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 (const Alphabet *alphabet, int initialState, double time)
	Builds a new MutationPath object with initial state 'initialState' and total time 'time'.
	MutationPath (const MutationPath &path)
MutationPath &	operator= (const MutationPath &path)
virtual	~MutationPath ()
const Alphabet *	getAlphabet () const
void	addEvent (int state, double time)
	Add a new mutation event.
int	getInitialState () const
	Retrieve the initial state.
double	getTotalTime () const
	Retrieve the total time of evolution.
size_t	getNumberOfEvents () const
	Retrieve the number of substitution events.
template<class Scalar >
void	getEventCounts (Matrix< Scalar > &counts) const
	Retrieve the number of substitution events per type of substitution.
template<class Scalar >
void	getEventCounts (std::vector< Scalar > &counts, const SubstitutionRegister &reg) const
	Retrieve the number of substitution events per type of substitution, defined by a SubstitutionRegister object.
int	getFinalState () const
	Retrieve the final state of this path.
Private Attributes
const Alphabet *	alphabet_
std::vector< int >	states_
	The states taken, without intiial state.
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_.
int	initialState_
	The initial state.
double	totalTime_
	Total time of evolution. Typically, this is a branch length.

Detailed Description

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

Author:: Julien Dutheil

Definition at line 56 of file MutationProcess.h.

Constructor & Destructor Documentation

bpp::MutationPath::MutationPath	(	const Alphabet *	alphabet,
		int	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 93 of file MutationProcess.h.

bpp::MutationPath::MutationPath ( const MutationPath & path ) [inline]

Definition at line 96 of file MutationProcess.h.

virtual bpp::MutationPath::~MutationPath ( ) [inline, virtual]

Definition at line 108 of file MutationProcess.h.

Member Function Documentation

void bpp::MutationPath::addEvent	(	int	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 123 of file MutationProcess.h.

References states_, and times_.

const Alphabet* bpp::MutationPath::getAlphabet ( ) const [inline]

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

Definition at line 115 of file MutationProcess.h.

References alphabet_.

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 155 of file MutationProcess.h.

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

template<class Scalar >

void bpp::MutationPath::getEventCounts	(	std::vector< Scalar > &	counts,
		const SubstitutionRegister &	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 174 of file MutationProcess.h.

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

int bpp::MutationPath::getFinalState ( ) const [inline]

Retrieve the final state of this path.