#include <Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h>

Inheritance diagram for bpp::GammaDiscreteRateDistribution:

Collaboration diagram for bpp::GammaDiscreteRateDistribution:

Public Member Functions
	GammaDiscreteRateDistribution (size_t nbClasses, double alpha=1.)

GammaDiscreteRateDistribution *	clone () const

std::string	getName () const

void	fireParameterChanged (const ParameterList &parameters)

double	randC () const

double	qProb (double x) const

double	pProb (double x) const

double	Expectation (double a) const

virtual void	restrictToConstraint (const ConstraintInterface &c)

virtual size_t	getNumberOfIndependentParameters () const=0

size_t	getNumberOfIndependentParameters () const

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

void	aliasParameters (const std::string &p1, const std::string &p2)

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

void	unaliasParameters (const std::string &p1, const std::string &p2)

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

virtual std::vector< std::string >	getAlias (const std::string &name) const

virtual std::map< std::string, std::string >	getAliases () const=0

virtual std::map< std::string, std::string >	getAliases () const

virtual bool	hasParameter (const std::string &name) const=0

bool	hasParameter (const std::string &name) const override

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

virtual const Parameter &	parameter (const std::string &name) const=0

const Parameter &	parameter (const std::string &name) const override

virtual double	getParameterValue (const std::string &name) const=0

double	getParameterValue (const std::string &name) const override

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

virtual void	setParameterValue (const std::string &name, double value)=0

void	setParameterValue (const std::string &name, double value) override

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

virtual void	removeConstraint (const std::string &name)=0

void	removeConstraint (const std::string &name) override

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual void	setNamespace (const std::string &prefix)=0

void	setNamespace (const std::string &prefix)

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

bool	hasIndependentParameter (const std::string &name) const

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

std::string	getFrom (const std::string &name) const

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

size_t	getNumberOfCategories () const

size_t	getNumberOfCategories () const

void	setNumberOfCategories (size_t nbClasses)

void	setNumberOfCategories (size_t nbClasses)

double	getCategory (size_t categoryIndex) const

double	getCategory (size_t categoryIndex) const

double	getProbability (size_t categoryIndex) const

double	getProbability (double category) const

double	getProbability (size_t categoryIndex) const

double	getProbability (double category) const

Vdouble	getCategories () const

Vdouble	getCategories () const

Vdouble	getProbabilities () const

Vdouble	getProbabilities () const

double	getValueCategory (double value) const

double	getValueCategory (double value) const

size_t	getCategoryIndex (double value) const

size_t	getCategoryIndex (double value) const

void	set (double category, double probability)

void	set (double category, double probability)

void	add (double category, double probability)

void	add (double category, double probability)

double	getInfCumulativeProbability (double category) const

double	getInfCumulativeProbability (double category) const

double	getIInfCumulativeProbability (double category) const

double	getIInfCumulativeProbability (double category) const

double	getSupCumulativeProbability (double category) const

double	getSupCumulativeProbability (double category) const

double	getSSupCumulativeProbability (double category) const

double	getSSupCumulativeProbability (double category) const

double	rand () const

double	rand () const

double	getBound (size_t i) const

double	getBound (size_t i) const

double	getLowerBound () const

double	getLowerBound () const

double	getUpperBound () const

double	getUpperBound () const

bool	strictLowerBound () const

bool	strictLowerBound () const

bool	strictUpperBound () const

bool	strictUpperBound () const

Vdouble	getBounds () const

Vdouble	getBounds () const

void	print (OutputStream &out) const

void	print (OutputStream &out) const

double	precision () const

double	precision () const

void	setMedian (bool median)

void	setMedian (bool median)

virtual void	discretize ()

virtual void	discretize ()

Static Public Attributes
static short	DISCRETIZATION_EQUAL_PROB

static short	DISCRETIZATION_EQUAL_INTERVAL

static short	DISCRETIZATION_EQUAL_PROB_WHEN_POSSIBLE

Protected Member Functions
const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	discretizeEqualProportions ()

void	discretizeEqualIntervals ()

virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

Protected Attributes
size_t	numberOfCategories_

std::map< double, double, Order >	distribution_

std::vector< double >	bounds_

std::shared_ptr< IntervalConstraint >	intMinMax_

bool	median_

short	discretizationScheme_

Private Attributes
double	alpha_

double	beta_

double	offset_

double	ga1_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_