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 ()

	AbstractSubstitutionMapping (const AbstractSubstitutionMapping &absm)

AbstractSubstitutionMapping *	clone () const =0

AbstractSubstitutionMapping &	operator= (const AbstractSubstitutionMapping &absm)

virtual	~AbstractSubstitutionMapping ()

size_t	getNumberOfSubstitutionTypes () const

virtual void	setNumberOfSubstitutionTypes (size_t numberOfTypes)

virtual double &	operator() (unsigned int branchId, size_t siteIndex, size_t type)=0

virtual const double &	operator() (unsigned int branchId, size_t siteIndex, size_t type) const =0

virtual size_t	getNumberOfSites () const =0

virtual const PhyloBranch &	getBranch (unsigned int branchId) const =0

virtual PhyloBranch &	getBranch (unsigned int branchId)=0

virtual size_t	getNumberOfBranches () const =0

virtual int	getSitePosition (size_t index) const =0

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

int	getSitePosition (size_t index) const

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

size_t	getNumberOfSites () const

virtual void	setNumberOfSites (size_t numberOfSites)

Protected Attributes
std::vector< int >	sitesPositions_

size_t	nbSites_

Private Attributes
size_t	numberOfTypes_

Detailed Description

Partial implementation of the substitution mapping interface.

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

Definition at line 55 of file SubstitutionMapping.h.

Constructor & Destructor Documentation

◆ AbstractSubstitutionMapping() [1/2]

bpp::AbstractSubstitutionMapping::AbstractSubstitutionMapping ( )

inline

Definition at line 63 of file SubstitutionMapping.h.

◆ AbstractSubstitutionMapping() [2/2]

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

inline

Definition at line 65 of file SubstitutionMapping.h.

◆ ~AbstractSubstitutionMapping()

virtual bpp::AbstractSubstitutionMapping::~AbstractSubstitutionMapping ( )

inlinevirtual

Definition at line 78 of file SubstitutionMapping.h.

Member Function Documentation

◆ clone()

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

pure virtual

Implements bpp::SubstitutionMapping.

Implemented in bpp::ProbabilisticSubstitutionMapping.

◆ getBranch() [1/2]

virtual const PhyloBranch& bpp::MappingInterface::getBranch ( unsigned int branchId ) const

pure virtualinherited

Returns: The PhyloBranchMapping to a given index

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

◆ getBranch() [2/2]

virtual PhyloBranch& bpp::MappingInterface::getBranch ( unsigned int branchId )

pure virtualinherited

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

◆ getNumberOfBranches()

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

pure virtualinherited

Returns: The number of branches mapped.

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

◆ getNumberOfSites() [1/2]

size_t bpp::AbstractMapping::getNumberOfSites ( ) const

inlinevirtualinherited

Returns: The number of sites mapped.

Implements bpp::MappingInterface.

Definition at line 111 of file Mapping.h.

References bpp::AbstractMapping::nbSites_.

Referenced by bpp::RewardMappingTools::computeSumForBranch(), bpp::SubstitutionMappingTools::getCountsForBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranch(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerType(), bpp::SubstitutionMappingTools::getTreeForType(), bpp::RewardMappingTools::writeToStream(), and bpp::SubstitutionMappingTools::writeToStream().

◆ getNumberOfSites() [2/2]

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

pure virtualinherited

Returns: The number of sites mapped.

Implemented in bpp::AbstractMapping.

◆ getNumberOfSubstitutionTypes()

size_t bpp::AbstractSubstitutionMapping::getNumberOfSubstitutionTypes ( ) const

inlinevirtual

Returns: The number of distinct types of substitutions mapped.

Implements bpp::SubstitutionMapping.

Definition at line 80 of file SubstitutionMapping.h.

References numberOfTypes_.

Referenced by bpp::SubstitutionMappingTools::computeNormalizedCounts(), bpp::SubstitutionMappingTools::getCountsForBranchPerType(), bpp::SubstitutionMappingTools::getCountsForSitePerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerType(), bpp::SubstitutionMappingTools::getCountsPerTypePerBranch(), and bpp::SubstitutionMappingTools::getNormForSite().

◆ getSitePosition() [1/2]

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

inlinevirtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implements bpp::MappingInterface.

Definition at line 98 of file Mapping.h.

References bpp::AbstractMapping::sitesPositions_.

◆ getSitePosition() [2/2]

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

pure virtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implemented in bpp::AbstractMapping.

◆ operator()() [1/2]

virtual const double& bpp::SubstitutionMapping::operator()	(	unsigned int	branchId,
		size_t	siteIndex,
		size_t	type
	)		const

pure virtualinherited

Implemented in bpp::ProbabilisticSubstitutionMapping.

◆ operator()() [2/2]

virtual double& bpp::SubstitutionMapping::operator()	(	unsigned int	branchId,
		size_t	siteIndex,
		size_t	type
	)

pure virtualinherited

Implemented in bpp::ProbabilisticSubstitutionMapping.

◆ operator=()

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

inline

Definition at line 70 of file SubstitutionMapping.h.

References numberOfTypes_, and 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 113 of file Mapping.h.

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

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

◆ setNumberOfSubstitutionTypes()

virtual void bpp::AbstractSubstitutionMapping::setNumberOfSubstitutionTypes ( size_t numberOfTypes )

inlinevirtual

Implements bpp::SubstitutionMapping.

Reimplemented in bpp::ProbabilisticSubstitutionMapping.

Definition at line 85 of file SubstitutionMapping.h.

References numberOfTypes_.

Referenced by bpp::ProbabilisticSubstitutionMapping::setNumberOfSitesAndTypes(), and bpp::ProbabilisticSubstitutionMapping::setNumberOfSubstitutionTypes().

◆ setSitePosition() [1/2]

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

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::MappingInterface.

Definition at line 103 of file Mapping.h.

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

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

◆ setSitePosition() [2/2]

virtual void bpp::MappingInterface::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.

Member Data Documentation

◆ nbSites_

size_t bpp::AbstractMapping::nbSites_

protectedinherited

Definition at line 82 of file Mapping.h.

Referenced by bpp::AbstractMapping::getNumberOfSites(), bpp::AbstractMapping::setNumberOfSites(), and bpp::AbstractMapping::setSitePosition().

◆ numberOfTypes_

size_t bpp::AbstractSubstitutionMapping::numberOfTypes_

private

Definition at line 60 of file SubstitutionMapping.h.

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

◆ sitesPositions_

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

protectedinherited

Definition at line 81 of file Mapping.h.

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

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

Bpp/Phyl/Mapping/SubstitutionMapping.h

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractSubstitutionMapping() [1/2]

◆ AbstractSubstitutionMapping() [2/2]

◆ ~AbstractSubstitutionMapping()

Member Function Documentation

◆ clone()

◆ getBranch() [1/2]

◆ getBranch() [2/2]

◆ getNumberOfBranches()

◆ getNumberOfSites() [1/2]

◆ getNumberOfSites() [2/2]

◆ getNumberOfSubstitutionTypes()

◆ getSitePosition() [1/2]

◆ getSitePosition() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ setNumberOfSites()

◆ setNumberOfSubstitutionTypes()

◆ setSitePosition() [1/2]

◆ setSitePosition() [2/2]

Member Data Documentation

◆ nbSites_

◆ numberOfTypes_

◆ sitesPositions_