bpp::LegacyRewardMappingInterface Class Reference

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

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

Inheritance diagram for bpp::LegacyRewardMappingInterface:

Collaboration diagram for bpp::LegacyRewardMappingInterface:

Public Member Functions
	LegacyRewardMappingInterface ()
virtual	~LegacyRewardMappingInterface ()
LegacyRewardMappingInterface *	clone () const override=0
virtual double &	operator() (size_t nodeIndex, size_t siteIndex)=0
virtual const double &	operator() (size_t nodeIndex, size_t siteIndex) const =0
virtual const Tree &	tree () 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
virtual void	setSitePosition (size_t index, int position)=0
	Set the position of a given site. More...

Detailed Description

Legacy 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 26 of file RewardMapping.h.

Constructor & Destructor Documentation

LegacyRewardMappingInterface()

bpp::LegacyRewardMappingInterface::LegacyRewardMappingInterface ( )

inline

Definition at line 30 of file RewardMapping.h.

~LegacyRewardMappingInterface()

virtual bpp::LegacyRewardMappingInterface::~LegacyRewardMappingInterface ( )

inlinevirtual

Definition at line 31 of file RewardMapping.h.

Member Function Documentation

clone()

LegacyRewardMappingInterface* bpp::LegacyRewardMappingInterface::clone ( ) const

overridepure virtual

Implements bpp::LegacyMappingInterface.

Implemented in bpp::LegacyAbstractRewardMapping, and bpp::LegacyProbabilisticRewardMapping.

getBranchLengths()

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

pure virtualinherited

Returns

A vector with all tree branch lengths.

Implemented in bpp::LegacyAbstractMapping.

getNodeIndex()

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.

getNumberOfBranches()

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().

getNumberOfSites()

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().

getSitePosition()

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.

isEmpty()

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.

operator()() [1/2]

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

pure virtual

Implemented in bpp::LegacyProbabilisticRewardMapping.

operator()() [2/2]

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

pure virtual

Implemented in bpp::LegacyProbabilisticRewardMapping.

setSitePosition()

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.

tree()

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

pure virtualinherited

Returns

Get the phylogenetic tree associated to this mapping.

Implemented in bpp::LegacyAbstractMapping.

---

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

• Bpp/Phyl/Legacy/Mapping/RewardMapping.h