bpp::RewardMappingInterface Class Reference

General interface for storing reward mapping data. More...

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

Inheritance diagram for bpp::RewardMappingInterface:

Collaboration diagram for bpp::RewardMappingInterface:

Public Member Functions
	RewardMappingInterface ()
virtual	~RewardMappingInterface ()
RewardMappingInterface *	clone () const override=0
virtual double &	operator() (uint branchId, size_t siteIndex)=0
virtual double	operator() (uint branchId, size_t siteIndex) 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 reward mapping data.

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

Definition at line 25 of file RewardMapping.h.

Constructor & Destructor Documentation

RewardMappingInterface()

bpp::RewardMappingInterface::RewardMappingInterface ( )

inline

Definition at line 29 of file RewardMapping.h.

~RewardMappingInterface()

virtual bpp::RewardMappingInterface::~RewardMappingInterface ( )

inlinevirtual

Definition at line 30 of file RewardMapping.h.

Member Function Documentation

clone()

RewardMappingInterface * bpp::RewardMappingInterface::clone ( ) const

overridepure virtual

Implements bpp::MappingInterface.

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

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::ProbabilisticRewardMapping, and bpp::ProbabilisticSubstitutionMapping.

getBranch() [2/2]

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

pure virtualinherited

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

getNumberOfBranches()

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

pure virtualinherited

Returns

The number of branches mapped.

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

getNumberOfSites()

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

pure virtualinherited

Returns

The number of sites mapped.

Implemented in bpp::AbstractMapping.

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 double bpp::RewardMappingInterface::operator() ( uint  branchId, size_t  siteIndex  ) const

pure virtual

Implemented in bpp::ProbabilisticRewardMapping.

operator()() [2/2]

virtual double & bpp::RewardMappingInterface::operator() ( uint  branchId, size_t  siteIndex  )

pure virtual

Implemented in bpp::ProbabilisticRewardMapping.

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/RewardMapping.h