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 (const Tree tree, const Alphabet alphabet, size_t ancestralState)

	SiteSimulationResult (const SiteSimulationResult &ssr)

SiteSimulationResult &	operator= (const SiteSimulationResult &ssr)

virtual	~SiteSimulationResult ()

virtual const Alphabet *	getAlphabet () const

virtual void	addNode (int nodeId, MutationPath path)

virtual size_t	getAncestralState (size_t i) const

virtual size_t	getAncestralState (int nodeId) const

virtual const MutationPath &	getMutationPath (size_t i) const

virtual const MutationPath &	getMutationPath (int nodeId) const

virtual size_t	getSubstitutionCount (size_t i) const

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

virtual size_t	getSubstitutionCount (int nodeId) const

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

virtual VVdouble	getSubstitutionVector (const SubstitutionRegister &reg) const

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

virtual Site *	getSite (const SubstitutionModel &model) const

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

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

size_t	currentIndex_

std::vector< MutationPath >	paths_

std::vector< size_t >	ancestralStates_

const Tree *	tree_

std::vector< int >	leavesId_

const Alphabet *	alphabet_

Detailed Description

Data structure to store the result of a DetailedSiteSimulator.

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

Definition at line 61 of file DetailedSiteSimulator.h.

Constructor & Destructor Documentation

◆ SiteSimulationResult() [1/2]

bpp::SiteSimulationResult::SiteSimulationResult	(	const Tree *	tree,
		const Alphabet *	alphabet,
		size_t	ancestralState
	)

inline

Definition at line 73 of file DetailedSiteSimulator.h.

References ancestralStates_, bpp::Tree::getRootId(), and indexes_.

◆ SiteSimulationResult() [2/2]

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

inline

Definition at line 87 of file DetailedSiteSimulator.h.

◆ ~SiteSimulationResult()

virtual bpp::SiteSimulationResult::~SiteSimulationResult ( )

inlinevirtual

Definition at line 109 of file DetailedSiteSimulator.h.

Member Function Documentation

◆ addNode()

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

inlinevirtual

Definition at line 117 of file DetailedSiteSimulator.h.

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

Referenced by bpp::NonHomogeneousSequenceSimulator::dEvolveInternal().

◆ getAlphabet()

virtual const Alphabet* bpp::SiteSimulationResult::getAlphabet ( ) const

inlinevirtual

Returns: The alphabet associated to this simulation.

Definition at line 115 of file DetailedSiteSimulator.h.

References alphabet_.

◆ getAncestralState() [1/2]

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

inlinevirtual

Definition at line 125 of file DetailedSiteSimulator.h.

References ancestralStates_.

◆ getAncestralState() [2/2]

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

inlinevirtual

Definition at line 127 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 159 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 185 of file DetailedSiteSimulator.h.

References bpp::Tree::getNodeName(), leavesId_, and tree_.

◆ getMutationPath() [1/2]

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

inlinevirtual

Definition at line 129 of file DetailedSiteSimulator.h.

References paths_.

◆ getMutationPath() [2/2]

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

inlinevirtual

Definition at line 131 of file DetailedSiteSimulator.h.

References indexes_, and paths_.

◆ getSite()

virtual Site* bpp::SiteSimulationResult::getSite ( const SubstitutionModel & model ) const

inlinevirtual

Returns: The site corresponding to this simulation.

Definition at line 173 of file DetailedSiteSimulator.h.

References alphabet_, bpp::SubstitutionModel::getAlphabetStateAsInt(), and getFinalStates().

◆ getSubstitutionCount() [1/4]

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

inlinevirtual

Definition at line 133 of file DetailedSiteSimulator.h.

References paths_.

◆ getSubstitutionCount() [2/4]

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

inlinevirtual

Definition at line 135 of file DetailedSiteSimulator.h.

References paths_.

◆ getSubstitutionCount() [3/4]

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

inlinevirtual

Definition at line 139 of file DetailedSiteSimulator.h.

References indexes_, and paths_.

◆ getSubstitutionCount() [4/4]

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

inlinevirtual

Definition at line 141 of file DetailedSiteSimulator.h.

References indexes_, and paths_.

◆ getSubstitutionVector()

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

inlinevirtual

Definition at line 145 of file DetailedSiteSimulator.h.

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

◆ operator=()

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

inline

Definition at line 97 of file DetailedSiteSimulator.h.

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

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::SiteSimulationResult::alphabet_

private

Definition at line 70 of file DetailedSiteSimulator.h.

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

◆ ancestralStates_

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

private

Definition at line 67 of file DetailedSiteSimulator.h.

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

◆ currentIndex_

size_t bpp::SiteSimulationResult::currentIndex_

private

Definition at line 65 of file DetailedSiteSimulator.h.

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

◆ indexes_

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

mutableprivate

Definition at line 64 of file DetailedSiteSimulator.h.

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

◆ leavesId_

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

private

Definition at line 69 of file DetailedSiteSimulator.h.

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

◆ paths_

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

private

Definition at line 66 of file DetailedSiteSimulator.h.

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

◆ tree_

const Tree* bpp::SiteSimulationResult::tree_

private

Definition at line 68 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()

◆ 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

◆ alphabet_

◆ ancestralStates_

◆ currentIndex_

◆ indexes_

◆ leavesId_

◆ paths_

◆ tree_