual

Parameters

yn	Enable/Disable verbose mode.

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

tree()

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

pure virtual

Returns

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

Implemented in bpp::AbstractAgglomerativeDistanceMethod.

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

---

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

• Bpp/Phyl/Distance/DistanceMethod.h