A simple implementation of hidden Markov models recursion. More...

#include <Bpp/Numeric/Hmm/LogsumHmmLikelihood.h>

Inheritance diagram for bpp::LogsumHmmLikelihood:

Collaboration diagram for bpp::LogsumHmmLikelihood:

Public Member Functions
	LogsumHmmLikelihood (HmmStateAlphabet hiddenAlphabet, HmmTransitionMatrix transitionMatrix, HmmEmissionProbabilities *emissionProbabilities, const std::string &prefix) throw (Exception)
	Build a new LogsumHmmLikelihood object.
	LogsumHmmLikelihood (const LogsumHmmLikelihood &lik)
LogsumHmmLikelihood &	operator= (const LogsumHmmLikelihood &lik)
virtual	~LogsumHmmLikelihood ()
LogsumHmmLikelihood *	clone () const
	Create a copy of this object and send a pointer to it.
const HmmStateAlphabet &	getHmmStateAlphabet () const
HmmStateAlphabet &	getHmmStateAlphabet ()
const HmmTransitionMatrix &	getHmmTransitionMatrix () const
HmmTransitionMatrix &	getHmmTransitionMatrix ()
const HmmEmissionProbabilities &	getHmmEmissionProbabilities () const
HmmEmissionProbabilities &	getHmmEmissionProbabilities ()
void	setBreakPoints (const std::vector< size_t > &breakPoints)
const std::vector< size_t > &	getBreakPoints () const
void	setParameters (const ParameterList &pl) throw (Exception)
	Set the point where the function must be computed.
double	getValue () const throw (Exception)
	Get the value of the function at the current point.
double	getLogLikelihood () const
void	fireParameterChanged (const ParameterList &pl)
	Notify the class when one or several parameters have changed.
void	getHiddenStatesPosteriorProbabilities (std::vector< std::vector< double > > &probs, bool append=false) const throw (Exception)
virtual double	f (const ParameterList &parameters) throw (Exception)
	Get the value of the function according to a given set of parameters.
virtual bool	hasParameter (const std::string &name) const =0
	Tell if there is a parameter with specified name.
virtual const ParameterList &	getParameters () const =0
	Get all parameters available.
virtual const Parameter &	getParameter (const std::string &name) const =0 throw (ParameterNotFoundException)
	Get the parameter with specified name.
virtual double	getParameterValue (const std::string &name) const =0 throw (ParameterNotFoundException)
	Get the value for parameter of name 'name'.
virtual void	setAllParametersValues (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException)
	Set the parameters values to be equals to those of parameters.
virtual void	setParameterValue (const std::string &name, double value)=0 throw (ParameterNotFoundException, ConstraintException)
	Set the value of parameter with name name to be equal to value.
virtual void	setParametersValues (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException)
	Update the parameters from parameters.
virtual bool	matchParametersValues (const ParameterList &parameters)=0 throw (ConstraintException)
	Update the parameters from parameters.
virtual size_t	getNumberOfParameters () const =0
	Get the number of parameters.
virtual void	setNamespace (const std::string &prefix)=0
	Set the namespace for the parameter names.
virtual std::string	getNamespace () const =0
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
	Resolves a parameter name according to the current namespace.
bool	hasParameter (const std::string &name) const
	Tell if there is a parameter with specified name.
const ParameterList &	getParameters () const
	Get all parameters available.
const Parameter &	getParameter (const std::string &name) const throw (ParameterNotFoundException)
	Get the parameter with specified name.
double	getParameterValue (const std::string &name) const throw (ParameterNotFoundException)
	Get the value for parameter of name 'name'.
void	setAllParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Set the parameters values to be equals to those of parameters.
void	setParameterValue (const std::string &name, double value) throw (ParameterNotFoundException, ConstraintException)
	Set the value of parameter with name name to be equal to value.
void	setParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Update the parameters from parameters.
bool	matchParametersValues (const ParameterList &parameters) throw (ConstraintException)
	Update the parameters from parameters.
size_t	getNumberOfParameters () const
	Get the number of parameters.
void	setNamespace (const std::string &prefix)
	Set the namespace for the parameter names.
std::string	getNamespace () const
std::string	getParameterNameWithoutNamespace (const std::string &name) const
	Resolves a parameter name according to the current namespace.
Protected Member Functions
void	computeForward_ ()
void	computeBackward_ (std::vector< std::vector< double > > &b) const
void	addParameter_ (Parameter *parameter)
void	addParameters_ (const ParameterList &parameters)
void	deleteParameter_ (size_t index) throw (IndexOutOfBoundsException)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name) throw (ParameterNotFoundException)
Parameter &	getParameter_ (size_t index) throw (IndexOutOfBoundsException)
const Parameter &	getParameter_ (size_t index) const throw (IndexOutOfBoundsException)
Parameter &	getParameterWithNamespace_ (const std::string &name) throw (ParameterNotFoundException)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const throw (ParameterNotFoundException)
ParameterList &	getParameters_ ()
Private Attributes
std::auto_ptr< HmmStateAlphabet >	hiddenAlphabet_
	The alphabet describing the hidden states.
std::auto_ptr < HmmTransitionMatrix >	transitionMatrix_
std::auto_ptr < HmmEmissionProbabilities >	emissionProbabilities_
std::vector< double >	logLikelihood_
	The likelihood array.
std::vector< double >	partialLogLikelihoods_
double	logLik_
std::vector< size_t >	breakPoints_
size_t	nbStates_
size_t	nbSites_

Detailed Description

A simple implementation of hidden Markov models recursion.

This implementation uses the logsum method described in Durbin et al "Biological sequence analysis", Cambridge University Press, and further developped in Tobias P. Mann "Numerically Stable Hidden Markov Model Implementation" (2006) http://bozeman.genome.washington.edu/compbio/mbt599_2006/hmm_scaling_revised.pdf . It also offer the possibility to specify "breakpoints", where the chain will be reset to the equilibrium frequencies.

Although probably more numerically accurate, this method is slower than the rescaling, as it involves one exponentiation per site and per hidden state!

See also:: RescaledHmmLikelihood

Definition at line 65 of file LogsumHmmLikelihood.h.

Constructor & Destructor Documentation

LogsumHmmLikelihood::LogsumHmmLikelihood	(	HmmStateAlphabet *	hiddenAlphabet,
		HmmTransitionMatrix *	transitionMatrix,
		HmmEmissionProbabilities *	emissionProbabilities,
		const std::string &	prefix
	)		throw (Exception)

Build a new LogsumHmmLikelihood object.

Warning:: the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to be destroyed with this object.

Definition at line 48 of file LogsumHmmLikelihood.cpp.

Referenced by clone().

bpp::LogsumHmmLikelihood::LogsumHmmLikelihood ( const LogsumHmmLikelihood & lik ) [inline]

Definition at line 106 of file LogsumHmmLikelihood.h.

References emissionProbabilities_, hiddenAlphabet_, and transitionMatrix_.

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

Definition at line 142 of file LogsumHmmLikelihood.h.

Member Function Documentation

void bpp::AbstractParametrizable::addParameter_ ( Parameter * parameter ) [inline, protected, inherited]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 136 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::TestFunction::TestFunction().

void bpp::AbstractParametrizable::addParameters_ ( const ParameterList & parameters ) [inline, protected, inherited]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 142 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters(), and bpp::AbstractParametrizable::parameters_.

LogsumHmmLikelihood* bpp::LogsumHmmLikelihood::clone ( ) const [inline, virtual]

Create a copy of this object and send a pointer to it.

Returns:: A pointer toward the copy object.

Implements bpp::HmmLikelihood.

Definition at line 149 of file LogsumHmmLikelihood.h.

References LogsumHmmLikelihood().

void LogsumHmmLikelihood::computeBackward_ ( std::vector< std::vector< double > > & b ) const [protected]

Definition at line 194 of file LogsumHmmLikelihood.cpp.

References bpp::NumTools::logsum().

void LogsumHmmLikelihood::computeForward_ ( ) [protected]

Definition at line 102 of file LogsumHmmLikelihood.cpp.

References bpp::NumTools::logsum().

Referenced by setBreakPoints().

void bpp::AbstractParametrizable::deleteParameter_ ( size_t index ) throw (IndexOutOfBoundsException) [inline, protected, inherited]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 147 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

virtual double bpp::Function::f ( const ParameterList & parameters ) throw (Exception) [inline, virtual, inherited]

Get the value of the function according to a given set of parameters.

Parameters:

parameters The parameter set to pass to the function.

Returns:: The value of the function with the given parameter set.

Exceptions:

Exception If an error occured.

Reimplemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, and bpp::AbstractNumericalDerivative.

Definition at line 117 of file Functions.h.

References bpp::Function::getValue(), and bpp::Function::setParameters().

Referenced by bpp::NewtonOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::BfgsMultiDimensions::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::GoldenSectionSearch::doStep(), bpp::BrentOneDimension::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::FunctionWrapper::f(), bpp::PowellMultiDimensions::optimize(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::AbstractOptimizer::step(), and bpp::DownhillSimplexMethod::tryExtrapolation().

void LogsumHmmLikelihood::fireParameterChanged ( const ParameterList & parameters ) [virtual]

Notify the class when one or several parameters have changed.

Parameters:

parameters A ParameterList object with parameters that changed.

Implements bpp::AbstractParametrizable.

Definition at line 86 of file LogsumHmmLikelihood.cpp.

const std::vector<size_t>& bpp::LogsumHmmLikelihood::getBreakPoints ( ) const [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 166 of file LogsumHmmLikelihood.h.

References breakPoints_.

void LogsumHmmLikelihood::getHiddenStatesPosteriorProbabilities	(	std::vector< std::vector< double > > &	probs,
		bool	append = `false`
	)		const throw (Exception) `[virtual]`

Implements bpp::HmmLikelihood.

Definition at line 256 of file LogsumHmmLikelihood.cpp.

const HmmEmissionProbabilities& bpp::LogsumHmmLikelihood::getHmmEmissionProbabilities ( ) const [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 158 of file LogsumHmmLikelihood.h.

References emissionProbabilities_.

HmmEmissionProbabilities& bpp::LogsumHmmLikelihood::getHmmEmissionProbabilities ( ) [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 159 of file LogsumHmmLikelihood.h.

References emissionProbabilities_.

const HmmStateAlphabet& bpp::LogsumHmmLikelihood::getHmmStateAlphabet ( ) const [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 152 of file LogsumHmmLikelihood.h.

References hiddenAlphabet_.

HmmStateAlphabet& bpp::LogsumHmmLikelihood::getHmmStateAlphabet ( ) [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 153 of file LogsumHmmLikelihood.h.

References hiddenAlphabet_.

const HmmTransitionMatrix& bpp::LogsumHmmLikelihood::getHmmTransitionMatrix ( ) const [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 155 of file LogsumHmmLikelihood.h.

References transitionMatrix_.

HmmTransitionMatrix& bpp::LogsumHmmLikelihood::getHmmTransitionMatrix ( ) [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 156 of file LogsumHmmLikelihood.h.

References transitionMatrix_.

double bpp::LogsumHmmLikelihood::getLogLikelihood ( ) const [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 175 of file LogsumHmmLikelihood.h.

References logLik_.

std::string bpp::AbstractParametrizable::getNamespace ( ) const [inline, virtual, inherited]

Returns:: The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 124 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

Referenced by bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::write().

virtual std::string bpp::Parametrizable::getNamespace ( ) const [pure virtual, inherited]

Returns:: The current namespace used. This is an empty string if no namespace is currently defined.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getNamespace().

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const [inline, virtual, inherited]

Get the number of parameters.

See also:: getNumberOfIndependentParameters If some parameters are aliased.

Returns:: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 120 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractParameterAliasable::operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const [pure virtual, inherited]

Get the number of parameters.

See also:: getNumberOfIndependentParameters If some parameters are aliased.

Returns:: The number of parameters.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::write().

const Parameter& bpp::AbstractParametrizable::getParameter ( const std::string & name ) const throw (ParameterNotFoundException) [inline, virtual, inherited]

Get the parameter with specified name.

Parameters:

name	The name of the parameter to look for.

Returns:: The parameter with given name.

Exceptions:

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 79 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::TestFunction::getValue().

virtual const Parameter& bpp::Parametrizable::getParameter ( const std::string & name ) const throw (ParameterNotFoundException) [pure virtual, inherited]

Get the parameter with specified name.

Parameters:

name	The name of the parameter to look for.

Returns:: The parameter with given name.

Exceptions:

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameter().

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string & name ) throw (ParameterNotFoundException) [inline, protected, inherited]

Parameters:

name	The name of the parameter.

Returns:: A reference toward the corresponding parameter.

Exceptions:

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 164 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index ) throw (IndexOutOfBoundsException) [inline, protected, inherited]

Definition at line 188 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index ) const throw (IndexOutOfBoundsException) [inline, protected, inherited]

Definition at line 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

std::string AbstractParametrizable::getParameterNameWithoutNamespace ( const std::string & name ) const [virtual, inherited]

Resolves a parameter name according to the current namespace.

Returns:: The parameter name without the namespace prefix, if any.

Implements bpp::Parametrizable.

Definition at line 63 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string & name ) const [pure virtual, inherited]

Resolves a parameter name according to the current namespace.

Returns:: The parameter name without the namespace prefix, if any.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), bpp::BppODiscreteDistributionFormat::read(), and bpp::BppOParametrizableFormat::write().

const ParameterList& bpp::AbstractParametrizable::getParameters ( ) const [inline, virtual, inherited]

Get all parameters available.

See also:: getIndependentParameters if some parameters are aliased.

Returns:: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 77 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::fireParameterChanged(), and bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions().

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const [pure virtual, inherited]

Get all parameters available.

See also:: getIndependentParameters if some parameters are aliased.

Returns:: A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::NewtonOneDimension::doStep(), bpp::FunctionWrapper::getParameters(), bpp::BppODiscreteDistributionFormat::read(), bpp::AbstractNumericalDerivative::setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().

ParameterList& bpp::AbstractParametrizable::getParameters_ ( ) [inline, protected, inherited]

Definition at line 201 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), and bpp::AbstractParameterAliasable::operator=().

double bpp::AbstractParametrizable::getParameterValue ( const std::string & name ) const throw (ParameterNotFoundException) [inline, virtual, inherited]

Get the value for parameter of name 'name'.

Parameters:

name	The name of the parameter.

Returns:: the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 84 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter(), and bpp::Parameter::getValue().

virtual double bpp::Parametrizable::getParameterValue ( const std::string & name ) const throw (ParameterNotFoundException) [pure virtual, inherited]

Get the value for parameter of name 'name'.

Parameters:

name	The name of the parameter.

Returns:: the value of parameter name.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterValue(), and bpp::BppODiscreteDistributionFormat::read().

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string & name ) throw (ParameterNotFoundException) [inline, protected, inherited]

Parameters:

name	The name of the parameter, including its namespace.

Returns:: A reference toward the corresponding parameter.

Exceptions:

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 174 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string & name ) const throw (ParameterNotFoundException) [inline, protected, inherited]

Parameters:

name	The name of the parameter, including its namespace.

Returns:: A reference toward the corresponding parameter.

Exceptions:

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 183 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

double bpp::LogsumHmmLikelihood::getValue ( ) const throw (Exception) [inline, virtual]

Get the value of the function at the current point.

Returns:: The value of the function.

Exceptions:

Exception If no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 173 of file LogsumHmmLikelihood.h.

References logLik_.

virtual bool bpp::Parametrizable::hasParameter ( const std::string & name ) const [pure virtual, inherited]

Tell if there is a parameter with specified name.

Parameters:

name	The name of the parameter to look for.

Returns:: y/n.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::hasParameter().

bool bpp::AbstractParametrizable::hasParameter ( const std::string & name ) const [inline, virtual, inherited]

Tell if there is a parameter with specified name.

Parameters:

name	The name of the parameter to look for.

Returns:: y/n.

Implements bpp::Parametrizable.

Definition at line 75 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::ConstantDistribution::fireParameterChanged().

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList & parameters ) throw (ConstraintException) [inline, virtual, inherited]

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters:

parameters A list of parameters.

Returns:: True if at least one parameter value has been changed.

Exceptions:

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 111 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::Simplex::setFrequencies(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::TestFunction::setParameters().

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList & parameters ) throw (ConstraintException) [pure virtual, inherited]

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters:

parameters A list of parameters.

Returns:: True if at least one parameter value has been changed.

Exceptions:

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

LogsumHmmLikelihood& bpp::LogsumHmmLikelihood::operator= ( const LogsumHmmLikelihood & lik ) [inline]

Definition at line 123 of file LogsumHmmLikelihood.h.

References breakPoints_, emissionProbabilities_, hiddenAlphabet_, logLik_, logLikelihood_, nbSites_, nbStates_, partialLogLikelihoods_, and transitionMatrix_.

void bpp::AbstractParametrizable::resetParameters_ ( ) [inline, protected, inherited]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 154 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::reset().

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList & parameters ) throw (ParameterNotFoundException, ConstraintException) [inline, virtual, inherited]

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters:

parameters A list with all parameters.

Exceptions:

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setAllParametersValues().

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList & parameters ) throw (ParameterNotFoundException, ConstraintException) [pure virtual, inherited]

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters:

parameters A list with all parameters.

Exceptions:

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

void bpp::LogsumHmmLikelihood::setBreakPoints ( const std::vector< size_t > & breakPoints ) [inline, virtual]

Implements bpp::HmmLikelihood.

Definition at line 161 of file LogsumHmmLikelihood.h.

References breakPoints_, and computeForward_().

void AbstractParametrizable::setNamespace ( const std::string & prefix ) [virtual, inherited]

Set the namespace for the parameter names.

Parameters:

prefix The 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implements bpp::Parametrizable.

Reimplemented in bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 45 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

virtual void bpp::Parametrizable::setNamespace ( const std::string & prefix ) [pure virtual, inherited]

Set the namespace for the parameter names.

Parameters:

prefix The 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::FunctionWrapper::setNamespace().

void bpp::LogsumHmmLikelihood::setParameters ( const ParameterList & parameters ) throw (Exception) [inline, virtual]

Set the point where the function must be computed.

Parameters:

parameters The parameter set to pass to the function.

Implements bpp::Function.

Definition at line 168 of file LogsumHmmLikelihood.h.

References bpp::AbstractParametrizable::setParametersValues().

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList & parameters ) throw (ParameterNotFoundException, ConstraintException) [inline, virtual, inherited]

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters:

parameters A list containing all parameters to update.

Exceptions:

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 104 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setParametersValues().

Referenced by bpp::RescaledHmmLikelihood::setParameters(), setParameters(), and bpp::LowMemoryRescaledHmmLikelihood::setParameters().

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList & parameters ) throw (ParameterNotFoundException, ConstraintException) [pure virtual, inherited]

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters:

parameters A list containing all parameters to update.

Exceptions:

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

void bpp::AbstractParametrizable::setParameterValue	(	const std::string &	name,
		double	value
	)		throw (ParameterNotFoundException, ConstraintException) `[inline, virtual, inherited]`

Set the value of parameter with name name to be equal to value.

Parameters:

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions:

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 97 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, bpp::ParameterList::setParameterValue(), and bpp::ParameterList::subList().

virtual void bpp::Parametrizable::setParameterValue	(	const std::string &	name,
		double	value
	)		throw (ParameterNotFoundException, ConstraintException) `[pure virtual, inherited]`

Set the value of parameter with name name to be equal to value.

Parameters:

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions:

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().