Likelihood data structure for rate across sites models, using a double-recursive algorithm. More...

#include <Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h>

Inheritance diagram for bpp::DRASDRTreeLikelihoodData:

Collaboration diagram for bpp::DRASDRTreeLikelihoodData:

Public Member Functions
	DRASDRTreeLikelihoodData (const TreeTemplate< Node > *tree, size_t nbClasses)

	DRASDRTreeLikelihoodData (const DRASDRTreeLikelihoodData &data)

DRASDRTreeLikelihoodData &	operator= (const DRASDRTreeLikelihoodData &data)

virtual	~DRASDRTreeLikelihoodData ()

DRASDRTreeLikelihoodData *	clone () const

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

DRASDRTreeLikelihoodNodeData &	getNodeData (int nodeId)

const DRASDRTreeLikelihoodNodeData &	getNodeData (int nodeId) const

DRASDRTreeLikelihoodLeafData &	getLeafData (int nodeId)

const DRASDRTreeLikelihoodLeafData &	getLeafData (int nodeId) const

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

const std::map< int, VVVdouble > &	getLikelihoodArrays (int nodeId) const

std::map< int, VVVdouble > &	getLikelihoodArrays (int nodeId)

VVVdouble &	getLikelihoodArray (int parentId, int neighborId)

const VVVdouble &	getLikelihoodArray (int parentId, int neighborId) const

Vdouble &	getDLikelihoodArray (int nodeId)

const Vdouble &	getDLikelihoodArray (int nodeId) const

Vdouble &	getD2LikelihoodArray (int nodeId)

const Vdouble &	getD2LikelihoodArray (int nodeId) const

VVdouble &	getLeafLikelihoods (int nodeId)

const VVdouble &	getLeafLikelihoods (int nodeId) const

VVVdouble &	getRootLikelihoodArray ()

const VVVdouble &	getRootLikelihoodArray () const

VVdouble &	getRootSiteLikelihoodArray ()

const VVdouble &	getRootSiteLikelihoodArray () const

Vdouble &	getRootRateSiteLikelihoodArray ()

const Vdouble &	getRootRateSiteLikelihoodArray () const

size_t	getNumberOfDistinctSites () const

size_t	getNumberOfSites () const

size_t	getNumberOfStates () const

size_t	getNumberOfClasses () const

const SiteContainer *	getShrunkData () const

void	initLikelihoods (const SiteContainer &sites, const SubstitutionModel &model) throw (Exception)
	Resize and initialize all likelihood arrays according to the given data set and substitution model. More...

void	reInit () throw (Exception)
	Rebuild likelihood arrays at inner nodes. More...

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

std::vector< size_t > &	getRootArrayPositions ()

const std::vector< size_t > &	getRootArrayPositions () const

size_t	getRootArrayPosition (const size_t site) const

unsigned int	getWeight (size_t pos) const

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

const Alphabet *	getAlphabet () const

const TreeTemplate< Node > *	getTree () const

Protected Member Functions
void	initLikelihoods (const Node *node, const SiteContainer &sites, const SubstitutionModel &model) throw (Exception)
	This method initializes the leaves according to a sequence container. More...

Protected Attributes
std::vector< size_t >	rootPatternLinks_
	Links between sites and patterns. More...

std::vector< unsigned int >	rootWeights_
	The frequency of each site. More...

const TreeTemplate< Node > *	tree_

const Alphabet *	alphabet_

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

std::map< int, DRASDRTreeLikelihoodLeafData >	leafData_

VVVdouble	rootLikelihoods_

VVdouble	rootLikelihoodsS_

Vdouble	rootLikelihoodsSR_

SiteContainer *	shrunkData_

size_t	nbSites_

size_t	nbStates_

size_t	nbClasses_

size_t	nbDistinctSites_

Detailed Description

Likelihood data structure for rate across sites models, using a double-recursive algorithm.

Definition at line 229 of file DRASDRTreeLikelihoodData.h.

Constructor & Destructor Documentation

bpp::DRASDRTreeLikelihoodData::DRASDRTreeLikelihoodData	(	const TreeTemplate< Node > *	tree,
		size_t	nbClasses
	)

inline

Definition at line 247 of file DRASDRTreeLikelihoodData.h.

Referenced by clone().

bpp::DRASDRTreeLikelihoodData::DRASDRTreeLikelihoodData ( const DRASDRTreeLikelihoodData & data )

inline

Definition at line 253 of file DRASDRTreeLikelihoodData.h.

References shrunkData_, shrunkData_, and shrunkData_.

virtual bpp::DRASDRTreeLikelihoodData::~DRASDRTreeLikelihoodData ( )

inlinevirtual

Definition at line 287 of file DRASDRTreeLikelihoodData.h.

References shrunkData_.

Member Function Documentation

DRASDRTreeLikelihoodData* bpp::DRASDRTreeLikelihoodData::clone ( ) const

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 289 of file DRASDRTreeLikelihoodData.h.

References DRASDRTreeLikelihoodData().

Referenced by bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::operator=(), and bpp::DRNonHomogeneousTreeLikelihood::operator=().

const Alphabet* bpp::AbstractTreeLikelihoodData::getAlphabet ( ) const

inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Definition at line 136 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::alphabet_.

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

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 336 of file DRASDRTreeLikelihoodData.h.

Vdouble& bpp::DRASDRTreeLikelihoodData::getD2LikelihoodArray ( int nodeId )

inline

Definition at line 371 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode().

const Vdouble& bpp::DRASDRTreeLikelihoodData::getD2LikelihoodArray ( int nodeId ) const

inline

Definition at line 376 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Vdouble& bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray ( int nodeId )

inline

Definition at line 361 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), and bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode().

const Vdouble& bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray ( int nodeId ) const

inline

Definition at line 366 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

DRASDRTreeLikelihoodLeafData& bpp::DRASDRTreeLikelihoodData::getLeafData ( int nodeId )

inline

Definition at line 326 of file DRASDRTreeLikelihoodData.h.

References leafData_.

const DRASDRTreeLikelihoodLeafData& bpp::DRASDRTreeLikelihoodData::getLeafData ( int nodeId ) const

inline

Definition at line 331 of file DRASDRTreeLikelihoodData.h.

References leafData_.

VVdouble& bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods ( int nodeId )

inline

Definition at line 381 of file DRASDRTreeLikelihoodData.h.

References leafData_.

const VVdouble& bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods ( int nodeId ) const

inline

Definition at line 386 of file DRASDRTreeLikelihoodData.h.

References leafData_.

VVVdouble& bpp::DRASDRTreeLikelihoodData::getLikelihoodArray	(	int	parentId,
		int	neighborId
	)

inline

Definition at line 351 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), and bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays().

const VVVdouble& bpp::DRASDRTreeLikelihoodData::getLikelihoodArray	(	int	parentId,
		int	neighborId
	)		const

inline

Definition at line 356 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

const std::map<int, VVVdouble>& bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays ( int nodeId ) const

inline

Definition at line 341 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), and bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix().

std::map<int, VVVdouble>& bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays ( int nodeId )

inline

Definition at line 346 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

DRASDRTreeLikelihoodNodeData& bpp::DRASDRTreeLikelihoodData::getNodeData ( int nodeId )

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 316 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

const DRASDRTreeLikelihoodNodeData& bpp::DRASDRTreeLikelihoodData::getNodeData ( int nodeId ) const

inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 321 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfClasses ( ) const

inline

Definition at line 406 of file DRASDRTreeLikelihoodData.h.

References nbClasses_.

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfDistinctSites ( ) const

inlinevirtual

Returns: The number of non redundant patterns.

Implements bpp::TreeLikelihoodData.

Definition at line 400 of file DRASDRTreeLikelihoodData.h.

References nbDistinctSites_.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate().

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfSites ( ) const

inlinevirtual

Returns: The total number of sites.

Implements bpp::TreeLikelihoodData.

Definition at line 402 of file DRASDRTreeLikelihoodData.h.

References nbSites_.

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfStates ( ) const

inlinevirtual

Returns: Get the number of states used in the model.

Implements bpp::TreeLikelihoodData.

Definition at line 404 of file DRASDRTreeLikelihoodData.h.

References nbStates_.

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

inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Reimplemented in bpp::DRASRTreeLikelihoodData.

Definition at line 123 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

std::vector<size_t>& bpp::AbstractTreeLikelihoodData::getRootArrayPositions ( )

inlineinherited

Definition at line 121 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

const std::vector<size_t>& bpp::AbstractTreeLikelihoodData::getRootArrayPositions ( ) const

inlineinherited

Definition at line 122 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

VVVdouble& bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray ( )

inline

Definition at line 391 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoods_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState().

const VVVdouble& bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray ( ) const

inline

Definition at line 392 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoods_.

Vdouble& bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray ( )

inline

Definition at line 397 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsSR_.

const Vdouble& bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray ( ) const

inline

Definition at line 398 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsSR_.

VVdouble& bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray ( )

inline

Definition at line 394 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsS_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass().

const VVdouble& bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray ( ) const

inline

Definition at line 395 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsS_.

const SiteContainer* bpp::DRASDRTreeLikelihoodData::getShrunkData ( ) const

inline

Definition at line 408 of file DRASDRTreeLikelihoodData.h.

References shrunkData_.

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

inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Definition at line 138 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::tree_.

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

inlinevirtualinherited

Returns: The frequency of a given pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 127 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootWeights_.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

const std::vector<unsigned int>& bpp::AbstractTreeLikelihoodData::getWeights ( ) const

inlinevirtualinherited

Returns: Frequencies for each pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 131 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootWeights_.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood().

void DRASDRTreeLikelihoodData::initLikelihoods	(	const SiteContainer &	sites,
		const SubstitutionModel &	model
	)		throw (Exception)

Resize and initialize all likelihood arrays according to the given data set and substitution model.

Parameters

sites	The sequences to use as data.
model	The substitution model to use.

Exceptions

Exception if an error occures.

Definition at line 51 of file DRASDRTreeLikelihoodData.cpp.

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

void DRASDRTreeLikelihoodData::initLikelihoods	(	const Node *	node,
		const SiteContainer &	sites,
		const SubstitutionModel &	model
	)		throw (Exception)

protected

This method initializes the leaves according to a sequence container.

Here the container shrunkData_ is used. Likelihood is set to 1 for the state corresponding to the sequence site, otherwise it is set to 0.

All likelihood arrays at each nodes are initialized according to alphabet size and sequences length, and filled with 1.

NB: This method is recursive.

Parameters

node	The node defining the subtree to analyse.
sites	The sequence container to use.
model	The model, used for initializing leaves' likelihoods.

Definition at line 104 of file DRASDRTreeLikelihoodData.cpp.

References bpp::DRASDRTreeLikelihoodNodeData::getD2LikelihoodArray(), bpp::DRASDRTreeLikelihoodNodeData::getDLikelihoodArray(), bpp::Node::getId(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodLeafData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrays(), bpp::Sequence::getValue(), bpp::Node::isLeaf(), bpp::DRASDRTreeLikelihoodLeafData::setNode(), and bpp::DRASDRTreeLikelihoodNodeData::setNode().

DRASDRTreeLikelihoodData& bpp::DRASDRTreeLikelihoodData::operator= ( const DRASDRTreeLikelihoodData & data )

inline

Definition at line 267 of file DRASDRTreeLikelihoodData.h.

References leafData_, leafData_, nbClasses_, nbClasses_, nbDistinctSites_, nbDistinctSites_, nbSites_, nbSites_, nbStates_, nbStates_, nodeData_, nodeData_, bpp::AbstractTreeLikelihoodData::operator=(), rootLikelihoods_, rootLikelihoods_, rootLikelihoodsS_, rootLikelihoodsS_, rootLikelihoodsSR_, rootLikelihoodsSR_, shrunkData_, shrunkData_, shrunkData_, shrunkData_, shrunkData_, and shrunkData_.

void DRASDRTreeLikelihoodData::reInit ( ) throw (Exception)

Rebuild likelihood arrays at inner nodes.

This method is to be called when the topology of the tree has changed. Node arrays relationship are rebuilt according to the new topology of the tree. The leaves likelihood remain unchanged, so as for the first and second order derivatives.

Definition at line 209 of file DRASDRTreeLikelihoodData.cpp.

References bpp::AbstractTreeLikelihoodData::tree_.

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

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

Definition at line 214 of file DRASDRTreeLikelihoodData.cpp.

References bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays(), bpp::DRASDRTreeLikelihoodNodeData::getD2LikelihoodArray(), bpp::DRASDRTreeLikelihoodNodeData::getDLikelihoodArray(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrayForNeighbor(), bpp::DRASDRTreeLikelihoodLeafData::setNode(), and bpp::DRASDRTreeLikelihoodNodeData::setNode().

void bpp::DRASDRTreeLikelihoodData::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 301 of file DRASDRTreeLikelihoodData.h.

References bpp::TreeTemplate< N >::getNode(), leafData_, leafData_, nodeData_, nodeData_, bpp::AbstractTreeLikelihoodData::tree_, bpp::AbstractTreeLikelihoodData::tree_, and bpp::AbstractTreeLikelihoodData::tree_.

Referenced by bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::operator=(), and bpp::DRNonHomogeneousTreeLikelihood::operator=().

Member Data Documentation

const Alphabet* bpp::AbstractTreeLikelihoodData::alphabet_

protectedinherited

Definition at line 95 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getAlphabet(), bpp::AbstractTreeLikelihoodData::operator=(), and bpp::AbstractTreeLikelihoodData::operator=().

std::map<int, DRASDRTreeLikelihoodLeafData> bpp::DRASDRTreeLikelihoodData::leafData_

mutableprivate

Definition at line 235 of file DRASDRTreeLikelihoodData.h.

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

size_t bpp::DRASDRTreeLikelihoodData::nbClasses_

private

Definition at line 243 of file DRASDRTreeLikelihoodData.h.

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

size_t bpp::DRASDRTreeLikelihoodData::nbDistinctSites_

private

Definition at line 244 of file DRASDRTreeLikelihoodData.h.

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

size_t bpp::DRASDRTreeLikelihoodData::nbSites_

private

Definition at line 241 of file DRASDRTreeLikelihoodData.h.

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

size_t bpp::DRASDRTreeLikelihoodData::nbStates_

private

Definition at line 242 of file DRASDRTreeLikelihoodData.h.

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

std::map<int, DRASDRTreeLikelihoodNodeData> bpp::DRASDRTreeLikelihoodData::nodeData_

mutableprivate

Definition at line 234 of file DRASDRTreeLikelihoodData.h.

Referenced by getD2LikelihoodArray(), getD2LikelihoodArray(), getDLikelihoodArray(), getDLikelihoodArray(), getLikelihoodArray(), getLikelihoodArray(), getLikelihoodArrays(), getLikelihoodArrays(), getNodeData(), getNodeData(), operator=(), operator=(), setTree(), and setTree().

VVVdouble bpp::DRASDRTreeLikelihoodData::rootLikelihoods_

mutableprivate

Definition at line 236 of file DRASDRTreeLikelihoodData.h.

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

VVdouble bpp::DRASDRTreeLikelihoodData::rootLikelihoodsS_

mutableprivate

Definition at line 237 of file DRASDRTreeLikelihoodData.h.

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

Vdouble bpp::DRASDRTreeLikelihoodData::rootLikelihoodsSR_

mutableprivate

Definition at line 238 of file DRASDRTreeLikelihoodData.h.

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

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

protectedinherited

Links between sites and patterns.

The size of this vector is equal to the number of sites in the container, each element corresponds to a site in the container and points to the corresponding column in the likelihood array of the root node. If the container contains no repeated site, there will be a strict equivalence between each site and the likelihood array of the root node. However, if this is not the case, some pointers may point toward the same element in the likelihood array.

Definition at line 86 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::AbstractTreeLikelihoodData::getRootArrayPositions(), bpp::AbstractTreeLikelihoodData::getRootArrayPositions(), bpp::AbstractTreeLikelihoodData::operator=(), and bpp::AbstractTreeLikelihoodData::operator=().