bpp::LegacySubstitutionMappingInterface Class Reference

Legacy interface for storing mapping data. More...

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

Inheritance diagram for bpp::LegacySubstitutionMappingInterface:

Collaboration diagram for bpp::LegacySubstitutionMappingInterface:

Public Member Functions
	LegacySubstitutionMappingInterface ()
virtual	~LegacySubstitutionMappingInterface ()
LegacySubstitutionMappingInterface *	clone () const override=0
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 &	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 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

LegacySubstitutionMappingInterface()

bpp::LegacySubstitutionMappingInterface::LegacySubstitutionMappingInterface ( )

inline

Definition at line 33 of file SubstitutionMapping.h.

~LegacySubstitutionMappingInterface()

virtual bpp::LegacySubstitutionMappingInterface::~LegacySubstitutionMappingInterface ( )

inlinevirtual

Definition at line 34 of file SubstitutionMapping.h.

Member Function Documentation

clone()

LegacySubstitutionMappingInterface* bpp::LegacySubstitutionMappingInterface::clone ( ) const

overridepure virtual

Implements bpp::LegacyMappingInterface.

Implemented in bpp::LegacyAbstractSubstitutionMapping, and bpp::LegacyProbabilisticSubstitutionMapping.

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().

getNumberOfSubstitutionTypes()

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

pure virtual

Returns

The number of distinct types of substitutions mapped.

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

Referenced by bpp::LegacySubstitutionMappingTools::computeNormForSite(), bpp::LegacySubstitutionMappingTools::computeSumForBranch(), bpp::LegacySubstitutionMappingTools::computeSumForSite(), bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerBranch(), and bpp::LegacySubstitutionMappingTools::computeTotalSubstitutionVectorForSitePerType().

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::LegacySubstitutionMappingInterface::operator() ( size_t  nodeIndex, size_t  siteIndex, size_t  type  ) const

pure virtual

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

operator()() [2/2]

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

pure virtual

Implemented in bpp::LegacyProbabilisticSubstitutionMapping.

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.

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

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