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

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

Inheritance diagram for bpp::LegacyProbabilisticRewardMapping:

Collaboration diagram for bpp::LegacyProbabilisticRewardMapping:

Public Member Functions
	LegacyProbabilisticRewardMapping (const Tree &tree, std::shared_ptr< const Reward > reward, size_t numberOfSites)
	Build a new LegacyProbabilisticRewardMapping object. More...

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

LegacyProbabilisticRewardMapping *	clone () const override

	LegacyProbabilisticRewardMapping (const LegacyProbabilisticRewardMapping &prm)=default

LegacyProbabilisticRewardMapping &	operator= (const LegacyProbabilisticRewardMapping &prm)=default

virtual	~LegacyProbabilisticRewardMapping ()

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) override

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

virtual const double &	operator() (size_t nodeIndex, size_t siteIndex) const override
	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 &	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 Reward >	reward_

std::vector< std::vector< double > >	mapping_
	Rewards 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 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 28 of file ProbabilisticRewardMapping.h.

Constructor & Destructor Documentation

◆ LegacyProbabilisticRewardMapping() [1/3]

bpp::LegacyProbabilisticRewardMapping::LegacyProbabilisticRewardMapping	(	const Tree &	tree,
		std::shared_ptr< const Reward >	reward,
		size_t	numberOfSites
	)

inline

Build a new LegacyProbabilisticRewardMapping 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 49 of file ProbabilisticRewardMapping.h.

References setNumberOfSites().

Referenced by clone().

◆ LegacyProbabilisticRewardMapping() [2/3]

bpp::LegacyProbabilisticRewardMapping::LegacyProbabilisticRewardMapping ( 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 62 of file ProbabilisticRewardMapping.h.

◆ LegacyProbabilisticRewardMapping() [3/3]

bpp::LegacyProbabilisticRewardMapping::LegacyProbabilisticRewardMapping ( const LegacyProbabilisticRewardMapping & prm )

default

◆ ~LegacyProbabilisticRewardMapping()

virtual bpp::LegacyProbabilisticRewardMapping::~LegacyProbabilisticRewardMapping ( )

inlinevirtual

Definition at line 78 of file ProbabilisticRewardMapping.h.

Member Function Documentation

◆ clone()

LegacyProbabilisticRewardMapping* bpp::LegacyProbabilisticRewardMapping::clone ( ) const

inlineoverridevirtual

Implements bpp::LegacyAbstractRewardMapping.

Definition at line 69 of file ProbabilisticRewardMapping.h.

References LegacyProbabilisticRewardMapping().

◆ 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 bpp::LegacyProbabilisticSubstitutionMapping::getNumberOfSubstitutions(), 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 setNumberOfSites(), bpp::LegacyProbabilisticSubstitutionMapping::setNumberOfSites(), setTree(), bpp::LegacyProbabilisticSubstitutionMapping::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 setTree(), bpp::LegacyProbabilisticSubstitutionMapping::setTree(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getReward()

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

inlinevirtual

Definition at line 81 of file ProbabilisticRewardMapping.h.

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

◆ 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::LegacyProbabilisticRewardMapping::operator()	(	size_t	nodeIndex,
		size_t	siteIndex
	)		const

inlineoverridevirtual

Direct access to rewards.

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

Implements bpp::LegacyRewardMappingInterface.

Definition at line 110 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ operator()() [2/2]

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

inlineoverridevirtual

Direct access to rewards.

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

Implements bpp::LegacyRewardMappingInterface.

Definition at line 100 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ operator=()

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

default

◆ operator[]() [1/2]

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

inline

Direct access to rewards.

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

Definition at line 120 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ operator[]() [2/2]

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

inline

Direct access to rewards.

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

Definition at line 130 of file ProbabilisticRewardMapping.h.

References mapping_.

◆ setNumberOfSites()

void LegacyProbabilisticRewardMapping::setNumberOfSites ( size_t numberOfSites )

overridevirtual

Reimplemented from bpp::LegacyAbstractMapping.

Definition at line 18 of file ProbabilisticRewardMapping.cpp.

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

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

◆ setSitePosition() [1/2]

void bpp::LegacyAbstractMapping::setSitePosition	(	size_t	index,
		int	position
	)

inlineoverridevirtualinherited

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::LegacyMappingInterface.

Definition at line 152 of file Mapping.h.

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

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

◆ setSitePosition() [2/2]

virtual void bpp::LegacyMappingInterface::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::LegacyAbstractMapping.

◆ setTree()

void LegacyProbabilisticRewardMapping::setTree ( const Tree & tree )

virtual

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

Parameters

tree	The new tree.

Definition at line 9 of file ProbabilisticRewardMapping.cpp.

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

◆ tree() [1/2]

virtual const Tree& bpp::LegacyMappingInterface::tree ( ) const

pure virtualinherited

Returns: Get the phylogenetic tree associated to this mapping.

Implemented in bpp::LegacyAbstractMapping.

◆ tree() [2/2]

const TreeTemplate<Node>& bpp::LegacyAbstractMapping::tree ( ) const

inlineoverridevirtualinherited

Returns: Get the phylogenetic tree associated to this mapping.

Implements bpp::LegacyMappingInterface.

Definition at line 132 of file Mapping.h.

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

Referenced by bpp::LegacyAbstractMapping::setTree(), setTree(), and bpp::LegacyProbabilisticSubstitutionMapping::setTree().

Member Data Documentation

◆ mapping_

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

private

Rewards storage.

Rewards are stored by sites.

Definition at line 39 of file ProbabilisticRewardMapping.h.

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

◆ nbBranches_

size_t bpp::LegacyAbstractMapping::nbBranches_

privateinherited

Definition at line 93 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getBranchLengths(), bpp::LegacyAbstractMapping::getNodeIndex(), bpp::LegacyAbstractMapping::getNumberOfBranches(), bpp::LegacyAbstractMapping::LegacyAbstractMapping(), bpp::LegacyAbstractMapping::operator=(), and bpp::LegacyAbstractMapping::setTree().

◆ nbSites_

size_t bpp::LegacyAbstractMapping::nbSites_

privateinherited

Definition at line 92 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getNumberOfSites(), bpp::LegacyAbstractMapping::operator=(), and bpp::LegacyAbstractMapping::setNumberOfSites().

◆ nodes_

std::vector<const Node*> bpp::LegacyAbstractMapping::nodes_

privateinherited

Definition at line 91 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getBranchLengths(), bpp::LegacyAbstractMapping::getNode(), bpp::LegacyAbstractMapping::getNodeIndex(), bpp::LegacyAbstractMapping::LegacyAbstractMapping(), bpp::LegacyAbstractMapping::operator=(), and bpp::LegacyAbstractMapping::setTree().

◆ reward_

std::shared_ptr<const Reward> bpp::LegacyProbabilisticRewardMapping::reward_

private

Definition at line 32 of file ProbabilisticRewardMapping.h.

◆ sitesPositions_

std::vector<int> bpp::LegacyAbstractMapping::sitesPositions_

privateinherited

Definition at line 90 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::getSitePosition(), bpp::LegacyAbstractMapping::operator=(), bpp::LegacyAbstractMapping::setNumberOfSites(), and bpp::LegacyAbstractMapping::setSitePosition().

◆ tree_

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

privateinherited

Definition at line 89 of file Mapping.h.

Referenced by bpp::LegacyAbstractMapping::isEmpty(), bpp::LegacyAbstractMapping::LegacyAbstractMapping(), bpp::LegacyAbstractMapping::operator=(), bpp::LegacyAbstractMapping::setTree(), and bpp::LegacyAbstractMapping::tree().

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

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ LegacyProbabilisticRewardMapping() [1/3]

◆ LegacyProbabilisticRewardMapping() [2/3]

◆ LegacyProbabilisticRewardMapping() [3/3]

◆ ~LegacyProbabilisticRewardMapping()

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]

◆ 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()

◆ tree() [1/2]

◆ tree() [2/2]

Member Data Documentation

◆ mapping_

◆ nbBranches_

◆ nbSites_

◆ nodes_

◆ reward_

◆ sitesPositions_

◆ tree_