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 =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 &	getTree () 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 throw (NodeNotFoundException)
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 65 of file SubstitutionMapping.h.

Constructor & Destructor Documentation

SubstitutionMapping()

bpp::SubstitutionMapping::SubstitutionMapping ( )

inline

Definition at line 70 of file SubstitutionMapping.h.

~SubstitutionMapping()

virtual bpp::SubstitutionMapping::~SubstitutionMapping ( )

inlinevirtual

Definition at line 71 of file SubstitutionMapping.h.

Member Function Documentation

clone()

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

pure virtual

Implements bpp::Mapping.

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

getBranchLengths()

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

pure virtualinherited

Returns

A vector with all tree branch lengths.

Implemented in bpp::AbstractMapping.

getNodeIndex()

virtual size_t bpp::Mapping::getNodeIndex ( int  nodeId ) const throw ( NodeNotFoundException )

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::AbstractMapping.

getNumberOfBranches()

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

pure virtualinherited

Returns

The number of branches mapped.

Implemented in bpp::AbstractMapping.

Referenced by bpp::SubstitutionMappingTools::computeNormForSite(), bpp::RewardMappingTools::computeSumForSite(), bpp::SubstitutionMappingTools::computeSumForSite(), and bpp::SubstitutionMappingTools::computeTotalSubstitutionVectorForSite().

getNumberOfSites()

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

pure virtualinherited

Returns

The number of sites mapped.

Implemented in bpp::AbstractMapping.

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

getNumberOfSubstitutionTypes()

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

pure virtual

Returns

The number of distinct types of substitutions mapped.

Implemented in bpp::ProbabilisticSubstitutionMapping.

Referenced by bpp::SubstitutionMappingTools::computeNormForSite(), bpp::SubstitutionMappingTools::computeSumForBranch(), bpp::SubstitutionMappingTools::computeSumForSite(), and bpp::SubstitutionMappingTools::computeTotalSubstitutionVectorForSite().

getSitePosition()

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

pure virtualinherited

Parameters

index

The site index.

Returns

The site position corresponding to the index.

Implemented in bpp::AbstractMapping.

getTree()

virtual const Tree& bpp::Mapping::getTree ( ) const

pure virtualinherited

Returns

Get the phylogenetic tree associated to this mapping.

Implemented in bpp::AbstractMapping.

isEmpty()

virtual bool bpp::Mapping::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::AbstractMapping.

operator()() [1/2]

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

pure virtual

Implemented in bpp::ProbabilisticSubstitutionMapping.

operator()() [2/2]

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

pure virtual

Implemented in bpp::ProbabilisticSubstitutionMapping.

setSitePosition()

virtual void bpp::Mapping::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