bpp::Mapping Class Reference

General interface for storing mapping data. More...

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

Inheritance diagram for bpp::Mapping:

Collaboration diagram for bpp::Mapping:

Public Member Functions
	Mapping ()
virtual	~Mapping ()
Mapping *	clone () 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.

Definition at line 59 of file Mapping.h.

Constructor & Destructor Documentation

Mapping()

bpp::Mapping::Mapping ( )

inline

Definition at line 64 of file Mapping.h.

~Mapping()

virtual bpp::Mapping::~Mapping ( )

inlinevirtual

Definition at line 65 of file Mapping.h.

Member Function Documentation

clone()

Mapping* bpp::Mapping::clone ( ) const

pure virtual

Implemented in bpp::AbstractMapping, bpp::AbstractSubstitutionMapping, bpp::ProbabilisticSubstitutionMapping, bpp::ProbabilisticRewardMapping, bpp::AbstractRewardMapping, bpp::SubstitutionMapping, and bpp::RewardMapping.

getBranchLengths()

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

pure virtual

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 virtual

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 virtual

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 virtual

Returns

The number of sites mapped.

Implemented in bpp::AbstractMapping.

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

getSitePosition()

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

pure virtual

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 virtual

Returns

Get the phylogenetic tree associated to this mapping.

Implemented in bpp::AbstractMapping.

isEmpty()

virtual bool bpp::Mapping::isEmpty ( ) const

pure virtual

Returns

True is the map is empty, that is, if no tree is associated to the map yet.

Implemented in bpp::AbstractMapping.

setSitePosition()

virtual void bpp::Mapping::setSitePosition ( size_t  index, int  position  )

pure virtual

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/Mapping.h