bpp::AbstractMapping Class Reference

Partial implementation of the mapping interface. More...

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

Inheritance diagram for bpp::AbstractMapping:

Collaboration diagram for bpp::AbstractMapping:

Public Member Functions
	AbstractMapping ()
	AbstractMapping (size_t nb)
	AbstractMapping (const AbstractMapping &absm)=default
AbstractMapping &	operator= (const AbstractMapping &absm)=default
virtual	~AbstractMapping ()
int	getSitePosition (size_t index) const
void	setSitePosition (size_t index, int position)
	Set the position of a given site. More...
size_t	getNumberOfSites () const
virtual void	setNumberOfSites (size_t numberOfSites)
MappingInterface *	clone () const override=0
virtual const PhyloBranch &	getBranch (unsigned int branchId) const =0
virtual PhyloBranch &	getBranch (unsigned int branchId)=0
virtual size_t	getNumberOfBranches () const =0

Protected Attributes
std::vector< int >	sitesPositions_
size_t	nbSites_

Detailed Description

Partial implementation of the mapping interface.

Here, there is no information about site compression.

Definition at line 77 of file Mapping.h.

Constructor & Destructor Documentation

AbstractMapping() [1/3]

bpp::AbstractMapping::AbstractMapping ( )

inline

Definition at line 85 of file Mapping.h.

AbstractMapping() [2/3]

bpp::AbstractMapping::AbstractMapping ( size_t  nb )

inline

Definition at line 88 of file Mapping.h.

AbstractMapping() [3/3]

bpp::AbstractMapping::AbstractMapping ( const AbstractMapping &  absm )

default

~AbstractMapping()

virtual bpp::AbstractMapping::~AbstractMapping ( )

inlinevirtual

Definition at line 95 of file Mapping.h.

Member Function Documentation

clone()

MappingInterface* bpp::MappingInterface::clone ( ) const

overridepure virtualinherited

Implements bpp::Clonable.

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

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::ProbabilisticSubstitutionMapping, and bpp::ProbabilisticRewardMapping.

getBranch() [2/2]

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

pure virtualinherited

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

getNumberOfBranches()

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

pure virtualinherited

Returns

The number of branches mapped.

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

getNumberOfSites()

size_t bpp::AbstractMapping::getNumberOfSites ( ) const

inlinevirtual

Returns

The number of sites mapped.

Implements bpp::MappingInterface.

Definition at line 111 of file Mapping.h.

References nbSites_.

Referenced by bpp::RewardMappingTools::computeSumForBranch(), bpp::SubstitutionMappingTools::getCountsForBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranch(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerType(), bpp::SubstitutionMappingTools::getTreeForType(), bpp::RewardMappingTools::writeToStream(), and bpp::SubstitutionMappingTools::writeToStream().

getSitePosition()

int bpp::AbstractMapping::getSitePosition ( size_t  index ) const

inlinevirtual

Parameters

index

The site index.

Returns

The site position corresponding to the index.

Implements bpp::MappingInterface.

Definition at line 98 of file Mapping.h.

References sitesPositions_.

operator=()

AbstractMapping& bpp::AbstractMapping::operator= ( const AbstractMapping &  absm )

default

Referenced by bpp::AbstractRewardMapping::operator=(), bpp::AbstractSubstitutionMapping::operator=(), and bpp::ProbabilisticRewardMapping::operator=().

setNumberOfSites()

virtual void bpp::AbstractMapping::setNumberOfSites ( size_t  numberOfSites )

inlinevirtual

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

Definition at line 113 of file Mapping.h.

References nbSites_, and sitesPositions_.

Referenced by bpp::ProbabilisticRewardMapping::setNumberOfSites(), bpp::ProbabilisticSubstitutionMapping::setNumberOfSites(), and bpp::ProbabilisticSubstitutionMapping::setNumberOfSitesAndTypes().

setSitePosition()

void bpp::AbstractMapping::setSitePosition ( size_t  index, int  position  )

inlinevirtual

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.

Implements bpp::MappingInterface.

Definition at line 103 of file Mapping.h.

References nbSites_, and sitesPositions_.

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

Member Data Documentation

nbSites_

size_t bpp::AbstractMapping::nbSites_

protected

Definition at line 82 of file Mapping.h.

Referenced by getNumberOfSites(), setNumberOfSites(), and setSitePosition().

sitesPositions_

std::vector<int> bpp::AbstractMapping::sitesPositions_

protected

Definition at line 81 of file Mapping.h.

Referenced by getSitePosition(), setNumberOfSites(), and setSitePosition().

---

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

• Bpp/Phyl/Mapping/Mapping.h