NNI topology search method. More...

#include <Bpp/Phyl/NNITopologySearch.h>

Inheritance diagram for bpp::NNITopologySearch:

Collaboration diagram for bpp::NNITopologySearch:

Public Member Functions
	NNITopologySearch (NNISearchable &tree, const std::string &algorithm=FAST, unsigned int verbose=2)

	NNITopologySearch (const NNITopologySearch &ts)

NNITopologySearch &	operator= (const NNITopologySearch &ts)

virtual	~NNITopologySearch ()

void	search () throw (Exception)
	Performs the search. More...

void	addTopologyListener (TopologyListener *listener)
	Add a listener to the list. More...

const Tree &	getTopology () const
	Retrieve the tree. More...

NNISearchable *	getSearchableObject ()

const NNISearchable *	getSearchableObject () const

Static Public Attributes
static const std::string	FAST = "Fast"

static const std::string	BETTER = "Better"

static const std::string	PHYML = "PhyML"

Protected Member Functions
void	searchFast () throw (Exception)

void	searchBetter () throw (Exception)

void	searchPhyML () throw (Exception)

void	notifyAllPerformed (const TopologyChangeEvent &event)
	Process a TopologyChangeEvent to all listeners. More...

void	notifyAllTested (const TopologyChangeEvent &event)
	Process a TopologyChangeEvent to all listeners. More...

void	notifyAllSuccessful (const TopologyChangeEvent &event)
	Process a TopologyChangeEvent to all listeners. More...

Private Attributes
NNISearchable *	searchableTree_

std::string	algorithm_

unsigned int	verbose_

std::vector< TopologyListener * >	topoListeners_

Detailed Description

NNI topology search method.

Several algorithm are implemented:

Fast algorithm: loop over all nodes, check all NNIs and perform the corresponding change if it improve the score. When a NNI is done, reloop from the first node without checking the remaining ones.
Better algorithm: loop over all nodes, check all NNIS. Then choose the NNI corresponding to the best improvement and perform it. Then re-loop over all nodes.
PhyML algorithm (not fully tested, use with care): as the previous one, but perform all NNI improving the score at the same time. Leads to faster convergence.

Definition at line 61 of file NNITopologySearch.h.

Constructor & Destructor Documentation

◆ NNITopologySearch() [1/2]

bpp::NNITopologySearch::NNITopologySearch	(	NNISearchable &	tree,
		const std::string &	algorithm = `FAST`,
		unsigned int	verbose = `2`
	)

inline

Definition at line 76 of file NNITopologySearch.h.

◆ NNITopologySearch() [2/2]

bpp::NNITopologySearch::NNITopologySearch ( const NNITopologySearch & ts )

inline

Definition at line 83 of file NNITopologySearch.h.

References topoListeners_.

◆ ~NNITopologySearch()

virtual bpp::NNITopologySearch::~NNITopologySearch ( )

inlinevirtual

Definition at line 107 of file NNITopologySearch.h.

References topoListeners_.

Member Function Documentation

◆ addTopologyListener()

void bpp::NNITopologySearch::addTopologyListener ( TopologyListener * listener )

inlinevirtual

Add a listener to the list.

All listeners will be notified in the order of the list. The first listener to be notified is the NNISearchable object itself.

The listener will be owned by this instance, and copied when needed.

Implements bpp::TopologySearch.

Definition at line 126 of file NNITopologySearch.h.

References topoListeners_.

Referenced by bpp::OptimizationTools::optimizeTreeNNI(), and bpp::OptimizationTools::optimizeTreeNNI2().

◆ getSearchableObject() [1/2]

NNISearchable* bpp::NNITopologySearch::getSearchableObject ( )

inline

Returns: The NNISearchable object associated to this instance.

Definition at line 143 of file NNITopologySearch.h.

References searchableTree_.

Referenced by bpp::OptimizationTools::optimizeTreeNNI(), and bpp::OptimizationTools::optimizeTreeNNI2().

◆ getSearchableObject() [2/2]

const NNISearchable* bpp::NNITopologySearch::getSearchableObject ( ) const

inline

Returns: The NNISearchable object associated to this instance.

Definition at line 147 of file NNITopologySearch.h.

References searchableTree_.

◆ getTopology()

const Tree& bpp::NNITopologySearch::getTopology ( ) const

inline

Retrieve the tree.

Returns: The tree associated to this instance.

Definition at line 138 of file NNITopologySearch.h.

References bpp::NNISearchable::getTopology(), and searchableTree_.

◆ notifyAllPerformed()

void NNITopologySearch::notifyAllPerformed ( const TopologyChangeEvent & event )

protected

Process a TopologyChangeEvent to all listeners.

Definition at line 58 of file NNITopologySearch.cpp.

◆ notifyAllSuccessful()

void NNITopologySearch::notifyAllSuccessful ( const TopologyChangeEvent & event )

protected

Process a TopologyChangeEvent to all listeners.

Definition at line 76 of file NNITopologySearch.cpp.

◆ notifyAllTested()

void NNITopologySearch::notifyAllTested ( const TopologyChangeEvent & event )

protected

Process a TopologyChangeEvent to all listeners.

Definition at line 67 of file NNITopologySearch.cpp.

◆ operator=()

NNITopologySearch& bpp::NNITopologySearch::operator= ( const NNITopologySearch & ts )

inline

Definition at line 94 of file NNITopologySearch.h.

References algorithm_, searchableTree_, topoListeners_, and verbose_.

◆ search()

void NNITopologySearch::search	(		)
throw	(	Exception
	)

virtual

Performs the search.

Implements bpp::TopologySearch.

Definition at line 85 of file NNITopologySearch.cpp.

Referenced by bpp::OptimizationTools::optimizeTreeNNI(), and bpp::OptimizationTools::optimizeTreeNNI2().

◆ searchBetter()

void NNITopologySearch::searchBetter	(		)
throw	(	Exception
	)

protected

Definition at line 149 of file NNITopologySearch.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), and bpp::TreeTemplate< N >::getNodes().

◆ searchFast()

void NNITopologySearch::searchFast	(		)
throw	(	Exception
	)

protected

Definition at line 97 of file NNITopologySearch.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), and bpp::TreeTemplate< N >::getNodes().

◆ searchPhyML()

void NNITopologySearch::searchPhyML	(		)
throw	(	Exception
	)

protected

Definition at line 214 of file NNITopologySearch.cpp.

References bpp::NNISearchable::clone(), bpp::Node::getFather(), bpp::Node::getId(), and bpp::TreeTemplate< N >::getNodes().

Member Data Documentation

◆ algorithm_

std::string bpp::NNITopologySearch::algorithm_

private

Definition at line 71 of file NNITopologySearch.h.

Referenced by operator=().

◆ BETTER

const string NNITopologySearch::BETTER = "Better"

static

Definition at line 66 of file NNITopologySearch.h.

Referenced by bpp::PhylogeneticsApplicationTools::optimizeParameters().

◆ FAST

const string NNITopologySearch::FAST = "Fast"

static

Definition at line 65 of file NNITopologySearch.h.

Referenced by bpp::PhylogeneticsApplicationTools::optimizeParameters().

◆ PHYML

const string NNITopologySearch::PHYML = "PhyML"

static

Definition at line 67 of file NNITopologySearch.h.

Referenced by bpp::PhylogeneticsApplicationTools::optimizeParameters(), and bpp::OptimizationTools::optimizeTreeNNI().

◆ searchableTree_

NNISearchable* bpp::NNITopologySearch::searchableTree_

private

Definition at line 70 of file NNITopologySearch.h.

Referenced by getSearchableObject(), getTopology(), and operator=().

◆ topoListeners_

std::vector<TopologyListener*> bpp::NNITopologySearch::topoListeners_

private

Definition at line 73 of file NNITopologySearch.h.

Referenced by addTopologyListener(), NNITopologySearch(), operator=(), and ~NNITopologySearch().

◆ verbose_

unsigned int bpp::NNITopologySearch::verbose_

private

Definition at line 72 of file NNITopologySearch.h.

Referenced by operator=().

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

Bpp/Phyl/NNITopologySearch.h
Bpp/Phyl/NNITopologySearch.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NNITopologySearch() [1/2]

◆ NNITopologySearch() [2/2]

◆ ~NNITopologySearch()

Member Function Documentation

◆ addTopologyListener()

◆ getSearchableObject() [1/2]

◆ getSearchableObject() [2/2]

◆ getTopology()

◆ notifyAllPerformed()

◆ notifyAllSuccessful()

◆ notifyAllTested()

◆ operator=()

◆ search()

◆ searchBetter()

◆ searchFast()

◆ searchPhyML()

Member Data Documentation

◆ algorithm_

◆ BETTER

◆ FAST

◆ PHYML

◆ searchableTree_

◆ topoListeners_

◆ verbose_