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

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

Inheritance diagram for bpp::SiteSimulationResult:

Collaboration diagram for bpp::SiteSimulationResult:

Public Member Functions
	SiteSimulationResult (std::shared_ptr< const ParametrizablePhyloTree > tree, std::shared_ptr< const StateMapInterface > statemap, size_t ancestralState)

	SiteSimulationResult (const SiteSimulationResult &ssr)

SiteSimulationResult &	operator= (const SiteSimulationResult &ssr)

virtual	~SiteSimulationResult ()

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

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

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 data structure stores each transitional state, and the time when it occurred.

Definition at line 24 of file DetailedSiteSimulator.h.

Constructor & Destructor Documentation

◆ SiteSimulationResult() [1/2]

bpp::SiteSimulationResult::SiteSimulationResult	(	std::shared_ptr< const ParametrizablePhyloTree >	tree,
		std::shared_ptr< const StateMapInterface >	statemap,
		size_t	ancestralState
	)

inline

Definition at line 36 of file DetailedSiteSimulator.h.

References ancestralStates_, getAlphabet(), indexes_, and paths_.

◆ SiteSimulationResult() [2/2]

bpp::SiteSimulationResult::SiteSimulationResult ( const SiteSimulationResult & ssr )

inline

Definition at line 54 of file DetailedSiteSimulator.h.

◆ ~SiteSimulationResult()

virtual bpp::SiteSimulationResult::~SiteSimulationResult ( )

inlinevirtual

Definition at line 76 of file DetailedSiteSimulator.h.

Member Function Documentation

◆ addNode()

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

inlinevirtual

Definition at line 86 of file DetailedSiteSimulator.h.

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

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

◆ alphabet()

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

inline

Definition at line 84 of file DetailedSiteSimulator.h.

References statemap_.

Referenced by getSite().

◆ getAlphabet()

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

inline

Returns: The alphabet associated to this simulation.

Definition at line 82 of file DetailedSiteSimulator.h.

References statemap_.

Referenced by SiteSimulationResult().

◆ getAncestralState() [1/2]

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

inlinevirtual

Definition at line 94 of file DetailedSiteSimulator.h.

References ancestralStates_.

◆ getAncestralState() [2/2]

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

inlinevirtual

Definition at line 96 of file DetailedSiteSimulator.h.

References ancestralStates_, and indexes_.

◆ getFinalStates()

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

inlinevirtual

Returns: The states at the leaves.

Definition at line 137 of file DetailedSiteSimulator.h.

References ancestralStates_, indexes_, and leavesId_.

Referenced by getSite().

◆ getLeaveNames()

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

inlinevirtual

Returns: A vector with the leaves names.

Definition at line 167 of file DetailedSiteSimulator.h.

References leavesId_, and tree_.

◆ getMutationPath() [1/2]

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

inlinevirtual

Definition at line 98 of file DetailedSiteSimulator.h.

References paths_.

◆ getMutationPath() [2/2]

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

inlinevirtual

Definition at line 100 of file DetailedSiteSimulator.h.

References indexes_, and paths_.

◆ getSite()

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

inlinevirtual

Returns: The site corresponding to this simulation.

Definition at line 151 of file DetailedSiteSimulator.h.

References alphabet(), getFinalStates(), and statemap_.

◆ getSubstitutionCount() [1/4]

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

inlinevirtual

Definition at line 102 of file DetailedSiteSimulator.h.

References paths_.

◆ getSubstitutionCount() [2/4]

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

inlinevirtual

Definition at line 104 of file DetailedSiteSimulator.h.

References paths_.

◆ getSubstitutionCount() [3/4]

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

inlinevirtual

Definition at line 112 of file DetailedSiteSimulator.h.

References indexes_, and paths_.

◆ getSubstitutionCount() [4/4]

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

inlinevirtual

Definition at line 114 of file DetailedSiteSimulator.h.

References indexes_, and paths_.

◆ getSubstitutionVector()

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

inlinevirtual

Definition at line 122 of file DetailedSiteSimulator.h.

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

◆ operator=()

SiteSimulationResult & bpp::SiteSimulationResult::operator= ( const SiteSimulationResult & ssr )

inline

Definition at line 64 of file DetailedSiteSimulator.h.

References ancestralStates_, currentIndex_, indexes_, leavesId_, paths_, statemap_, and tree_.

Member Data Documentation

◆ ancestralStates_

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

private

Definition at line 30 of file DetailedSiteSimulator.h.

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

◆ currentIndex_

size_t bpp::SiteSimulationResult::currentIndex_

private

Definition at line 28 of file DetailedSiteSimulator.h.

Referenced by addNode(), and operator=().

◆ indexes_

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

mutableprivate

Definition at line 27 of file DetailedSiteSimulator.h.

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

◆ leavesId_

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

private

Definition at line 32 of file DetailedSiteSimulator.h.

Referenced by getFinalStates(), getLeaveNames(), and operator=().

◆ paths_

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

private

Definition at line 29 of file DetailedSiteSimulator.h.

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

◆ statemap_

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

private

Definition at line 33 of file DetailedSiteSimulator.h.

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

◆ tree_

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

private

Definition at line 31 of file DetailedSiteSimulator.h.

Referenced by getLeaveNames(), and operator=().

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

Bpp/Phyl/Simulation/DetailedSiteSimulator.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SiteSimulationResult() [1/2]

◆ SiteSimulationResult() [2/2]

◆ ~SiteSimulationResult()

Member Function Documentation

◆ addNode()

◆ alphabet()

◆ getAlphabet()

◆ getAncestralState() [1/2]

◆ getAncestralState() [2/2]

◆ getFinalStates()

◆ getLeaveNames()

◆ getMutationPath() [1/2]

◆ getMutationPath() [2/2]

◆ getSite()

◆ getSubstitutionCount() [1/4]

◆ getSubstitutionCount() [2/4]

◆ getSubstitutionCount() [3/4]

◆ getSubstitutionCount() [4/4]

◆ getSubstitutionVector()

◆ operator=()

Member Data Documentation

◆ ancestralStates_

◆ currentIndex_

◆ indexes_

◆ leavesId_

◆ paths_

◆ statemap_

◆ tree_