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 (std::shared_ptr< TreeTemplate< Node > > tree, std::shared_ptr< const SiteContainerInterface > data, bool verbose=true, bool includeGaps=false)

	DRTreeParsimonyScore (std::shared_ptr< TreeTemplate< Node > > tree, std::shared_ptr< const SiteContainerInterface > data, std::shared_ptr< const StateMapInterface > statesMap, bool verbose=true)

	DRTreeParsimonyScore (const DRTreeParsimonyScore &tp)

DRTreeParsimonyScore &	operator= (const DRTreeParsimonyScore &tp)

virtual	~DRTreeParsimonyScore ()

DRTreeParsimonyScore *	clone () const override

unsigned int	getScore () const override
	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 override
	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...

const Tree &	tree () const override
	Get the tree for which scores are computed. More...

virtual const TreeTemplate< Node > &	treeTemplate () const

virtual std::shared_ptr< const TreeTemplate< Node > >	getTreeTemplate () const

std::vector< unsigned int >	getScorePerSite () const override
	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...

const StateMapInterface &	stateMap () const override
	Get the state map associated to this instance. More...

std::shared_ptr< const StateMapInterface >	getStateMap () const override
	Get the state map associated to this instance. More...

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

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

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

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

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

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

void	topologyChangeSuccessful (const TopologyChangeEvent &event) override
	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...

virtual Tree &	tree_ ()

virtual TreeTemplate< Node > &	treeTemplate_ ()

virtual std::shared_ptr< TreeTemplate< Node > >	getTreeTemplate_ ()

Private Member Functions
void	init_ (std::shared_ptr< const SiteContainerInterface > data, bool verbose)

Private Attributes
std::unique_ptr< DRTreeParsimonyData >	parsimonyData_

size_t	nbDistinctSites_

std::shared_ptr< TreeTemplate< Node > >	treePtr_

std::shared_ptr< const SiteContainerInterface >	data_

std::shared_ptr< const Alphabet >	alphabet_

std::shared_ptr< const StateMapInterface >	statesMap_

size_t	nbStates_

Parsimony solution
static std::string	PARSIMONY_SOLUTION_STATE = "state"

void	setNodeState (Node *node, size_t state)
	Sets the state of a node in a mapping. More...

size_t	getNodeState (const Node *node)
	Extracts the state of a node in a mapping. More...

void	computeSolution ()
	Compute a maximum parsimony solution in DELTRAN manner. More...

Detailed Description

Double recursive implementation of interface TreeParsimonyScore.

Uses a DRTreeParsimonyData object for data storage.

Definition at line 21 of file DRTreeParsimonyScore.h.

Constructor & Destructor Documentation

◆ DRTreeParsimonyScore() [1/3]

DRTreeParsimonyScore::DRTreeParsimonyScore	(	std::shared_ptr< TreeTemplate< Node > >	tree,
		std::shared_ptr< const SiteContainerInterface >	data,
		bool	verbose = `true`,
		bool	includeGaps = `false`
	)

Definition at line 18 of file DRTreeParsimonyScore.cpp.

References init_().

Referenced by clone().

◆ DRTreeParsimonyScore() [2/3]

DRTreeParsimonyScore::DRTreeParsimonyScore	(	std::shared_ptr< TreeTemplate< Node > >	tree,
		std::shared_ptr< const SiteContainerInterface >	data,
		std::shared_ptr< const StateMapInterface >	statesMap,
		bool	verbose = `true`
	)

Definition at line 30 of file DRTreeParsimonyScore.cpp.

References init_().

◆ DRTreeParsimonyScore() [3/3]

DRTreeParsimonyScore::DRTreeParsimonyScore ( const DRTreeParsimonyScore & tp )

Definition at line 58 of file DRTreeParsimonyScore.cpp.

References bpp::AbstractTreeParsimonyScore::getTreeTemplate(), and parsimonyData_.

◆ ~DRTreeParsimonyScore()

DRTreeParsimonyScore::~DRTreeParsimonyScore ( )

virtual

Definition at line 79 of file DRTreeParsimonyScore.cpp.

Member Function Documentation

◆ clone()

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

inlineoverridevirtual

Implements bpp::NNISearchable.

Definition at line 48 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 83 of file DRTreeParsimonyScore.cpp.

References computeScoresForNode(), computeScoresPostorder(), computeScoresPreorder(), parsimonyData_, and bpp::AbstractTreeParsimonyScore::treeTemplate().

Referenced by init_(), and 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 203 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 scores of 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 239 of file DRTreeParsimonyScore.cpp.

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

◆ computeScoresPostorder()

void DRTreeParsimonyScore::computeScoresPostorder ( const Node * node )

protectedvirtual

Compute scores (postorder algorithm).

Definition at line 93 of file DRTreeParsimonyScore.cpp.

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

Referenced by computeScores(), and computeScoresPostorder().

◆ 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 124 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 146 of file DRTreeParsimonyScore.cpp.

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

Referenced by computeScores(), and computeScoresPreorder().

◆ 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 182 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().

◆ computeSolution()

void DRTreeParsimonyScore::computeSolution ( )

Compute a maximum parsimony solution in DELTRAN manner.

Definition at line 392 of file DRTreeParsimonyScore.cpp.

References bpp::TreeIterator::begin(), bpp::TreeIterator::end(), getNodeState(), bpp::StateMapInterface::getNumberOfModelStates(), bpp::TreeIterator::next(), parsimonyData_, bpp::RandomTools::pickOne(), setNodeState(), bpp::AbstractTreeParsimonyScore::stateMap(), and bpp::AbstractTreeParsimonyScore::treeTemplate_().

◆ doNNI()

void DRTreeParsimonyScore::doNNI ( int nodeId )

overridevirtual

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 352 of file DRTreeParsimonyScore.cpp.

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

◆ getNodeState()

size_t DRTreeParsimonyScore::getNodeState ( const Node * node )

Extracts the state of a node in a mapping.

Parameters

node	The node to get the state of

Returns: Node state is int

Definition at line 385 of file DRTreeParsimonyScore.cpp.

References bpp::Node::getNodeProperty(), and PARSIMONY_SOLUTION_STATE.

Referenced by computeSolution().

◆ getScore()

unsigned int DRTreeParsimonyScore::getScore ( ) const

overridevirtual

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::TreeParsimonyScoreInterface.

Definition at line 222 of file DRTreeParsimonyScore.cpp.

References nbDistinctSites_, and parsimonyData_.

Referenced by getTopologyValue(), and testNNI().

◆ getScoreForSite()

unsigned int DRTreeParsimonyScore::getScoreForSite ( size_t site ) const

overridevirtual

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::TreeParsimonyScoreInterface.

Definition at line 233 of file DRTreeParsimonyScore.cpp.

References parsimonyData_.

◆ getScorePerSite()

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

overridevirtualinherited

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::TreeParsimonyScoreInterface.

Definition at line 69 of file AbstractTreeParsimonyScore.cpp.

References bpp::AbstractTreeParsimonyScore::data_, and bpp::TreeParsimonyScoreInterface::getScoreForSite().

◆ getStateMap()

std::shared_ptr< const StateMapInterface > bpp::AbstractTreeParsimonyScore::getStateMap ( ) const

inlineoverridevirtualinherited

Get the state map associated to this instance.

Returns: A shared pointer toward the underlying state map.

Implements bpp::TreeParsimonyScoreInterface.

Definition at line 54 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::statesMap_.

Referenced by init_().

◆ getTopologyValue()

double bpp::DRTreeParsimonyScore::getTopologyValue ( ) const

inlineoverridevirtual

Get the current score of this NNISearchable object.

Returns: The current score of this instance.

Implements bpp::NNISearchable.

Definition at line 133 of file DRTreeParsimonyScore.h.

References getScore().

◆ getTreeTemplate()

virtual std::shared_ptr< const TreeTemplate< Node > > bpp::AbstractTreeParsimonyScore::getTreeTemplate ( ) const

inlinevirtualinherited

Definition at line 51 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::treePtr_.

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

◆ getTreeTemplate_()

virtual std::shared_ptr< TreeTemplate< Node > > bpp::AbstractTreeParsimonyScore::getTreeTemplate_ ( )

inlineprotectedvirtualinherited

Definition at line 59 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::treePtr_.

◆ init_()

void DRTreeParsimonyScore::init_	(	std::shared_ptr< const SiteContainerInterface >	data,
		bool	verbose
	)

private

Definition at line 42 of file DRTreeParsimonyScore.cpp.

References computeScores(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::AbstractTreeParsimonyScore::getStateMap(), nbDistinctSites_, parsimonyData_, and bpp::TextTools::toString().

Referenced by DRTreeParsimonyScore().

◆ operator=()

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

Definition at line 68 of file DRTreeParsimonyScore.cpp.

References bpp::AbstractTreeParsimonyScore::getTreeTemplate(), nbDistinctSites_, and parsimonyData_.

◆ setNodeState()

void DRTreeParsimonyScore::setNodeState	(	Node *	node,
		size_t	state
	)

Sets the state of a node in a mapping.

Parameters

node	The node to get the state of
state	The state that needs to be assigned to the node

Definition at line 377 of file DRTreeParsimonyScore.cpp.

References PARSIMONY_SOLUTION_STATE, and bpp::Node::setNodeProperty().

Referenced by computeSolution().

◆ stateMap()

const StateMapInterface & bpp::AbstractTreeParsimonyScore::stateMap ( ) const

inlineoverridevirtualinherited

Get the state map associated to this instance.

Returns: The underlying state map.

Implements bpp::TreeParsimonyScoreInterface.

Definition at line 53 of file AbstractTreeParsimonyScore.h.

References bpp::AbstractTreeParsimonyScore::statesMap_.

Referenced by computeSolution().

◆ testNNI()

double DRTreeParsimonyScore::testNNI ( int nodeId ) const

overridevirtual

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.