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

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

Inheritance diagram for bpp::ProbabilisticRewardMapping:

Collaboration diagram for bpp::ProbabilisticRewardMapping:

Public Member Functions
	ProbabilisticRewardMapping (const Tree &tree, const Reward *reward, size_t numberOfSites)
	Build a new ProbabilisticRewardMapping object. More...

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

ProbabilisticRewardMapping *	clone () const

	ProbabilisticRewardMapping (const ProbabilisticRewardMapping &prm)

ProbabilisticRewardMapping &	operator= (const ProbabilisticRewardMapping &prm)

virtual	~ProbabilisticRewardMapping ()

virtual double	getReward (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)
	Direct access to rewards. More...

virtual const double &	operator() (size_t nodeIndex, size_t siteIndex) const
	Direct access to rewards. More...

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

const std::vector< double > &	operator[] (size_t siteIndex) const
	Direct access to rewards. 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 Reward *	reward_

std::vector< std::vector< double > >	mapping_
	Rewards storage. More...

Detailed Description

Data storage class for probabilistic rewards mappings.

A 'probabilistic' mapping contains an single value for each branch and each site. This number is an average reward. Probabilistic was coined there by opposition to the'stochastic' mapping, where a path (sequence of rewards along the branch) is available for each branch and site.

Definition at line 64 of file ProbabilisticRewardMapping.h.

Constructor & Destructor Documentation

◆ ProbabilisticRewardMapping() [1/3]

bpp::ProbabilisticRewardMapping::ProbabilisticRewardMapping	(	const Tree &	tree,
		const Reward *	reward,
		size_t	numberOfSites
	)

inline

Build a new ProbabilisticRewardMapping object.

Parameters

tree	The tree object to use. It will be cloned for internal use.
reward	A pointer toward the Reward object that has been used for the mapping, if any.
numberOfSites	The number of sites to map.

Definition at line 85 of file ProbabilisticRewardMapping.h.

References setNumberOfSites().

Referenced by clone().

◆ ProbabilisticRewardMapping() [2/3]

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

inline

Build a new ProbabilisticRewardMapping object.

Parameters

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

Definition at line 96 of file ProbabilisticRewardMapping.h.

◆ ProbabilisticRewardMapping() [3/3]

bpp::ProbabilisticRewardMapping::ProbabilisticRewardMapping ( const ProbabilisticRewardMapping & prm )

inline

Definition at line 103 of file ProbabilisticRewardMapping.h.

◆ ~ProbabilisticRewardMapping()

virtual bpp::ProbabilisticRewardMapping::~ProbabilisticRewardMapping ( )

inlinevirtual

Definition at line 115 of file ProbabilisticRewardMapping.h.

Member Function Documentation

◆ clone()

ProbabilisticRewardMapping* bpp::ProbabilisticRewardMapping::clone ( ) const

inlinevirtual

Implements bpp::AbstractRewardMapping.

Definition at line 101 of file ProbabilisticRewardMapping.h.

References ProbabilisticRewardMapping().

◆ 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(), bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutions(), 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 setNumberOfSites(), bpp::ProbabilisticSubstitutionMapping::setNumberOfSites(), setTree(), and bpp::ProbabilisticSubstitutionMapping::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(), setTree(), and bpp::ProbabilisticSubstitutionMapping::setTree().

◆ getReward()

virtual double bpp::ProbabilisticRewardMapping::getReward	(	int	nodeId,
		size_t	siteIndex
	)		const

inlinevirtual

Definition at line 119 of file ProbabilisticRewardMapping.h.

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

◆ 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::ProbabilisticRewardMapping::operator()	(	size_t	nodeIndex,
		size_t	siteIndex
	)

inlinevirtual

Direct access to rewards.

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

Implements bpp::RewardMapping.

Definition at line 138 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ operator()() [2/2]

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

inlinevirtual

Direct access to rewards.

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

Implements bpp::RewardMapping.

Definition at line 148 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ operator=()

ProbabilisticRewardMapping& bpp::ProbabilisticRewardMapping::operator= ( const ProbabilisticRewardMapping & prm )

inline

Definition at line 107 of file ProbabilisticRewardMapping.h.

References mapping_, bpp::AbstractRewardMapping::operator=(), and reward_.

◆ operator[]() [1/2]

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

inline

Direct access to rewards.

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

Definition at line 158 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ operator[]() [2/2]

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

inline

Direct access to rewards.

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

Definition at line 168 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ setNumberOfSites()

void ProbabilisticRewardMapping::setNumberOfSites ( size_t numberOfSites )

virtual

Reimplemented from bpp::AbstractMapping.

Definition at line 51 of file ProbabilisticRewardMapping.cpp.

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

Referenced by ProbabilisticRewardMapping().

◆ 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 ProbabilisticRewardMapping::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 ProbabilisticRewardMapping.cpp.

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

Member Data Documentation

◆ mapping_

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

private

Rewards storage.

Rewards are stored by sites.

Definition at line 74 of file ProbabilisticRewardMapping.h.

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

◆ reward_

const Reward* bpp::ProbabilisticRewardMapping::reward_

private

Definition at line 68 of file ProbabilisticRewardMapping.h.

Referenced by operator=().

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

Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h
Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProbabilisticRewardMapping() [1/3]

◆ ProbabilisticRewardMapping() [2/3]

◆ ProbabilisticRewardMapping() [3/3]

◆ ~ProbabilisticRewardMapping()

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]

◆ getReward()

◆ 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_

◆ reward_