This class is used by MutationProcess to store detailed results of simulations. More...

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

Collaboration diagram for bpp::MutationPath:

Public Member Functions
	MutationPath (std::shared_ptr< const Alphabet > alphabet, size_t initialState, double time)
	Builds a new MutationPath object with initial state 'initialState' and total time 'time'. More...

	MutationPath (const MutationPath &path)

MutationPath &	operator= (const MutationPath &path)

virtual	~MutationPath ()

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

const Alphabet &	alphabet () const

void	addEvent (size_t state, double time)
	Add a new mutation event. More...

void	clear ()

size_t	getInitialState () const
	Retrieve the initial state. More...

double	getTotalTime () const
	Retrieve the total time of evolution. More...

size_t	getNumberOfEvents () const
	Retrieve the number of substitution events. More...

template<class Scalar >
void	getEventCounts (Matrix< Scalar > &counts) const
	Retrieve the number of substitution events per type of substitution. More...

template<class Scalar >
void	getEventCounts (std::vector< Scalar > &counts, const SubstitutionRegisterInterface &reg) const
	Retrieve the number of substitution events per type of substitution, defined by a SubstitutionRegister object. More...

size_t	getFinalState () const
	Retrieve the final state of this path. More...

Private Attributes
std::shared_ptr< const Alphabet >	alphabet_

std::vector< size_t >	states_
	The states taken, without initial state. More...

std::vector< double >	times_
	Times between states. The first element in array is the time between the initial state and the first state in states_. More...

size_t	initialState_
	The initial state. More...

double	totalTime_
	Total time of evolution. Typically, this is a branch length. More...

Detailed Description

This class is used by MutationProcess to store detailed results of simulations.

Author: Julien Dutheil

Definition at line 20 of file MutationProcess.h.

Constructor & Destructor Documentation

◆ MutationPath() [1/2]

bpp::MutationPath::MutationPath	(	std::shared_ptr< const Alphabet >	alphabet,
		size_t	initialState,
		double	time
	)

inline

Builds a new MutationPath object with initial state 'initialState' and total time 'time'.

Parameters

alphabet	The alphabet associated to the states in this path.
initialState	The initial state.
time	The total time of evolution.

Definition at line 55 of file MutationProcess.h.

◆ MutationPath() [2/2]

bpp::MutationPath::MutationPath ( const MutationPath & path )

inline

Definition at line 61 of file MutationProcess.h.

◆ ~MutationPath()

virtual bpp::MutationPath::~MutationPath ( )

inlinevirtual

Definition at line 74 of file MutationProcess.h.

Member Function Documentation

◆ addEvent()

void bpp::MutationPath::addEvent	(	size_t	state,
		double	time
	)

inline

Add a new mutation event.

Parameters

state	The new state after mutation event.
time	The time between this mutation and previous mutation (or initial state).

Definition at line 93 of file MutationProcess.h.

References states_, and times_.

Referenced by bpp::AbstractMutationProcess::detailedEvolve().

◆ alphabet()

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

inline

Returns: A reference toward the alphabet associated to this path.

Definition at line 85 of file MutationProcess.h.

References alphabet_.

◆ clear()

void bpp::MutationPath::clear ( )

inline

Definition at line 103 of file MutationProcess.h.

References states_, and times_.

Referenced by bpp::AbstractMutationProcess::detailedEvolve().

◆ getAlphabet()

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

inline

Returns: A pointer toward the alphabet associated to this path.

Definition at line 80 of file MutationProcess.h.

References alphabet_.

◆ getEventCounts() [1/2]

template<class Scalar >

void bpp::MutationPath::getEventCounts ( Matrix< Scalar > & counts ) const

inline

Retrieve the number of substitution events per type of substitution.

Parameters

counts A matrix with the same size as the alphabet. The substitution counts will be incremented according to the mutation path, which allows to efficiently sum various mutation paths with a look.

Definition at line 136 of file MutationProcess.h.

References alphabet_, bpp::Matrix< class >::getNumberOfColumns(), bpp::Matrix< class >::getNumberOfRows(), initialState_, and states_.

◆ getEventCounts() [2/2]

template<class Scalar >

void bpp::MutationPath::getEventCounts	(	std::vector< Scalar > &	counts,
		const SubstitutionRegisterInterface &	reg
	)		const

inline

Retrieve the number of substitution events per type of substitution, defined by a SubstitutionRegister object.

Parameters

counts	A vector with the appropriate size, as defined by SubstitutionRegister::getNumberOfSubstitutionTypes(). The substitution counts will be incremented according to the mutation path, which allows to efficiently sum various mutation paths with a look.
reg	The substitution register to use to categorize substitutions.

Definition at line 157 of file MutationProcess.h.

References bpp::SubstitutionRegisterInterface::getNumberOfSubstitutionTypes(), bpp::SubstitutionRegisterInterface::getType(), initialState_, and states_.

◆ getFinalState()

size_t bpp::MutationPath::getFinalState ( ) const

inline

Retrieve the final state of this path.

Returns: The initial state if no mutation occurred, otherwise sends the state after last mutation event.

Definition at line 176 of file MutationProcess.h.

References initialState_, and states_.

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

◆ getInitialState()

size_t bpp::MutationPath::getInitialState ( ) const

inline

Retrieve the initial state.

Returns: The initial state of this path.

Definition at line 114 of file MutationProcess.h.

References initialState_.

◆ getNumberOfEvents()

size_t bpp::MutationPath::getNumberOfEvents ( ) const

inline

Retrieve the number of substitution events.

Returns: The number of substitution events, i.e. the number of states (without initial state).

Definition at line 128 of file MutationProcess.h.

References states_.

◆ getTotalTime()

double bpp::MutationPath::getTotalTime ( ) const

inline

Retrieve the total time of evolution.

Returns: The total time of evolution.

Definition at line 121 of file MutationProcess.h.

References totalTime_.

◆ operator=()

MutationPath& bpp::MutationPath::operator= ( const MutationPath & path )

inline

Definition at line 64 of file MutationProcess.h.

References alphabet_, initialState_, states_, times_, and totalTime_.

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::MutationPath::alphabet_

private

Definition at line 23 of file MutationProcess.h.

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

◆ initialState_

size_t bpp::MutationPath::initialState_

private

The initial state.

Definition at line 39 of file MutationProcess.h.

Referenced by getEventCounts(), getFinalState(), getInitialState(), and operator=().

◆ states_

std::vector<size_t> bpp::MutationPath::states_

private

The states taken, without initial state.

Definition at line 28 of file MutationProcess.h.

Referenced by addEvent(), clear(), getEventCounts(), getFinalState(), getNumberOfEvents(), and operator=().

◆ times_

std::vector<double> bpp::MutationPath::times_

private

Times between states. The first element in array is the time between the initial state and the first state in states_.

Definition at line 34 of file MutationProcess.h.

Referenced by addEvent(), clear(), and operator=().

◆ totalTime_

double bpp::MutationPath::totalTime_

private

Total time of evolution. Typically, this is a branch length.

Definition at line 45 of file MutationProcess.h.

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

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

Bpp/Phyl/Simulation/MutationProcess.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MutationPath() [1/2]

◆ MutationPath() [2/2]

◆ ~MutationPath()

Member Function Documentation

◆ addEvent()

◆ alphabet()

◆ clear()

◆ getAlphabet()

◆ getEventCounts() [1/2]

◆ getEventCounts() [2/2]

◆ getFinalState()

◆ getInitialState()

◆ getNumberOfEvents()

◆ getTotalTime()

◆ operator=()

Member Data Documentation

◆ alphabet_

◆ initialState_

◆ states_

◆ times_

◆ totalTime_