Parsimony data structure for double-recursive (DR) algorithm. More...

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

Inheritance diagram for bpp::DRTreeParsimonyData:

Collaboration diagram for bpp::DRTreeParsimonyData:

Public Member Functions
	DRTreeParsimonyData (const TreeTemplate< Node > *tree)

	DRTreeParsimonyData (const DRTreeParsimonyData &data)

DRTreeParsimonyData &	operator= (const DRTreeParsimonyData &data)

virtual	~DRTreeParsimonyData ()

DRTreeParsimonyData *	clone () const

void	setTree (const TreeTemplate< Node > *tree)
	Set the tree associated to the data. More...

DRTreeParsimonyNodeData &	getNodeData (int nodeId)

const DRTreeParsimonyNodeData &	getNodeData (int nodeId) const

DRTreeParsimonyLeafData &	getLeafData (int nodeId)

const DRTreeParsimonyLeafData &	getLeafData (int nodeId) const

std::vector< Bitset > &	getBitsetsArray (int nodeId, int neighborId)

const std::vector< Bitset > &	getBitsetsArray (int nodeId, int neighborId) const

std::vector< unsigned int > &	getScoresArray (int nodeId, int neighborId)

const std::vector< unsigned int > &	getScoresArray (int nodeId, int neighborId) const

size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition) const

std::vector< Bitset > &	getRootBitsets ()

const std::vector< Bitset > &	getRootBitsets () const

const Bitset &	getRootBitset (size_t i) const

std::vector< unsigned int > &	getRootScores ()

const std::vector< unsigned int > &	getRootScores () const

unsigned int	getRootScore (size_t i) const

size_t	getNumberOfDistinctSites () const

size_t	getNumberOfSites () const

size_t	getNumberOfStates () const

void	init (const SiteContainer &sites, const StateMap &stateMap) throw (Exception)

void	reInit () throw (Exception)

size_t	getRootArrayPosition (size_t site) const

unsigned int	getWeight (size_t pos) const

const TreeTemplate< Node > *	getTree () const

Protected Member Functions
void	init (const Node *node, const SiteContainer &sites, const StateMap &stateMap) throw (Exception)

void	reInit (const Node *node) throw (Exception)

void	setTreeP_ (const TreeTemplate< Node > *tree)

const TreeTemplate< Node > *	getTreeP_ () const

Protected Attributes
std::vector< size_t >	rootPatternLinks_

std::vector< unsigned int >	rootWeights_

const TreeTemplate< Node > *	tree_

Private Attributes
std::map< int, DRTreeParsimonyNodeData >	nodeData_

std::map< int, DRTreeParsimonyLeafData >	leafData_

std::vector< Bitset >	rootBitsets_

std::vector< unsigned int >	rootScores_

SiteContainer *	shrunkData_

size_t	nbSites_

size_t	nbStates_

size_t	nbDistinctSites_

Detailed Description

Parsimony data structure for double-recursive (DR) algorithm.

States are coded using bitsets for faster computing (

See also: AbstractTreeParsimonyData). For each inner node in the tree, we store a DRTreeParsimonyNodeData object in nodeData_. For each leaf node in the tree, we store a DRTreeParsimonyLeafData object in leafData_.

The dataset is first compressed, removing all identical sites. The resulting dataset is stored in shrunkData_. The corresponding positions are stored in rootPatternLinks_, inherited from AbstractTreeParsimonyData.

Definition at line 195 of file DRTreeParsimonyData.h.

Constructor & Destructor Documentation

◆ DRTreeParsimonyData() [1/2]

bpp::DRTreeParsimonyData::DRTreeParsimonyData ( const TreeTemplate< Node > * tree )

inline

Definition at line 209 of file DRTreeParsimonyData.h.

Referenced by clone().

◆ DRTreeParsimonyData() [2/2]

DRTreeParsimonyData::DRTreeParsimonyData ( const DRTreeParsimonyData & data )

Definition at line 52 of file DRTreeParsimonyData.cpp.

References shrunkData_.

◆ ~DRTreeParsimonyData()

virtual bpp::DRTreeParsimonyData::~DRTreeParsimonyData ( )

inlinevirtual

Definition at line 225 of file DRTreeParsimonyData.h.

References shrunkData_.

Member Function Documentation

◆ clone()

DRTreeParsimonyData* bpp::DRTreeParsimonyData::clone ( ) const

inlinevirtual

Implements bpp::TreeParsimonyData.

Definition at line 227 of file DRTreeParsimonyData.h.

References DRTreeParsimonyData().

Referenced by bpp::DRTreeParsimonyScore::operator=().

◆ getArrayPosition()

size_t bpp::DRTreeParsimonyData::getArrayPosition	(	int	parentId,
		int	sonId,
		size_t	currentPosition
	)		const

inlinevirtual

Implements bpp::TreeParsimonyData.

Definition at line 290 of file DRTreeParsimonyData.h.

◆ getBitsetsArray() [1/2]

std::vector<Bitset>& bpp::DRTreeParsimonyData::getBitsetsArray	(	int	nodeId,
		int	neighborId
	)

inline

Definition at line 272 of file DRTreeParsimonyData.h.

References nodeData_.

◆ getBitsetsArray() [2/2]

const std::vector<Bitset>& bpp::DRTreeParsimonyData::getBitsetsArray	(	int	nodeId,
		int	neighborId
	)		const

inline

Definition at line 276 of file DRTreeParsimonyData.h.

References nodeData_.

◆ getLeafData() [1/2]

DRTreeParsimonyLeafData& bpp::DRTreeParsimonyData::getLeafData ( int nodeId )

inline

Definition at line 263 of file DRTreeParsimonyData.h.

References leafData_.

Referenced by bpp::DRTreeParsimonyScore::computeScoresPostorder(), and bpp::DRTreeParsimonyScore::computeScoresPreorder().

◆ getLeafData() [2/2]

const DRTreeParsimonyLeafData& bpp::DRTreeParsimonyData::getLeafData ( int nodeId ) const

inline

Definition at line 267 of file DRTreeParsimonyData.h.

References leafData_.

◆ getNodeData() [1/2]

DRTreeParsimonyNodeData& bpp::DRTreeParsimonyData::getNodeData ( int nodeId )

inlinevirtual

Implements bpp::TreeParsimonyData.

Definition at line 254 of file DRTreeParsimonyData.h.

References nodeData_.

Referenced by bpp::DRTreeParsimonyScore::computeScores(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), and bpp::DRTreeParsimonyScore::computeScoresPreorder().

◆ getNodeData() [2/2]

const DRTreeParsimonyNodeData& bpp::DRTreeParsimonyData::getNodeData ( int nodeId ) const

inlinevirtual

Implements bpp::TreeParsimonyData.

Definition at line 258 of file DRTreeParsimonyData.h.

References nodeData_.

◆ getNumberOfDistinctSites()

size_t bpp::DRTreeParsimonyData::getNumberOfDistinctSites ( ) const

inline

Definition at line 303 of file DRTreeParsimonyData.h.

References nbDistinctSites_.

◆ getNumberOfSites()

size_t bpp::DRTreeParsimonyData::getNumberOfSites ( ) const

inline

Definition at line 304 of file DRTreeParsimonyData.h.

References nbSites_.

◆ getNumberOfStates()

size_t bpp::DRTreeParsimonyData::getNumberOfStates ( ) const

inline

Definition at line 305 of file DRTreeParsimonyData.h.

References nbStates_.

◆ getRootArrayPosition()

size_t bpp::AbstractTreeParsimonyData::getRootArrayPosition ( size_t site ) const

inlinevirtualinherited

Implements bpp::TreeParsimonyData.

Definition at line 99 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::rootPatternLinks_.

Referenced by bpp::DRTreeParsimonyScore::getScoreForSite().

◆ getRootBitset()

const Bitset& bpp::DRTreeParsimonyData::getRootBitset ( size_t i ) const

inline

Definition at line 297 of file DRTreeParsimonyData.h.

References rootBitsets_.

◆ getRootBitsets() [1/2]

std::vector<Bitset>& bpp::DRTreeParsimonyData::getRootBitsets ( )

inline

Definition at line 295 of file DRTreeParsimonyData.h.

References rootBitsets_.

Referenced by bpp::DRTreeParsimonyScore::computeScores().

◆ getRootBitsets() [2/2]

const std::vector<Bitset>& bpp::DRTreeParsimonyData::getRootBitsets ( ) const

inline

Definition at line 296 of file DRTreeParsimonyData.h.

References rootBitsets_.

◆ getRootScore()

unsigned int bpp::DRTreeParsimonyData::getRootScore ( size_t i ) const

inline

Definition at line 301 of file DRTreeParsimonyData.h.

References rootScores_.

Referenced by bpp::DRTreeParsimonyScore::getScore(), and bpp::DRTreeParsimonyScore::getScoreForSite().

◆ getRootScores() [1/2]

std::vector<unsigned int>& bpp::DRTreeParsimonyData::getRootScores ( )

inline

Definition at line 299 of file DRTreeParsimonyData.h.

References rootScores_.

Referenced by bpp::DRTreeParsimonyScore::computeScores().

◆ getRootScores() [2/2]

const std::vector<unsigned int>& bpp::DRTreeParsimonyData::getRootScores ( ) const

inline

Definition at line 300 of file DRTreeParsimonyData.h.

References rootScores_.

◆ getScoresArray() [1/2]

std::vector<unsigned int>& bpp::DRTreeParsimonyData::getScoresArray	(	int	nodeId,
		int	neighborId
	)

inline

Definition at line 281 of file DRTreeParsimonyData.h.

References nodeData_.

◆ getScoresArray() [2/2]

const std::vector<unsigned int>& bpp::DRTreeParsimonyData::getScoresArray	(	int	nodeId,
		int	neighborId
	)		const

inline

Definition at line 285 of file DRTreeParsimonyData.h.

References nodeData_.

◆ getTree()

const TreeTemplate<Node>* bpp::AbstractTreeParsimonyData::getTree ( ) const

inlinevirtualinherited

Implements bpp::TreeParsimonyData.

Definition at line 109 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::tree_.

◆ getTreeP_()

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

inlineprotectedinherited

Definition at line 113 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::tree_.

Referenced by reInit().

◆ getWeight()

unsigned int bpp::AbstractTreeParsimonyData::getWeight ( size_t pos ) const

inlineinherited

Definition at line 104 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::rootWeights_.

Referenced by bpp::DRTreeParsimonyScore::getScore().

◆ init() [1/2]

void DRTreeParsimonyData::init	(	const SiteContainer &	sites,
		const StateMap &	stateMap
	)
throw	(	Exception
	)

Definition at line 90 of file DRTreeParsimonyData.cpp.

References bpp::SitePatterns::getIndices(), bpp::SitePatterns::getSites(), and bpp::SitePatterns::getWeights().

◆ init() [2/2]

void DRTreeParsimonyData::init	(	const Node *	node,
		const SiteContainer &	sites,
		const StateMap &	stateMap
	)
throw	(	Exception
	)

protected

Definition at line 112 of file DRTreeParsimonyData.cpp.

References bpp::DRTreeParsimonyNodeData::eraseNeighborArrays(), bpp::DRTreeParsimonyLeafData::getBitsetsArray(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), bpp::DRTreeParsimonyNodeData::setNode(), and bpp::DRTreeParsimonyLeafData::setNode().

◆ operator=()

DRTreeParsimonyData & DRTreeParsimonyData::operator= ( const DRTreeParsimonyData & data )

Definition at line 71 of file DRTreeParsimonyData.cpp.

References leafData_, nbDistinctSites_, nbSites_, nbStates_, nodeData_, bpp::AbstractTreeParsimonyData::operator=(), rootBitsets_, rootScores_, and shrunkData_.

◆ reInit() [1/2]

void DRTreeParsimonyData::reInit	(		)
throw	(	Exception
	)

Definition at line 178 of file DRTreeParsimonyData.cpp.

References bpp::AbstractTreeParsimonyData::getTreeP_().

Referenced by bpp::DRTreeParsimonyScore::topologyChangeTested().

◆ reInit() [2/2]

void DRTreeParsimonyData::reInit	(	const Node *	node	)
throw	(	Exception
	)

protected

Definition at line 184 of file DRTreeParsimonyData.cpp.

References bpp::DRTreeParsimonyNodeData::eraseNeighborArrays(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), and bpp::DRTreeParsimonyNodeData::setNode().

◆ setTree()

void bpp::DRTreeParsimonyData::setTree ( const TreeTemplate< Node > * tree )

inline

Set the tree associated to the data.

All node data will be actualized accordingly by calling the setNode() method on the corresponding nodes.

Warning: : the old tree and the new tree must be two clones! And particularly, they have to share the same topology and nodes id.

Parameters

tree	The tree to be associated to this data.

Definition at line 239 of file DRTreeParsimonyData.h.

References leafData_, nodeData_, bpp::AbstractTreeParsimonyData::setTreeP_(), and bpp::AbstractTreeParsimonyData::tree_.

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

◆ setTreeP_()

void bpp::AbstractTreeParsimonyData::setTreeP_ ( const TreeTemplate< Node > * tree )

inlineprotectedinherited

Definition at line 112 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::tree_.

Referenced by setTree().

Member Data Documentation

◆ leafData_

std::map<int, DRTreeParsimonyLeafData> bpp::DRTreeParsimonyData::leafData_

mutableprivate

Definition at line 200 of file DRTreeParsimonyData.h.

Referenced by getLeafData(), operator=(), and setTree().

◆ nbDistinctSites_

size_t bpp::DRTreeParsimonyData::nbDistinctSites_

private

Definition at line 206 of file DRTreeParsimonyData.h.

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

◆ nbSites_

size_t bpp::DRTreeParsimonyData::nbSites_

private

Definition at line 204 of file DRTreeParsimonyData.h.

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

◆ nbStates_

size_t bpp::DRTreeParsimonyData::nbStates_

private

Definition at line 205 of file DRTreeParsimonyData.h.

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

◆ nodeData_

std::map<int, DRTreeParsimonyNodeData> bpp::DRTreeParsimonyData::nodeData_

mutableprivate

Definition at line 199 of file DRTreeParsimonyData.h.

Referenced by getBitsetsArray(), getNodeData(), getScoresArray(), operator=(), and setTree().

◆ rootBitsets_

std::vector<Bitset> bpp::DRTreeParsimonyData::rootBitsets_

mutableprivate

Definition at line 201 of file DRTreeParsimonyData.h.

Referenced by getRootBitset(), getRootBitsets(), and operator=().

◆ rootPatternLinks_

std::vector<size_t> bpp::AbstractTreeParsimonyData::rootPatternLinks_

protectedinherited

Definition at line 70 of file AbstractTreeParsimonyData.h.

Referenced by bpp::AbstractTreeParsimonyData::getRootArrayPosition(), and bpp::AbstractTreeParsimonyData::operator=().

◆ rootScores_

std::vector<unsigned int> bpp::DRTreeParsimonyData::rootScores_

mutableprivate

Definition at line 202 of file DRTreeParsimonyData.h.

Referenced by getRootScore(), getRootScores(), and operator=().

◆ rootWeights_

std::vector<unsigned int> bpp::AbstractTreeParsimonyData::rootWeights_

protectedinherited

Definition at line 71 of file AbstractTreeParsimonyData.h.

Referenced by bpp::AbstractTreeParsimonyData::getWeight(), and bpp::AbstractTreeParsimonyData::operator=().

◆ shrunkData_

SiteContainer* bpp::DRTreeParsimonyData::shrunkData_

private

Definition at line 203 of file DRTreeParsimonyData.h.

Referenced by DRTreeParsimonyData(), operator=(), and ~DRTreeParsimonyData().

◆ tree_

const TreeTemplate<Node>* bpp::AbstractTreeParsimonyData::tree_

protectedinherited

Definition at line 72 of file AbstractTreeParsimonyData.h.

Referenced by bpp::AbstractTreeParsimonyData::getTree(), bpp::AbstractTreeParsimonyData::getTreeP_(), bpp::AbstractTreeParsimonyData::operator=(), setTree(), and bpp::AbstractTreeParsimonyData::setTreeP_().

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

Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DRTreeParsimonyData() [1/2]

◆ DRTreeParsimonyData() [2/2]

◆ ~DRTreeParsimonyData()

Member Function Documentation

◆ clone()

◆ getArrayPosition()

◆ getBitsetsArray() [1/2]

◆ getBitsetsArray() [2/2]

◆ getLeafData() [1/2]

◆ getLeafData() [2/2]

◆ getNodeData() [1/2]

◆ getNodeData() [2/2]

◆ getNumberOfDistinctSites()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getRootArrayPosition()

◆ getRootBitset()

◆ getRootBitsets() [1/2]

◆ getRootBitsets() [2/2]

◆ getRootScore()

◆ getRootScores() [1/2]

◆ getRootScores() [2/2]

◆ getScoresArray() [1/2]

◆ getScoresArray() [2/2]

◆ getTree()

◆ getTreeP_()

◆ getWeight()

◆ init() [1/2]

◆ init() [2/2]

◆ operator=()

◆ reInit() [1/2]

◆ reInit() [2/2]

◆ setTree()

◆ setTreeP_()

Member Data Documentation

◆ leafData_

◆ nbDistinctSites_

◆ nbSites_

◆ nbStates_

◆ nodeData_

◆ rootBitsets_

◆ rootPatternLinks_

◆ rootScores_

◆ rootWeights_

◆ shrunkData_

◆ tree_