Data structure to store the result of a DetailedSiteSimulator. More...

#include <Bpp/Phyl/Simulation/DetailedSiteSimulator.h>

Inheritance diagram for bpp::RASiteSimulationResult:

Collaboration diagram for bpp::RASiteSimulationResult:

Public Member Functions
	RASiteSimulationResult (std::shared_ptr< const ParametrizablePhyloTree > tree, std::shared_ptr< const StateMapInterface > stateMap, size_t ancestralStateIndex, double rate)

virtual	~RASiteSimulationResult ()

virtual double	getRate () const

std::shared_ptr< const Alphabet >	getAlphabet () const

const Alphabet &	alphabet () const

virtual void	addNode (unsigned int nodeId, MutationPath path)

virtual size_t	getAncestralState (size_t i) const

virtual size_t	getAncestralState (unsigned int nodeId) const

virtual const MutationPath &	getMutationPath (size_t i) const

virtual const MutationPath &	getMutationPath (unsigned int nodeId) const

virtual size_t	getSubstitutionCount (size_t i) const

virtual void	getSubstitutionCount (size_t i, const SubstitutionRegisterInterface &reg, std::vector< double > &counts) const

virtual size_t	getSubstitutionCount (unsigned int nodeId) const

virtual void	getSubstitutionCount (unsigned int nodeId, const SubstitutionRegisterInterface &reg, std::vector< double > &counts) const

virtual VVdouble	getSubstitutionVector (const SubstitutionRegisterInterface &reg) const

virtual std::vector< size_t >	getFinalStates () const

virtual std::unique_ptr< SiteInterface >	getSite (const TransitionModelInterface &model) const

virtual std::vector< std::string >	getLeaveNames () const

Protected Attributes
double	rate_

Private Attributes
std::map< uint, size_t >	indexes_

size_t	currentIndex_

std::vector< MutationPath >	paths_

std::vector< size_t >	ancestralStates_

std::shared_ptr< const ParametrizablePhyloTree >	tree_

std::vector< unsigned int >	leavesId_

std::shared_ptr< const StateMapInterface >	statemap_

Detailed Description

Data structure to store the result of a DetailedSiteSimulator.

This structure inherits from the SequenceSimulationResult class, and add support for rate variation across sites.

Definition at line 185 of file DetailedSiteSimulator.h.

Constructor & Destructor Documentation

◆ RASiteSimulationResult()

bpp::RASiteSimulationResult::RASiteSimulationResult	(	std::shared_ptr< const ParametrizablePhyloTree >	tree,
		std::shared_ptr< const StateMapInterface >	stateMap,
		size_t	ancestralStateIndex,
		double	rate
	)

inline

Definition at line 192 of file DetailedSiteSimulator.h.

◆ ~RASiteSimulationResult()

virtual bpp::RASiteSimulationResult::~RASiteSimulationResult ( )

inlinevirtual

Definition at line 200 of file DetailedSiteSimulator.h.

Member Function Documentation

◆ addNode()

virtual void bpp::SiteSimulationResult::addNode	(	unsigned int	nodeId,
		MutationPath	path
	)

inlinevirtualinherited

Definition at line 85 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_, bpp::SiteSimulationResult::currentIndex_, bpp::MutationPath::getFinalState(), bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

Referenced by bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), and bpp::SimpleSubstitutionProcessSiteSimulator::evolveInternal().

◆ alphabet()

const Alphabet& bpp::SiteSimulationResult::alphabet ( ) const

inlineinherited

Definition at line 83 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::statemap_.

Referenced by bpp::SiteSimulationResult::getSite().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::SiteSimulationResult::getAlphabet ( ) const

inlineinherited

Returns: The alphabet associated to this simulation.

Definition at line 81 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::statemap_.

◆ getAncestralState() [1/2]

virtual size_t bpp::SiteSimulationResult::getAncestralState ( size_t i ) const

inlinevirtualinherited

Definition at line 93 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_.

◆ getAncestralState() [2/2]

virtual size_t bpp::SiteSimulationResult::getAncestralState ( unsigned int nodeId ) const

inlinevirtualinherited

Definition at line 95 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_, and bpp::SiteSimulationResult::indexes_.

◆ getFinalStates()

virtual std::vector<size_t> bpp::SiteSimulationResult::getFinalStates ( ) const

inlinevirtualinherited

Returns: The states at the leaves.

Definition at line 136 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_, bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::leavesId_.

Referenced by bpp::SiteSimulationResult::getSite().

◆ getLeaveNames()

virtual std::vector<std::string> bpp::SiteSimulationResult::getLeaveNames ( ) const

inlinevirtualinherited

Returns: A vector with the leaves names.

Definition at line 165 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::leavesId_, and bpp::SiteSimulationResult::tree_.

◆ getMutationPath() [1/2]

virtual const MutationPath& bpp::SiteSimulationResult::getMutationPath ( size_t i ) const

inlinevirtualinherited

Definition at line 97 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::paths_.

◆ getMutationPath() [2/2]

virtual const MutationPath& bpp::SiteSimulationResult::getMutationPath ( unsigned int nodeId ) const

inlinevirtualinherited

Definition at line 99 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

◆ getRate()

virtual double bpp::RASiteSimulationResult::getRate ( ) const

inlinevirtual

Returns: The rate of this simulation.

Definition at line 206 of file DetailedSiteSimulator.h.

References rate_.

◆ getSite()

virtual std::unique_ptr<SiteInterface> bpp::SiteSimulationResult::getSite ( const TransitionModelInterface & model ) const

inlinevirtualinherited

Returns: The site corresponding to this simulation.

Definition at line 150 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::alphabet(), bpp::SiteSimulationResult::getFinalStates(), and bpp::SiteSimulationResult::statemap_.

◆ getSubstitutionCount() [1/4]

virtual size_t bpp::SiteSimulationResult::getSubstitutionCount ( size_t i ) const

inlinevirtualinherited

Definition at line 101 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::paths_.

◆ getSubstitutionCount() [2/4]

virtual void bpp::SiteSimulationResult::getSubstitutionCount	(	size_t	i,
		const SubstitutionRegisterInterface &	reg,
		std::vector< double > &	counts
	)		const

inlinevirtualinherited

Definition at line 103 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::paths_.

◆ getSubstitutionCount() [3/4]

virtual size_t bpp::SiteSimulationResult::getSubstitutionCount ( unsigned int nodeId ) const

inlinevirtualinherited

Definition at line 111 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

◆ getSubstitutionCount() [4/4]

virtual void bpp::SiteSimulationResult::getSubstitutionCount	(	unsigned int	nodeId,
		const SubstitutionRegisterInterface &	reg,
		std::vector< double > &	counts
	)		const

inlinevirtualinherited

Definition at line 113 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

◆ getSubstitutionVector()

virtual VVdouble bpp::SiteSimulationResult::getSubstitutionVector ( const SubstitutionRegisterInterface & reg ) const

inlinevirtualinherited

Definition at line 121 of file DetailedSiteSimulator.h.

References bpp::SubstitutionRegisterInterface::getNumberOfSubstitutionTypes(), and bpp::SiteSimulationResult::paths_.

Member Data Documentation

◆ ancestralStates_

std::vector<size_t> bpp::SiteSimulationResult::ancestralStates_

privateinherited

Definition at line 30 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::addNode(), bpp::SiteSimulationResult::getAncestralState(), bpp::SiteSimulationResult::getFinalStates(), bpp::SiteSimulationResult::operator=(), and bpp::SiteSimulationResult::SiteSimulationResult().

◆ currentIndex_

size_t bpp::SiteSimulationResult::currentIndex_

privateinherited

Definition at line 28 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::addNode(), and bpp::SiteSimulationResult::operator=().

◆ indexes_

std::map<uint, size_t> bpp::SiteSimulationResult::indexes_

mutableprivateinherited

Definition at line 27 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::addNode(), bpp::SiteSimulationResult::getAncestralState(), bpp::SiteSimulationResult::getFinalStates(), bpp::SiteSimulationResult::getMutationPath(), bpp::SiteSimulationResult::getSubstitutionCount(), bpp::SiteSimulationResult::operator=(), and bpp::SiteSimulationResult::SiteSimulationResult().

◆ leavesId_

std::vector<unsigned int> bpp::SiteSimulationResult::leavesId_

privateinherited

Definition at line 32 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::getFinalStates(), bpp::SiteSimulationResult::getLeaveNames(), and bpp::SiteSimulationResult::operator=().

◆ paths_

std::vector<MutationPath> bpp::SiteSimulationResult::paths_

privateinherited

Definition at line 29 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::addNode(), bpp::SiteSimulationResult::getMutationPath(), bpp::SiteSimulationResult::getSubstitutionCount(), bpp::SiteSimulationResult::getSubstitutionVector(), and bpp::SiteSimulationResult::operator=().

◆ rate_

double bpp::RASiteSimulationResult::rate_

protected

Definition at line 189 of file DetailedSiteSimulator.h.

Referenced by getRate().

◆ statemap_

std::shared_ptr<const StateMapInterface> bpp::SiteSimulationResult::statemap_

privateinherited

Definition at line 33 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::alphabet(), bpp::SiteSimulationResult::getAlphabet(), bpp::SiteSimulationResult::getSite(), and bpp::SiteSimulationResult::operator=().

◆ tree_

std::shared_ptr<const ParametrizablePhyloTree> bpp::SiteSimulationResult::tree_

privateinherited

Definition at line 31 of file DetailedSiteSimulator.h.

Referenced by bpp::SiteSimulationResult::getLeaveNames(), and bpp::SiteSimulationResult::operator=().

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

Bpp/Phyl/Simulation/DetailedSiteSimulator.h

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RASiteSimulationResult()

◆ ~RASiteSimulationResult()

Member Function Documentation

◆ addNode()

◆ alphabet()

◆ getAlphabet()

◆ getAncestralState() [1/2]

◆ getAncestralState() [2/2]

◆ getFinalStates()

◆ getLeaveNames()

◆ getMutationPath() [1/2]

◆ getMutationPath() [2/2]

◆ getRate()

◆ getSite()

◆ getSubstitutionCount() [1/4]

◆ getSubstitutionCount() [2/4]

◆ getSubstitutionCount() [3/4]

◆ getSubstitutionCount() [4/4]

◆ getSubstitutionVector()

Member Data Documentation

◆ ancestralStates_

◆ currentIndex_

◆ indexes_

◆ leavesId_

◆ paths_

◆ rate_

◆ statemap_

◆ tree_