Double recursive implementation of interface TreeParsimonyScore. More...

#include <Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h>

Inheritance diagram for bpp::DRTreeParsimonyScore:

Collaboration diagram for bpp::DRTreeParsimonyScore:

Public Member Functions
	DRTreeParsimonyScore (const Tree &tree, const SiteContainer &data, bool verbose=true, bool includeGaps=false) throw (Exception)

	DRTreeParsimonyScore (const Tree &tree, const SiteContainer &data, const StateMap *statesMap, bool verbose=true) throw (Exception)

	DRTreeParsimonyScore (const DRTreeParsimonyScore &tp)

DRTreeParsimonyScore &	operator= (const DRTreeParsimonyScore &tp)

virtual	~DRTreeParsimonyScore ()

DRTreeParsimonyScore *	clone () const

unsigned int	getScore () const
	Get the score for the current tree, i.e. the total minimum number of changes in the tree. More...

unsigned int	getScoreForSite (size_t site) const
	Get the score for a given site for the current tree, i.e. the total minimum number of changes in the tree for this site. More...

virtual const Tree &	getTree () const
	Get the tree for wich scores are computed. More...

virtual std::vector< unsigned int >	getScoreForEachSite () const
	Get the score for each site for the current tree, i.e. the total minimum number of changes in the tree for each site. More...

virtual const StateMap &	getStateMap () const

virtual void	topologyChangePerformed (const TopologyChangeEvent &event)
	Notify a topology change event. More...

Thee NNISearchable interface.
double	getTopologyValue () const throw (Exception)
	Get the current score of this NNISearchable object. More...

double	testNNI (int nodeId) const throw (NodeException)
	Send the score of a NNI movement, without performing it. More...

void	doNNI (int nodeId) throw (NodeException)
	Perform a NNI movement. More...

const Tree &	getTopology () const
	Get the tree associated to this NNISearchable object. More...

void	topologyChangeTested (const TopologyChangeEvent &event)
	Notify a topology change event. More...

void	topologyChangeSuccessful (const TopologyChangeEvent &event)
	Tell that a topology change is definitive. More...

Static Public Member Functions
static void	computeScoresPostorderForNode (const DRTreeParsimonyNodeData &pData, std::vector< Bitset > &rBitsets, std::vector< unsigned int > &rScores)
	Compute bitsets and scores for each site for a node, in postorder. More...

static void	computeScoresPreorderForNode (const DRTreeParsimonyNodeData &pData, const Node *source, std::vector< Bitset > &rBitsets, std::vector< unsigned int > &rScores)
	Compute bitsets and scores for each site for a node, in preorder. More...

static void	computeScoresForNode (const DRTreeParsimonyNodeData &pData, std::vector< Bitset > &rBitsets, std::vector< unsigned int > &rScores)
	Compute bitsets and scores for each site for a node, in all directions. More...

static void	computeScoresFromArrays (const std::vector< const std::vector< Bitset > > &iBitsets, const std::vector< const std::vector< unsigned int > > &iScores, std::vector< Bitset > &oBitsets, std::vector< unsigned int > &oScores)
	Compute bitsets and scores from an array of arrays. More...

Protected Member Functions
virtual void	computeScores ()
	Compute all scores. More...

virtual void	computeScoresPreorder (const Node *)
	Compute scores (preorder algorithm). More...

virtual void	computeScoresPostorder (const Node *)
	Compute scores (postorder algorithm). More...

const TreeTemplate< Node > *	getTreeP_ () const

TreeTemplate< Node > *	getTreeP_ ()

Private Member Functions
void	init_ (const SiteContainer &data, bool verbose)

Private Attributes
DRTreeParsimonyData *	parsimonyData_

size_t	nbDistinctSites_

Detailed Description

Double recursive implementation of interface TreeParsimonyScore.

Uses a DRTreeParsimonyData object for data storage.

Definition at line 55 of file DRTreeParsimonyScore.h.

Constructor & Destructor Documentation

◆ DRTreeParsimonyScore() [1/3]

DRTreeParsimonyScore::DRTreeParsimonyScore	(	const Tree &	tree,
		const SiteContainer &	data,
		bool	verbose = `true`,
		bool	includeGaps = `false`
	)
throw	(	Exception
	)

Definition at line 52 of file DRTreeParsimonyScore.cpp.

Referenced by clone().

◆ DRTreeParsimonyScore() [2/3]

DRTreeParsimonyScore::DRTreeParsimonyScore	(	const Tree &	tree,
		const SiteContainer &	data,
		const StateMap *	statesMap,
		bool	verbose = `true`
	)
throw	(	Exception
	)

Definition at line 65 of file DRTreeParsimonyScore.cpp.

◆ DRTreeParsimonyScore() [3/3]

DRTreeParsimonyScore::DRTreeParsimonyScore ( const DRTreeParsimonyScore & tp )

Definition at line 94 of file DRTreeParsimonyScore.cpp.

References bpp::AbstractTreeParsimonyScore::getTreeP_(), parsimonyData_, and bpp::DRTreeParsimonyData::setTree().

◆ ~DRTreeParsimonyScore()

DRTreeParsimonyScore::~DRTreeParsimonyScore ( )

virtual

Definition at line 115 of file DRTreeParsimonyScore.cpp.

References parsimonyData_.

Member Function Documentation

◆ clone()

DRTreeParsimonyScore* bpp::DRTreeParsimonyScore::clone ( ) const

inlinevirtual

Implements bpp::NNISearchable.

Definition at line 89 of file DRTreeParsimonyScore.h.

References DRTreeParsimonyScore().

◆ computeScores()

void DRTreeParsimonyScore::computeScores ( )

protectedvirtual

Compute all scores.

Call the computeScoresPreorder and computeScoresPostorder methods, and then initialize rootBitsets_ and rootScores_.

Definition at line 121 of file DRTreeParsimonyScore.cpp.

References computeScoresForNode(), computeScoresPostorder(), computeScoresPreorder(), bpp::DRTreeParsimonyData::getNodeData(), bpp::DRTreeParsimonyData::getRootBitsets(), bpp::DRTreeParsimonyData::getRootScores(), bpp::AbstractTreeParsimonyScore::getTree(), bpp::AbstractTreeParsimonyScore::getTreeP_(), and parsimonyData_.

Referenced by topologyChangeTested().

◆ computeScoresForNode()

void DRTreeParsimonyScore::computeScoresForNode	(	const DRTreeParsimonyNodeData &	pData,
		std::vector< Bitset > &	rBitsets,
		std::vector< unsigned int > &	rScores
	)

static

Compute bitsets and scores for each site for a node, in all directions.

Parameters

pData	The node data to use.
rBitsets	The bitset array where to store the resulting bitsets.
rScores	The score array where to write the resulting scores.

Definition at line 239 of file DRTreeParsimonyScore.cpp.

References computeScoresFromArrays(), bpp::Node::degree(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::Node::getNeighbors(), bpp::DRTreeParsimonyNodeData::getNode(), and bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor().

Referenced by computeScores().

◆ computeScoresFromArrays()

void DRTreeParsimonyScore::computeScoresFromArrays	(	const std::vector< const std::vector< Bitset > *> &	iBitsets,
		const std::vector< const std::vector< unsigned int > *> &	iScores,
		std::vector< Bitset > &	oBitsets,
		std::vector< unsigned int > &	oScores
	)

static

Compute bitsets and scores from an array of arrays.

This method is the more general score computation. Depending on what is passed as input, it may computes scroes fo a subtree or the whole tree.

Parameters

iBitsets	The vector of bitset arrays to use.
iScores	The vector of score arrays to use.
oBitsets	The bitset array where to store the resulting bitsets.
oScores	The score array where to write the resulting scores.

Definition at line 275 of file DRTreeParsimonyScore.cpp.

Referenced by computeScoresForNode(), computeScoresPostorderForNode(), and computeScoresPreorderForNode().

◆ computeScoresPostorder()

void DRTreeParsimonyScore::computeScoresPostorder ( const Node * node )

protectedvirtual

Compute scores (postorder algorithm).

Definition at line 131 of file DRTreeParsimonyScore.cpp.

References computeScoresPostorderForNode(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::DRTreeParsimonyData::getLeafData(), bpp::DRTreeParsimonyData::getNodeData(), bpp::Node::getNumberOfSons(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), bpp::Node::getSon(), bpp::Node::isLeaf(), and parsimonyData_.

Referenced by computeScores().

◆ computeScoresPostorderForNode()

void DRTreeParsimonyScore::computeScoresPostorderForNode	(	const DRTreeParsimonyNodeData &	pData,
		std::vector< Bitset > &	rBitsets,
		std::vector< unsigned int > &	rScores
	)

static

Compute bitsets and scores for each site for a node, in postorder.

Parameters

pData	The node data to use.
rBitsets	The bitset array where to store the resulting bitsets.
rScores	The score array where to write the resulting scores.

Definition at line 161 of file DRTreeParsimonyScore.cpp.

References computeScoresFromArrays(), bpp::Node::degree(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNeighbors(), bpp::DRTreeParsimonyNodeData::getNode(), and bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor().

Referenced by computeScoresPostorder().

◆ computeScoresPreorder()

void DRTreeParsimonyScore::computeScoresPreorder ( const Node * node )

protectedvirtual

Compute scores (preorder algorithm).

Definition at line 183 of file DRTreeParsimonyScore.cpp.

References computeScoresPreorderForNode(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRTreeParsimonyData::getLeafData(), bpp::DRTreeParsimonyData::getNodeData(), bpp::Node::getNumberOfSons(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), and parsimonyData_.

Referenced by computeScores().

◆ computeScoresPreorderForNode()

void DRTreeParsimonyScore::computeScoresPreorderForNode	(	const DRTreeParsimonyNodeData &	pData,
		const Node *	source,
		std::vector< Bitset > &	rBitsets,
		std::vector< unsigned int > &	rScores
	)

static

Compute bitsets and scores for each site for a node, in preorder.

Parameters

pData	The node data to use.
source	The node where we are coming from.
rBitsets	The bitset array where to store the resulting bitsets.
rScores	The score array where to write the resulting scores.

Definition at line 218 of file DRTreeParsimonyScore.cpp.

References computeScoresFromArrays(), bpp::Node::degree(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::Node::getNeighbors(), bpp::DRTreeParsimonyNodeData::getNode(), and bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor().

Referenced by computeScoresPreorder().

◆ doNNI()

void DRTreeParsimonyScore::doNNI	(	int	nodeId	)
throw	(	NodeException
	)

virtual

Perform a NNI movement.

Parameters

nodeId The id of the node defining the NNI movement.

Exceptions

NodeException If the node does not define a valid NNI.

Implements bpp::NNISearchable.

Definition at line 385 of file DRTreeParsimonyScore.cpp.

References bpp::Node::addSon(), bpp::Node::getFather(), bpp::Node::getSon(), bpp::Node::getSonPosition(), bpp::Node::hasFather(), and bpp::Node::removeSon().

◆ getScore()

unsigned int DRTreeParsimonyScore::getScore ( ) const

virtual

Get the score for the current tree, i.e. the total minimum number of changes in the tree.

Returns: The minimum total number of changes in the tree.

Implements bpp::TreeParsimonyScore.

Definition at line 258 of file DRTreeParsimonyScore.cpp.

References bpp::DRTreeParsimonyData::getRootScore(), bpp::AbstractTreeParsimonyData::getWeight(), nbDistinctSites_, and parsimonyData_.

Referenced by getTopologyValue().

◆ getScoreForEachSite()

std::vector< unsigned int > AbstractTreeParsimonyScore::getScoreForEachSite ( ) const

virtualinherited

Get the score for each site for the current tree, i.e. the total minimum number of changes in the tree for each site.

Returns: The minimum total number of changes in the tree for each site.

Implements bpp::TreeParsimonyScore.

Definition at line 99 of file AbstractTreeParsimonyScore.cpp.

◆ getScoreForSite()

unsigned int DRTreeParsimonyScore::getScoreForSite ( size_t site ) const

virtual

Get the score for a given site for the current tree, i.e. the total minimum number of changes in the tree for this site.

Parameters

site	The corresponding site.

Returns: The minimum total number of changes in the tree for site 'site'.

Implements bpp::TreeParsimonyScore.

Definition at line 269 of file DRTreeParsimonyScore.cpp.

References bpp::AbstractTreeParsimonyData::getRootArrayPosition(), bpp::DRTreeParsimonyData::getRootScore(), and parsimonyData_.

◆ getStateMap()

virtual const StateMap& bpp::AbstractTreeParsimonyScore::getStateMap ( ) const

inlinevirtualinherited

Definition at line 113 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::statesMap_.

◆ getTopology()

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

inlinevirtual

Get the tree associated to this NNISearchable object.

Returns: The tree associated to this instance.

Implements bpp::NNISearchable.

Definition at line 181 of file DRTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::getTree().

◆ getTopologyValue()

double bpp::DRTreeParsimonyScore::getTopologyValue	(		)	const
throw	(	Exception
	)

inlinevirtual

Get the current score of this NNISearchable object.

Returns: The current score of this instance.

Implements bpp::NNISearchable.

Definition at line 174 of file DRTreeParsimonyScore.h.

References getScore().

◆ getTree()

virtual const Tree& bpp::AbstractTreeParsimonyScore::getTree ( ) const

inlinevirtualinherited

Get the tree for wich scores are computed.

Returns: The tree associated to this object.

Implements bpp::TreeParsimonyScore.

Definition at line 111 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::tree_.

Referenced by computeScores(), and getTopology().

◆ getTreeP_() [1/2]

const TreeTemplate<Node>* bpp::AbstractTreeParsimonyScore::getTreeP_ ( ) const

inlineprotectedinherited

Definition at line 116 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::tree_.

Referenced by computeScores(), DRTreeParsimonyScore(), and operator=().

◆ getTreeP_() [2/2]

TreeTemplate<Node>* bpp::AbstractTreeParsimonyScore::getTreeP_ ( )

inlineprotectedinherited

Definition at line 117 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::tree_.

◆ init_()

void DRTreeParsimonyScore::init_	(	const SiteContainer &	data,
		bool	verbose
	)

private

Definition at line 78 of file DRTreeParsimonyScore.cpp.

◆ operator=()

DRTreeParsimonyScore & DRTreeParsimonyScore::operator= ( const DRTreeParsimonyScore & tp )

Definition at line 104 of file DRTreeParsimonyScore.cpp.

References bpp::DRTreeParsimonyData::clone(), bpp::AbstractTreeParsimonyScore::getTreeP_(), nbDistinctSites_, bpp::AbstractTreeParsimonyScore::operator=(), parsimonyData_, and bpp::DRTreeParsimonyData::setTree().

◆ testNNI()

double DRTreeParsimonyScore::testNNI	(	int	nodeId	)	const
throw	(	NodeException
	)

virtual

Send the score of a NNI movement, without performing it.

This methods sends the score variation. This variation must be negative if the new point is better, i.e. the object is to be used with a minimizing optimization (for consistence with Optimizer objects).

Parameters

nodeId The id of the node defining the NNI movement.

Returns: The score variation of the NNI.

Exceptions

NodeException If the node does not define a valid NNI.

Implements bpp::NNISearchable.

Definition at line 313 of file DRTreeParsimonyScore.cpp.

References bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeTemplateTools::getRemainingNeighbors(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), bpp::Node::getSon(), bpp::Node::getSonPosition(), and bpp::Node::hasFather().

◆ topologyChangePerformed()

virtual void bpp::TopologyListener::topologyChangePerformed ( const TopologyChangeEvent & event )

inlinevirtualinherited

Notify a topology change event.

This method is to be invoked after one or several NNI are performed. It allows appropriate recomputations.

In most case, this is the same as topologyChangeTested() + topologyChangeSuccessful().

Parameters

event The topology change event.

Definition at line 105 of file TopologySearch.h.

References bpp::TopologyListener::topologyChangeSuccessful(), and bpp::TopologyListener::topologyChangeTested().

◆ topologyChangeSuccessful()

void bpp::DRTreeParsimonyScore::topologyChangeSuccessful ( const TopologyChangeEvent & event )

inlinevirtual

Tell that a topology change is definitive.

This method is called after the topologyChangeTested() method.

Parameters

event The topology change event.

Implements bpp::TopologyListener.

Definition at line 189 of file DRTreeParsimonyScore.h.

◆ topologyChangeTested()

void bpp::DRTreeParsimonyScore::topologyChangeTested ( const TopologyChangeEvent & event )

inlinevirtual

Notify a topology change event.

Parameters

event The topology change event.

Implements bpp::TopologyListener.

Definition at line 183 of file DRTreeParsimonyScore.h.

References computeScores(), parsimonyData_, and bpp::DRTreeParsimonyData::reInit().

Member Data Documentation

◆ nbDistinctSites_

size_t bpp::DRTreeParsimonyScore::nbDistinctSites_

private

Definition at line 61 of file DRTreeParsimonyScore.h.

Referenced by getScore(), and operator=().

◆ parsimonyData_

DRTreeParsimonyData* bpp::DRTreeParsimonyScore::parsimonyData_

private

Definition at line 60 of file DRTreeParsimonyScore.h.

Referenced by computeScores(), computeScoresPostorder(), computeScoresPreorder(), DRTreeParsimonyScore(), getScore(), getScoreForSite(), operator=(), topologyChangeTested(), and ~DRTreeParsimonyScore().

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

Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DRTreeParsimonyScore() [1/3]

◆ DRTreeParsimonyScore() [2/3]

◆ DRTreeParsimonyScore() [3/3]

◆ ~DRTreeParsimonyScore()

Member Function Documentation

◆ clone()

◆ computeScores()

◆ computeScoresForNode()

◆ computeScoresFromArrays()

◆ computeScoresPostorder()

◆ computeScoresPostorderForNode()

◆ computeScoresPreorder()

◆ computeScoresPreorderForNode()

◆ doNNI()

◆ getScore()

◆ getScoreForEachSite()

◆ getScoreForSite()

◆ getStateMap()

◆ getTopology()

◆ getTopologyValue()

◆ getTree()

◆ getTreeP_() [1/2]

◆ getTreeP_() [2/2]

◆ init_()

◆ operator=()

◆ testNNI()

◆ topologyChangePerformed()

◆ topologyChangeSuccessful()

◆ topologyChangeTested()

Member Data Documentation

◆ nbDistinctSites_

◆ parsimonyData_