bpp::SubstitutionMapping Class Reference

General interface for storing mapping data. More...

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

Inheritance diagram for bpp::SubstitutionMapping:

Collaboration diagram for bpp::SubstitutionMapping:

Public Member Functions
	SubstitutionMapping ()
virtual	~SubstitutionMapping ()
SubstitutionMapping *	clone () const override=0
virtual size_t	getNumberOfSubstitutionTypes () const =0
virtual void	setNumberOfSubstitutionTypes (size_t numberOfTypes)=0
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...

Detailed Description

General interface for storing mapping data.

There are several kinds of mapping:

• Exact mapping, storing the positions of each substitution onto each branch,
• Probabilistic mapping, storing the number of substitutions onto each branch.

Since only probabilistic substitution mapping is implemented for now, the basal interface only contains a few methods. More methods are expected to be added later.

Definition at line 29 of file SubstitutionMapping.h.

Constructor & Destructor Documentation

SubstitutionMapping()

bpp::SubstitutionMapping::SubstitutionMapping ( )

inline

Definition at line 33 of file SubstitutionMapping.h.

~SubstitutionMapping()

virtual bpp::SubstitutionMapping::~SubstitutionMapping ( )

inlinevirtual

Definition at line 34 of file SubstitutionMapping.h.

Member Function Documentation

clone()

SubstitutionMapping* bpp::SubstitutionMapping::clone ( ) const

overridepure virtual

Implements bpp::MappingInterface.

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

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()

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

pure virtualinherited

Returns

The number of sites mapped.

Implemented in bpp::AbstractMapping.

getNumberOfSubstitutionTypes()

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

pure virtual

Returns

The number of distinct types of substitutions mapped.

Implemented in bpp::AbstractSubstitutionMapping.

getSitePosition()

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 virtual

Implemented in bpp::ProbabilisticSubstitutionMapping.

operator()() [2/2]

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

pure virtual

Implemented in bpp::ProbabilisticSubstitutionMapping.

setNumberOfSubstitutionTypes()

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

pure virtual

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

setSitePosition()

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.

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

• Bpp/Phyl/Mapping/SubstitutionMapping.h