Partial implementation of the substitution mapping interface. More...

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

Inheritance diagram for bpp::AbstractSubstitutionMapping:

Collaboration diagram for bpp::AbstractSubstitutionMapping:

Public Member Functions
	AbstractSubstitutionMapping (const Tree &tree)

	AbstractSubstitutionMapping (const AbstractSubstitutionMapping &absm)

AbstractSubstitutionMapping *	clone () const =0

AbstractSubstitutionMapping &	operator= (const AbstractSubstitutionMapping &absm)

virtual	~AbstractSubstitutionMapping ()

virtual size_t	getNumberOfSubstitutionTypes () const =0

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

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

virtual const Tree &	getTree () const =0

virtual bool	isEmpty () const =0

virtual size_t	getNumberOfSites () const =0

virtual size_t	getNumberOfBranches () const =0

virtual int	getSitePosition (size_t index) const =0

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

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

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

bool	isEmpty () const

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

void	setTree (const Tree &tree)

int	getSitePosition (size_t index) const throw (Exception)

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

size_t	getNumberOfSites () const

size_t	getNumberOfBranches () const

virtual const Node *	getNode (size_t nodeIndex) const

virtual void	setNumberOfSites (size_t numberOfSites)

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

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

Detailed Description

Partial implementation of the substitution mapping interface.

This implementation copies the input tree in a TreeTemplate<Node> object.

Definition at line 94 of file SubstitutionMapping.h.

Constructor & Destructor Documentation

◆ AbstractSubstitutionMapping() [1/2]

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

inline

Definition at line 101 of file SubstitutionMapping.h.

◆ AbstractSubstitutionMapping() [2/2]

bpp::AbstractSubstitutionMapping::AbstractSubstitutionMapping ( const AbstractSubstitutionMapping & absm )

inline

Definition at line 103 of file SubstitutionMapping.h.

◆ ~AbstractSubstitutionMapping()

virtual bpp::AbstractSubstitutionMapping::~AbstractSubstitutionMapping ( )

inlinevirtual

Definition at line 116 of file SubstitutionMapping.h.

Member Function Documentation

◆ clone()

AbstractSubstitutionMapping* bpp::AbstractSubstitutionMapping::clone ( ) const

pure virtual

Implements bpp::AbstractMapping.

Implemented in bpp::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(), bpp::ProbabilisticSubstitutionMapping::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(), bpp::ProbabilisticSubstitutionMapping::setNumberOfSites(), bpp::ProbabilisticRewardMapping::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(), bpp::ProbabilisticRewardMapping::setTree(), and bpp::ProbabilisticSubstitutionMapping::setTree().

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::SubstitutionMapping::getNumberOfSubstitutionTypes ( ) const

pure virtualinherited

Returns: The number of distinct types of substitutions mapped.

Implemented in bpp::ProbabilisticSubstitutionMapping.

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

◆ 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::SubstitutionMapping::operator()	(	size_t	nodeIndex,
		size_t	siteIndex,
		size_t	type
	)

pure virtualinherited

Implemented in bpp::ProbabilisticSubstitutionMapping.

◆ operator()() [2/2]

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

pure virtualinherited

Implemented in bpp::ProbabilisticSubstitutionMapping.

◆ operator=()

AbstractSubstitutionMapping& bpp::AbstractSubstitutionMapping::operator= ( const AbstractSubstitutionMapping & absm )

inline

Definition at line 110 of file SubstitutionMapping.h.

References bpp::AbstractMapping::operator=().

Referenced by bpp::ProbabilisticSubstitutionMapping::operator=().

◆ setNumberOfSites()

virtual void bpp::AbstractMapping::setNumberOfSites ( size_t numberOfSites )

inlinevirtualinherited

Reimplemented in bpp::ProbabilisticSubstitutionMapping, and bpp::ProbabilisticRewardMapping.

Definition at line 214 of file Mapping.h.

References bpp::AbstractMapping::nbSites_, and bpp::AbstractMapping::sitesPositions_.

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

◆ 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 bpp::AbstractMapping::setTree ( const Tree & tree )

inlineinherited

Definition at line 188 of file Mapping.h.

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

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

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

Bpp/Phyl/Mapping/SubstitutionMapping.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AbstractSubstitutionMapping() [1/2]

◆ AbstractSubstitutionMapping() [2/2]

◆ ~AbstractSubstitutionMapping()

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]

◆ 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=()

◆ setNumberOfSites()

◆ setSitePosition() [1/2]

◆ setSitePosition() [2/2]

◆ setTree()