Legacy data storage class for probabilistic substitution mappings. More...

#include <Bpp/Phyl/Legacy/Mapping/ProbabilisticSubstitutionMapping.h>

Inheritance diagram for bpp::LegacyProbabilisticSubstitutionMapping:

Collaboration diagram for bpp::LegacyProbabilisticSubstitutionMapping:

Public Member Functions
	LegacyProbabilisticSubstitutionMapping (const Tree &tree, std::shared_ptr< const SubstitutionCountInterface > sc, size_t numberOfSites)
	Build a new LegacyProbabilisticSubstitutionMapping object. More...

	LegacyProbabilisticSubstitutionMapping (const Tree &tree)
	Build a new ProbabilisticSubstitutionMapping object. More...

LegacyProbabilisticSubstitutionMapping *	clone () const override

	LegacyProbabilisticSubstitutionMapping (const LegacyProbabilisticSubstitutionMapping &psm)=default

LegacyProbabilisticSubstitutionMapping &	operator= (const LegacyProbabilisticSubstitutionMapping &psm)=default

virtual	~LegacyProbabilisticSubstitutionMapping ()

size_t	getNumberOfSubstitutionTypes () const override

double	getNumberOfSubstitutions (int nodeId, size_t siteIndex, size_t type) const

virtual std::vector< double >	getNumberOfSubstitutions (int nodeId, size_t siteIndex) const

virtual void	setTree (const Tree &tree)
	(Re)-set the phylogenetic tree associated to this mapping. More...

virtual void	setNumberOfSites (size_t numberOfSites) override

virtual double &	operator() (size_t nodeIndex, size_t siteIndex, size_t type) override
	Direct access to substitution numbers. More...

virtual const double &	operator() (size_t nodeIndex, size_t siteIndex, size_t type) const override
	Direct access to substitution numbers. More...

std::vector< std::vector< double > > &	operator[] (size_t siteIndex)
	Direct access to substitution numbers. More...

const std::vector< std::vector< double > > &	operator[] (size_t siteIndex) const
	Direct access to substitution numbers. More...

virtual const Tree &	tree () const =0

const TreeTemplate< Node > &	tree () const override

virtual bool	isEmpty () const =0

bool	isEmpty () const override

virtual size_t	getNumberOfSites () const =0

size_t	getNumberOfSites () const override

virtual size_t	getNumberOfBranches () const =0

size_t	getNumberOfBranches () const override

virtual int	getSitePosition (size_t index) const =0

int	getSitePosition (size_t index) const override

virtual std::vector< double >	getBranchLengths () const =0

virtual std::vector< double >	getBranchLengths () const override

virtual size_t	getNodeIndex (int nodeId) const =0

virtual size_t	getNodeIndex (int nodeId) const override

virtual void	setSitePosition (size_t index, int position)=0
	Set the position of a given site. More...

void	setSitePosition (size_t index, int position) override
	Set the position of a given site. More...

virtual const Node *	getNode (size_t nodeIndex) const

Private Attributes
std::shared_ptr< const SubstitutionCountInterface >	substitutionCount_

std::vector< std::vector< std::vector< double > > >	mapping_
	Substitution numbers storage. More...

std::unique_ptr< const TreeTemplate< Node > >	tree_

std::vector< int >	sitesPositions_

std::vector< const Node * >	nodes_

size_t	nbSites_

size_t	nbBranches_

Detailed Description

Legacy data storage class for probabilistic substitution mappings.

A 'probabilistic' mapping contains an single value for each branch and each site. This number can be an average number of substitutions, optionally waited, or a probability of observing a certain number of substitutions. Probabilistic was coined there by opposition to the'stochastic' mapping, where a path (number of susbstitutions + there position along the branch) is available for each branch and site. The probabilistic mapping can however be extended to contain a matrix will all types of substitutions, instead of their total number.

Definition at line 27 of file ProbabilisticSubstitutionMapping.h.

Constructor & Destructor Documentation

◆ LegacyProbabilisticSubstitutionMapping() [1/3]

bpp::LegacyProbabilisticSubstitutionMapping::LegacyProbabilisticSubstitutionMapping	(	const Tree &	tree,
		std::shared_ptr< const SubstitutionCountInterface >	sc,
		size_t	numberOfSites
	)

inline

Build a new LegacyProbabilisticSubstitutionMapping object.

Parameters

tree	The tree object to use. It will be cloned for internal use.
sc	A pointer toward the substitution count object that has been used for the mapping, if any. This object allows to get the substitution types description, if there are several. If set to 0, then the mapping will be considered as having only one type of substitution mapped.
numberOfSites	The number of sites to map.

Definition at line 50 of file ProbabilisticSubstitutionMapping.h.

References setNumberOfSites().

Referenced by clone().

◆ LegacyProbabilisticSubstitutionMapping() [2/3]

bpp::LegacyProbabilisticSubstitutionMapping::LegacyProbabilisticSubstitutionMapping ( const Tree & tree )

inline

Build a new ProbabilisticSubstitutionMapping object.

Parameters

tree	The tree object to use. It will be cloned for internal use.

Definition at line 63 of file ProbabilisticSubstitutionMapping.h.

◆ LegacyProbabilisticSubstitutionMapping() [3/3]

bpp::LegacyProbabilisticSubstitutionMapping::LegacyProbabilisticSubstitutionMapping ( const LegacyProbabilisticSubstitutionMapping & psm )

default

◆ ~LegacyProbabilisticSubstitutionMapping()

virtual bpp::LegacyProbabilisticSubstitutionMapping::~LegacyProbabilisticSubstitutionMapping ( )

inlinevirtual

Definition at line 79 of file ProbabilisticSubstitutionMapping.h.

Member Function Documentation

◆ clone()

LegacyProbabilisticSubstitutionMapping* bpp::LegacyProbabilisticSubstitutionMapping::clone ( ) const

inlineoverridevirtual

Implements bpp::LegacyAbstractSubstitutionMapping.

Definition at line 70 of file ProbabilisticSubstitutionMapping.h.

References LegacyProbabilisticSubstitutionMapping().

◆ getBranchLengths() [1/2]

virtual std::vector<double> bpp::LegacyMappingInterface::getBranchLengths ( ) const

pure virtualinherited

Returns: A vector with all tree branch lengths.

Implemented in bpp::LegacyAbstractMapping.

◆ getBranchLengths() [2/2]

virtual std::vector<double> bpp::LegacyAbstractMapping::getBranchLengths ( ) const

inlineoverridevirtualinherited

Returns: A vector with all tree branch lengths.

Implements bpp::LegacyMappingInterface.

Definition at line 174 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_, and bpp::LegacyAbstractMapping::nodes_.

◆ getNode()

virtual const Node* bpp::LegacyAbstractMapping::getNode ( size_t nodeIndex ) const

inlinevirtualinherited

Definition at line 162 of file Mapping.h.

References bpp::LegacyAbstractMapping::nodes_.

Referenced by bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getNodeIndex() [1/2]

virtual size_t bpp::LegacyMappingInterface::getNodeIndex ( int nodeId ) const

pure virtualinherited

Parameters

nodeId An id of the node to look for in the map.

Returns: The mapping index for the specified node id.

Implemented in bpp::LegacyAbstractMapping.

◆ getNodeIndex() [2/2]

virtual size_t bpp::LegacyAbstractMapping::getNodeIndex ( int nodeId ) const

inlineoverridevirtualinherited

Parameters

nodeId An id of the node to look for in the map.

Returns: The mapping index for the specified node id.

Implements bpp::LegacyMappingInterface.

Definition at line 184 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_, bpp::LegacyAbstractMapping::nodes_, and bpp::TextTools::toString().

Referenced by getNumberOfSubstitutions(), bpp::LegacyProbabilisticRewardMapping::getReward(), bpp::LegacyRewardMappingTools::readFromStream(), and bpp::LegacySubstitutionMappingTools::readFromStream().

◆ getNumberOfBranches() [1/2]

virtual size_t bpp::LegacyMappingInterface::getNumberOfBranches ( ) const

pure virtualinherited

Returns: The number of branches mapped.

Implemented in bpp::LegacyAbstractMapping.

Referenced by bpp::LegacySubstitutionMappingTools::computeNormForSite(), bpp::LegacyRewardMappingTools::computeSumForSite(), bpp::LegacySubstitutionMappingTools::computeSumForSite(), bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerBranch(), and bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerType().

◆ getNumberOfBranches() [2/2]

size_t bpp::LegacyAbstractMapping::getNumberOfBranches ( ) const

inlineoverridevirtualinherited

Returns: The number of branches mapped.

Implements bpp::LegacyMappingInterface.

Definition at line 160 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbBranches_.

Referenced by bpp::LegacyProbabilisticRewardMapping::setNumberOfSites(), setNumberOfSites(), bpp::LegacyProbabilisticRewardMapping::setTree(), setTree(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getNumberOfSites() [1/2]

virtual size_t bpp::LegacyMappingInterface::getNumberOfSites ( ) const

pure virtualinherited

Returns: The number of sites mapped.

Implemented in bpp::LegacyAbstractMapping.

Referenced by bpp::LegacyRewardMappingTools::computeSumForBranch(), and bpp::LegacySubstitutionMappingTools::computeSumForBranch().

◆ getNumberOfSites() [2/2]

size_t bpp::LegacyAbstractMapping::getNumberOfSites ( ) const

inlineoverridevirtualinherited

Returns: The number of sites mapped.

Implements bpp::LegacyMappingInterface.

Definition at line 158 of file Mapping.h.

References bpp::LegacyAbstractMapping::nbSites_.

Referenced by bpp::LegacyProbabilisticRewardMapping::setTree(), setTree(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getNumberOfSubstitutions() [1/2]

virtual std::vector<double> bpp::LegacyProbabilisticSubstitutionMapping::getNumberOfSubstitutions	(	int	nodeId,
		size_t	siteIndex
	)		const

inlinevirtual

Definition at line 93 of file ProbabilisticSubstitutionMapping.h.

References bpp::LegacyAbstractMapping::getNodeIndex(), and mapping_.

◆ getNumberOfSubstitutions() [2/2]

double bpp::LegacyProbabilisticSubstitutionMapping::getNumberOfSubstitutions	(	int	nodeId,
		size_t	siteIndex,
		size_t	type
	)		const

inline

Definition at line 88 of file ProbabilisticSubstitutionMapping.h.

References bpp::LegacyAbstractMapping::getNodeIndex(), and mapping_.

◆ getNumberOfSubstitutionTypes()

size_t bpp::LegacyProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes ( ) const

inlineoverridevirtual

Returns: The number of distinct types of substitutions mapped.

Implements bpp::LegacySubstitutionMappingInterface.

Definition at line 82 of file ProbabilisticSubstitutionMapping.h.

References substitutionCount_.

Referenced by setNumberOfSites().

◆ getSitePosition() [1/2]

virtual int bpp::LegacyMappingInterface::getSitePosition ( size_t index ) const

pure virtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implemented in bpp::LegacyAbstractMapping.

◆ getSitePosition() [2/2]

int bpp::LegacyAbstractMapping::getSitePosition ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implements bpp::LegacyMappingInterface.

Definition at line 146 of file Mapping.h.

References bpp::LegacyAbstractMapping::isEmpty(), and bpp::LegacyAbstractMapping::sitesPositions_.

◆ isEmpty() [1/2]

virtual bool bpp::LegacyMappingInterface::isEmpty ( ) const

pure virtualinherited

Returns: True is the map is empty, that is, if no tree is associated to the map yet.

Implemented in bpp::LegacyAbstractMapping.

◆ isEmpty() [2/2]

bool bpp::LegacyAbstractMapping::isEmpty ( ) const

inlineoverridevirtualinherited

Returns: True is the map is empty, that is, if no tree is associated to the map yet.

Implements bpp::LegacyMappingInterface.

Definition at line 130 of file Mapping.h.

References bpp::LegacyAbstractMapping::tree_.

Referenced by bpp::LegacyAbstractMapping::getSitePosition(), bpp::LegacyAbstractMapping::setSitePosition(), and bpp::LegacyAbstractMapping::tree().

◆ operator()() [1/2]

virtual const double& bpp::LegacyProbabilisticSubstitutionMapping::operator()	(	size_t	nodeIndex,
		size_t	siteIndex,
		size_t	type
	)		const

inlineoverridevirtual

Direct access to substitution numbers.

Warning: No index checking is performed, use with care!

Implements bpp::LegacySubstitutionMappingInterface.

Definition at line 122 of file ProbabilisticSubstitutionMapping.h.

References mapping_.

◆ operator()() [2/2]

virtual double& bpp::LegacyProbabilisticSubstitutionMapping::operator()	(	size_t	nodeIndex,
		size_t	siteIndex,
		size_t	type
	)

inlineoverridevirtual

Direct access to substitution numbers.

Warning: No index checking is performed, use with care!

Implements bpp::LegacySubstitutionMappingInterface.

Definition at line 112 of file ProbabilisticSubstitutionMapping.h.

References mapping_.

◆ operator=()

LegacyProbabilisticSubstitutionMapping& bpp::LegacyProbabilisticSubstitutionMapping::operator= ( const LegacyProbabilisticSubstitutionMapping & psm )

default