Data storage class for probabilistic substitution mappings. More...

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

Inheritance diagram for bpp::ProbabilisticSubstitutionMapping:

Collaboration diagram for bpp::ProbabilisticSubstitutionMapping:

Public Member Functions
	ProbabilisticSubstitutionMapping (const Tree &tree, const SubstitutionCount *sc, size_t numberOfSites)
	Build a new ProbabilisticSubstitutionMapping object. More...

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

ProbabilisticSubstitutionMapping *	clone () const

	ProbabilisticSubstitutionMapping (const ProbabilisticSubstitutionMapping &psm)

ProbabilisticSubstitutionMapping &	operator= (const ProbabilisticSubstitutionMapping &psm)

virtual	~ProbabilisticSubstitutionMapping ()

size_t	getNumberOfSubstitutionTypes () const

virtual 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)

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

virtual const double &	operator() (size_t nodeIndex, size_t siteIndex, size_t type) const
	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 &	getTree () const =0

const TreeTemplate< Node > &	getTree () const throw (Exception)

virtual bool	isEmpty () const =0

bool	isEmpty () const

virtual size_t	getNumberOfSites () const =0

size_t	getNumberOfSites () const

virtual size_t	getNumberOfBranches () const =0

size_t	getNumberOfBranches () const

virtual int	getSitePosition (size_t index) const =0

int	getSitePosition (size_t index) const throw (Exception)

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

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

virtual size_t	getNodeIndex (int nodeId) const =0 throw (NodeNotFoundException)

virtual size_t	getNodeIndex (int nodeId) const throw (NodeNotFoundException)

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

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

virtual const Node *	getNode (size_t nodeIndex) const

Private Attributes
const SubstitutionCount *	substitutionCount_

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

Detailed Description

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 63 of file ProbabilisticSubstitutionMapping.h.

Constructor & Destructor Documentation

◆ ProbabilisticSubstitutionMapping() [1/3]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping	(	const Tree &	tree,
		const SubstitutionCount *	sc,
		size_t	numberOfSites
	)

inline

Build a new ProbabilisticSubstitutionMapping 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 86 of file ProbabilisticSubstitutionMapping.h.

References setNumberOfSites().

Referenced by clone().

◆ ProbabilisticSubstitutionMapping() [2/3]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping ( 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 97 of file ProbabilisticSubstitutionMapping.h.

◆ ProbabilisticSubstitutionMapping() [3/3]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping ( const ProbabilisticSubstitutionMapping & psm )

inline

Definition at line 104 of file ProbabilisticSubstitutionMapping.h.

◆ ~ProbabilisticSubstitutionMapping()

virtual bpp::ProbabilisticSubstitutionMapping::~ProbabilisticSubstitutionMapping ( )

inlinevirtual

Definition at line 116 of file ProbabilisticSubstitutionMapping.h.

Member Function Documentation

◆ clone()

ProbabilisticSubstitutionMapping* bpp::ProbabilisticSubstitutionMapping::clone ( ) const

inlinevirtual

Implements bpp::AbstractSubstitutionMapping.

Definition at line 102 of file ProbabilisticSubstitutionMapping.h.

References ProbabilisticSubstitutionMapping().

◆ getBranchLengths() [1/2]

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

pure virtualinherited

Returns: A vector with all tree branch lengths.

Implemented in bpp::AbstractMapping.

◆ getBranchLengths() [2/2]

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

inlinevirtualinherited

Returns: A vector with all tree branch lengths.

Implements bpp::Mapping.

Definition at line 222 of file Mapping.h.

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

◆ getNode()

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

inlinevirtualinherited

Definition at line 212 of file Mapping.h.

References bpp::AbstractMapping::nodes_.

◆ getNodeIndex() [1/2]

virtual size_t bpp::Mapping::getNodeIndex	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

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::AbstractMapping.

◆ getNodeIndex() [2/2]

virtual size_t bpp::AbstractMapping::getNodeIndex	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtualinherited

Parameters

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

Returns: The mapping index for the specified node id.

Implements bpp::Mapping.

Definition at line 230 of file Mapping.h.

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

Referenced by bpp::SubstitutionMappingTools::getCountsPerBranch(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), getNumberOfSubstitutions(), bpp::ProbabilisticRewardMapping::getReward(), bpp::SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite(), and bpp::SubstitutionMappingTools::outputTotalCountsPerBranchPerSite().

◆ getNumberOfBranches() [1/2]

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

pure virtualinherited

Returns: The number of branches mapped.

Implemented in bpp::AbstractMapping.

Referenced by bpp::SubstitutionMappingTools::computeNormForSite(), bpp::RewardMappingTools::computeSumForSite(), bpp::SubstitutionMappingTools::computeSumForSite(), and bpp::SubstitutionMappingTools::computeTotalSubstitutionVectorForSite().

◆ getNumberOfBranches() [2/2]

size_t bpp::AbstractMapping::getNumberOfBranches ( ) const

inlinevirtualinherited

Returns: The number of branches mapped.

Implements bpp::Mapping.

Definition at line 210 of file Mapping.h.

References bpp::AbstractMapping::nbBranches_.

Referenced by bpp::ProbabilisticRewardMapping::setNumberOfSites(), setNumberOfSites(), bpp::ProbabilisticRewardMapping::setTree(), and setTree().

◆ getNumberOfSites() [1/2]

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

pure virtualinherited

Returns: The number of sites mapped.

Implemented in bpp::AbstractMapping.

Referenced by bpp::RewardMappingTools::computeSumForBranch(), and bpp::SubstitutionMappingTools::computeSumForBranch().

◆ getNumberOfSites() [2/2]

size_t bpp::AbstractMapping::getNumberOfSites ( ) const

inlinevirtualinherited

Returns: The number of sites mapped.

Implements bpp::Mapping.

Definition at line 208 of file Mapping.h.

References bpp::AbstractMapping::nbSites_.

Referenced by bpp::SubstitutionMappingTools::getCountsPerBranch(), bpp::SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite(), bpp::SubstitutionMappingTools::outputTotalCountsPerBranchPerSite(), bpp::ProbabilisticRewardMapping::setTree(), and setTree().

◆ getNumberOfSubstitutions() [1/2]

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

inlinevirtual

Definition at line 126 of file ProbabilisticSubstitutionMapping.h.

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

◆ getNumberOfSubstitutions() [2/2]

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

inlinevirtual

Definition at line 131 of file ProbabilisticSubstitutionMapping.h.

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

◆ getNumberOfSubstitutionTypes()

size_t bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

Returns: The number of distinct types of substitutions mapped.

Implements bpp::SubstitutionMapping.

Definition at line 120 of file ProbabilisticSubstitutionMapping.h.

References bpp::SubstitutionCount::getNumberOfSubstitutionTypes(), and substitutionCount_.

Referenced by bpp::SubstitutionMappingTools::getCountsPerBranch(), and setNumberOfSites().

◆ getSitePosition() [1/2]

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

pure virtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implemented in bpp::AbstractMapping.

◆ getSitePosition() [2/2]

int bpp::AbstractMapping::getSitePosition	(	size_t	index	)	const
throw	(	Exception
	)

inlinevirtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implements bpp::Mapping.

Definition at line 196 of file Mapping.h.

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

◆ getTree() [1/2]

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

pure virtualinherited

Returns: Get the phylogenetic tree associated to this mapping.

Implemented in bpp::AbstractMapping.

◆ getTree() [2/2]

const TreeTemplate<Node>& bpp::AbstractMapping::getTree	(		)	const
throw	(	Exception
	)

inlinevirtualinherited

Returns: Get the phylogenetic tree associated to this mapping.

Implements bpp::Mapping.

Definition at line 182 of file Mapping.h.

References bpp::AbstractMapping::isEmpty(), and bpp::AbstractMapping::tree_.

◆ isEmpty() [1/2]

virtual bool bpp::Mapping::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::AbstractMapping.

◆ isEmpty() [2/2]

bool bpp::AbstractMapping::isEmpty ( ) const

inlinevirtualinherited

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

Implements bpp::Mapping.

Definition at line 180 of file Mapping.h.

References bpp::AbstractMapping::tree_.

Referenced by bpp::AbstractMapping::getSitePosition(), bpp::AbstractMapping::getTree(), and bpp::AbstractMapping::setSitePosition().

◆ operator()() [1/2]

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

inlinevirtual

Direct access to substitution numbers.

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

Implements bpp::SubstitutionMapping.

Definition at line 150 of file ProbabilisticSubstitutionMapping.h.

References mapping_.

◆ operator()() [2/2]

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

inlinevirtual

Direct access to substitution numbers.

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

Implements bpp::SubstitutionMapping.

Definition at line 160 of file ProbabilisticSubstitutionMapping.h.

References mapping_.

◆ operator=()

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

inline

Definition at line 108 of file ProbabilisticSubstitutionMapping.h.

References mapping_, bpp::AbstractSubstitutionMapping::operator=(), and substitutionCount_.

◆ operator[]() [1/2]

std::vector< std::vector<double> >& bpp::ProbabilisticSubstitutionMapping::operator[] ( size_t siteIndex )

inline

Direct access to substitution numbers.

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

Definition at line 170 of file ProbabilisticSubstitutionMapping.h.

References mapping_.

◆ operator[]() [2/2]

const std::vector< std::vector<double> >& bpp::ProbabilisticSubstitutionMapping::operator[] ( size_t siteIndex ) const

inline

Direct access to substitution numbers.

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

Definition at line 180 of file ProbabilisticSubstitutionMapping.h.

References mapping_.

◆ setNumberOfSites()

void ProbabilisticSubstitutionMapping::setNumberOfSites ( size_t numberOfSites )

virtual

Reimplemented from bpp::AbstractMapping.

Definition at line 55 of file ProbabilisticSubstitutionMapping.cpp.

References bpp::AbstractMapping::getNumberOfBranches(), getNumberOfSubstitutionTypes(), mapping_, and bpp::AbstractMapping::setNumberOfSites().

Referenced by ProbabilisticSubstitutionMapping().

◆ setSitePosition() [1/2]

virtual void bpp::Mapping::setSitePosition	(	size_t	index,
		int	position
	)

pure virtualinherited

Set the position of a given site.

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

Parameters

index	The site index.
position	The position of the site.

Implemented in bpp::AbstractMapping.

◆ setSitePosition() [2/2]

void bpp::AbstractMapping::setSitePosition	(	size_t	index,
		int	position
	)
throw	(	Exception
	)

inlinevirtualinherited

Set the position of a given site.

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

Parameters

index	The site index.
position	The position of the site.

Implements bpp::Mapping.

Definition at line 202 of file Mapping.h.

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

◆ setTree()

void ProbabilisticSubstitutionMapping::setTree ( const Tree & tree )

virtual

(Re)-set the phylogenetic tree associated to this mapping.

Parameters

tree	The new tree.

Definition at line 44 of file ProbabilisticSubstitutionMapping.cpp.

References bpp::AbstractMapping::getNumberOfBranches(), bpp::AbstractMapping::getNumberOfSites(), mapping_, and bpp::AbstractMapping::setTree().

Member Data Documentation

◆ mapping_

std::vector< std::vector< std::vector<double> > > bpp::ProbabilisticSubstitutionMapping::mapping_

private

Substitution numbers storage.

Numbers are stored by sites.

Definition at line 73 of file ProbabilisticSubstitutionMapping.h.

Referenced by getNumberOfSubstitutions(), operator()(), operator=(), operator[](), setNumberOfSites(), and setTree().

◆ substitutionCount_

const SubstitutionCount* bpp::ProbabilisticSubstitutionMapping::substitutionCount_

private

Definition at line 67 of file ProbabilisticSubstitutionMapping.h.

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

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

Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h
Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProbabilisticSubstitutionMapping() [1/3]

◆ ProbabilisticSubstitutionMapping() [2/3]

◆ ProbabilisticSubstitutionMapping() [3/3]

◆ ~ProbabilisticSubstitutionMapping()

Member Function Documentation

◆ clone()

◆ getBranchLengths() [1/2]

◆ getBranchLengths() [2/2]

◆ getNode()

◆ getNodeIndex() [1/2]

◆ getNodeIndex() [2/2]

◆ getNumberOfBranches() [1/2]

◆ getNumberOfBranches() [2/2]

◆ getNumberOfSites() [1/2]

◆ getNumberOfSites() [2/2]

◆ getNumberOfSubstitutions() [1/2]

◆ getNumberOfSubstitutions() [2/2]

◆ getNumberOfSubstitutionTypes()

◆ getSitePosition() [1/2]

◆ getSitePosition() [2/2]

◆ getTree() [1/2]

◆ getTree() [2/2]

◆ isEmpty() [1/2]

◆ isEmpty() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setNumberOfSites()

◆ setSitePosition() [1/2]

◆ setSitePosition() [2/2]

◆ setTree()

Member Data Documentation

◆ mapping_

◆ substitutionCount_