bpp-core3
3.0.0
|
A simple implementation of hidden Markov models recursion. More...
#include <Bpp/Numeric/Hmm/LogsumHmmLikelihood.h>
Public Member Functions | |
LogsumHmmLikelihood (HmmStateAlphabet *hiddenAlphabet, HmmTransitionMatrix *transitionMatrix, HmmEmissionProbabilities *emissionProbabilities, bool ownsPointers_=true, const std::string &prefix="") | |
Build a new LogsumHmmLikelihood object. More... | |
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. More... | |
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) |
Set the point where the function must be computed. More... | |
double | getValue () const |
Get the value of the function at the current point. More... | |
double | getLogLikelihood () const |
double | getLikelihoodForASite (size_t site) const |
Get the likelihood for a site, and its derivatives. More... | |
double | getDLogLikelihoodForASite (size_t site) const |
double | getD2LogLikelihoodForASite (size_t site) const |
Vdouble | getLikelihoodForEachSite () const |
Get the likelihood for each site. More... | |
void | setNamespace (const std::string &nameSpace) |
Set the namespace for the parameter names. More... | |
void | fireParameterChanged (const ParameterList &pl) |
Notify the class when one or several parameters have changed. More... | |
Vdouble | getHiddenStatesPosteriorProbabilitiesForASite (size_t site) const |
void | getHiddenStatesPosteriorProbabilities (std::vector< std::vector< double > > &probs, bool append=false) const |
void | computeLikelihood () |
void | enableFirstOrderDerivatives (bool yn) |
Tell if derivatives must be computed. More... | |
bool | enableFirstOrderDerivatives () const |
Tell if derivatives must be computed. More... | |
double | getFirstOrderDerivative (const std::string &variable) const |
Get the derivative of the function at the current point. More... | |
double | getDLogLikelihood () const |
void | enableSecondOrderDerivatives (bool yn) |
Tell if derivatives must be computed. More... | |
bool | enableSecondOrderDerivatives () const |
Tell if derivatives must be computed. More... | |
double | getSecondOrderDerivative (const std::string &variable) const |
Get the second order derivative of the function at the current point. More... | |
double | getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const |
Get the value of the cross derivative of the function according to a given set of parameters. More... | |
double | getD2LogLikelihood () const |
virtual double | d2f (const std::string &variable, const ParameterList ¶meters) |
Get the value of the second order derivative of the function according to a given set of parameters. More... | |
virtual double | d2f (const std::string &variable1, const std::string &variable2, const ParameterList ¶meters) |
Get the value of the cross derivative of the function according to a given set of parameters. More... | |
virtual double | df (const std::string &variable, const ParameterList ¶meters) |
Get the value of the first derivative of the function according to a given set of parameters. More... | |
virtual double | f (const ParameterList ¶meters) |
Get the value of the function according to a given set of parameters. More... | |
virtual bool | hasParameter (const std::string &name) const =0 |
Tell if there is a parameter with specified name. More... | |
virtual const ParameterList & | getParameters () const =0 |
Get all parameters available. More... | |
virtual const Parameter & | getParameter (const std::string &name) const =0 |
Get the parameter with specified name. More... | |
virtual double | getParameterValue (const std::string &name) const =0 |
Get the value for parameter of name 'name'. More... | |
virtual void | setAllParametersValues (const ParameterList ¶meters)=0 |
Set the parameters values to be equals to those of parameters. More... | |
virtual void | setParameterValue (const std::string &name, double value)=0 |
Set the value of parameter with name name to be equal to value. More... | |
virtual void | setParametersValues (const ParameterList ¶meters)=0 |
Update the parameters from parameters. More... | |
virtual bool | matchParametersValues (const ParameterList ¶meters)=0 |
Update the parameters from parameters. More... | |
virtual size_t | getNumberOfParameters () const =0 |
Get the number of parameters. More... | |
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. More... | |
bool | hasParameter (const std::string &name) const |
Tell if there is a parameter with specified name. More... | |
const ParameterList & | getParameters () const |
Get all parameters available. More... | |
const Parameter & | getParameter (const std::string &name) const |
Get the parameter with specified name. More... | |
const std::shared_ptr< Parameter > & | getSharedParameter (const std::string &name) const |
double | getParameterValue (const std::string &name) const |
Get the value for parameter of name 'name'. More... | |
void | setAllParametersValues (const ParameterList ¶meters) |
Set the parameters values to be equals to those of parameters. More... | |
void | setParameterValue (const std::string &name, double value) |
Set the value of parameter with name name to be equal to value. More... | |
void | setParametersValues (const ParameterList ¶meters) |
Update the parameters from parameters. More... | |
bool | matchParametersValues (const ParameterList ¶meters) |
Update the parameters from parameters. More... | |
size_t | getNumberOfParameters () const |
Get the number of parameters. More... | |
std::string | getNamespace () const |
std::string | getParameterNameWithoutNamespace (const std::string &name) const |
Resolves a parameter name according to the current namespace. More... | |
Protected Member Functions | |
void | computeForward_ () |
void | computeBackward_ () const |
void | computeDLikelihood_ () const |
void | computeD2Likelihood_ () const |
void | computeDForward_ () const |
void | computeD2Forward_ () const |
virtual ParameterList & | getParameters_ ()=0 |
Get all parameters available. More... | |
const std::shared_ptr< Parameter > & | getSharedParameter (size_t i) const |
std::shared_ptr< Parameter > & | getSharedParameter (size_t i) |
virtual void | addParameter_ (Parameter *parameter) |
virtual void | addParameters_ (const ParameterList ¶meters) |
virtual void | shareParameter_ (const std::shared_ptr< Parameter > ¶meter) |
virtual void | shareParameters_ (const ParameterList ¶meters) |
virtual void | includeParameters_ (const ParameterList ¶meters) |
virtual void | deleteParameter_ (size_t index) |
virtual void | deleteParameter_ (std::string &name) |
virtual 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 |
ParameterList & | getParameters_ () |
Get all parameters available. More... | |
Protected Attributes | |
HmmStateAlphabet * | hiddenAlphabet_ |
The alphabet describing the hidden states. More... | |
HmmTransitionMatrix * | transitionMatrix_ |
HmmEmissionProbabilities * | emissionProbabilities_ |
bool | ownsPointers_ |
Owns previous objects. More... | |
std::vector< double > | logLikelihood_ |
The likelihood array. More... | |
std::vector< double > | partialLogLikelihoods_ |
double | logLik_ |
std::vector< std::vector< double > > | dLogLikelihood_ |
The DLogLikelihood arrays. More... | |
std::vector< double > | partialDLogLikelihoods_ |
std::vector< std::vector< double > > | d2LogLikelihood_ |
std::vector< double > | partialD2LogLikelihoods_ |
std::vector< std::vector< double > > | backLogLikelihood_ |
backward logLikelihood More... | |
bool | backLogLikelihoodUpToDate_ |
std::vector< size_t > | breakPoints_ |
size_t | nbStates_ |
size_t | nbSites_ |
double | dLogLik_ |
std::string | dVariable_ |
double | d2LogLik_ |
std::string | d2Variable_ |
Private Attributes | |
ParameterList | parameters_ |
std::string | prefix_ |
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!
Definition at line 67 of file LogsumHmmLikelihood.h.
LogsumHmmLikelihood::LogsumHmmLikelihood | ( | HmmStateAlphabet * | hiddenAlphabet, |
HmmTransitionMatrix * | transitionMatrix, | ||
HmmEmissionProbabilities * | emissionProbabilities, | ||
bool | ownsPointers_ = true , |
||
const std::string & | prefix = "" |
||
) |
Build a new LogsumHmmLikelihood object.
Definition at line 50 of file LogsumHmmLikelihood.cpp.
References bpp::AbstractParametrizable::addParameters_(), computeForward_(), emissionProbabilities_, bpp::HmmEmissionProbabilities::getHmmStateAlphabet(), bpp::HmmTransitionMatrix::getHmmStateAlphabet(), bpp::HmmEmissionProbabilities::getNumberOfPositions(), bpp::HmmStateAlphabet::getNumberOfStates(), bpp::Parametrizable::getParameters(), hiddenAlphabet_, logLikelihood_, nbSites_, nbStates_, transitionMatrix_, and bpp::HmmStateAlphabet::worksWith().
Referenced by clone().
|
inline |
Definition at line 149 of file LogsumHmmLikelihood.h.
References bpp::Clonable::clone(), bpp::HmmEmissionProbabilities::clone(), emissionProbabilities_, hiddenAlphabet_, ownsPointers_, bpp::HmmEmissionProbabilities::setHmmStateAlphabet(), bpp::HmmTransitionMatrix::setHmmStateAlphabet(), and transitionMatrix_.
|
inlinevirtual |
Definition at line 226 of file LogsumHmmLikelihood.h.
References emissionProbabilities_, hiddenAlphabet_, ownsPointers_, and transitionMatrix_.
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 137 of file AbstractParametrizable.h.
References bpp::ParameterList::addParameter(), and bpp::AbstractParametrizable::parameters_.
Referenced by bpp::AbstractParameterAliasable::addParameter_(), bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(), and bpp::TestFunction::TestFunction().
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 143 of file AbstractParametrizable.h.
References bpp::ParameterList::addParameters(), and bpp::AbstractParametrizable::parameters_.
Referenced by bpp::AbstractParameterAliasable::addParameters_(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), LogsumHmmLikelihood(), bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(), and bpp::RescaledHmmLikelihood::RescaledHmmLikelihood().
|
inlinevirtual |
Create a copy of this object and send a pointer to it.
Implements bpp::HmmLikelihood.
Definition at line 237 of file LogsumHmmLikelihood.h.
References LogsumHmmLikelihood().
|
protected |
Definition at line 244 of file LogsumHmmLikelihood.cpp.
References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, bpp::NumTools::logsum(), nbSites_, nbStates_, bpp::HmmTransitionMatrix::Pij(), and transitionMatrix_.
Referenced by getHiddenStatesPosteriorProbabilities(), and getHiddenStatesPosteriorProbabilitiesForASite().
|
protected |
Definition at line 522 of file LogsumHmmLikelihood.cpp.
References breakPoints_, bpp::AbstractHmmLikelihood::d2LogLik_, d2LogLikelihood_, bpp::AbstractHmmLikelihood::d2Variable_, dLogLikelihood_, emissionProbabilities_, bpp::ColMatrix< Scalar >::getCol(), bpp::HmmEmissionProbabilities::getD2EmissionProbabilities(), bpp::HmmEmissionProbabilities::getDEmissionProbabilities(), bpp::AbstractHmmLikelihood::getFirstOrderDerivative(), bpp::HmmTransitionMatrix::getPij(), logLikelihood_, nbSites_, nbStates_, partialD2LogLikelihoods_, partialDLogLikelihoods_, bpp::VectorTools::sumExp(), transitionMatrix_, and bpp::VectorTools::whichMax().
Referenced by computeD2Likelihood_().
|
inlineprotectedvirtual |
Implements bpp::HmmLikelihood.
Definition at line 295 of file LogsumHmmLikelihood.h.
References computeD2Forward_().
|
protected |
Definition at line 417 of file LogsumHmmLikelihood.cpp.
References breakPoints_, bpp::AbstractHmmLikelihood::dLogLik_, dLogLikelihood_, emissionProbabilities_, bpp::ColMatrix< Scalar >::getCol(), bpp::HmmEmissionProbabilities::getDEmissionProbabilities(), bpp::HmmTransitionMatrix::getPij(), logLikelihood_, nbSites_, nbStates_, partialDLogLikelihoods_, bpp::VectorTools::sumExp(), transitionMatrix_, and bpp::VectorTools::whichMax().
Referenced by computeDLikelihood_().
|
inlineprotectedvirtual |
Implements bpp::HmmLikelihood.
Definition at line 290 of file LogsumHmmLikelihood.h.
References computeDForward_().
|
protected |
Definition at line 137 of file LogsumHmmLikelihood.cpp.
References breakPoints_, bpp::HmmTransitionMatrix::getEquilibriumFrequencies(), logLik_, logLikelihood_, bpp::NumTools::logsum(), nbSites_, nbStates_, partialLogLikelihoods_, bpp::HmmTransitionMatrix::Pij(), and transitionMatrix_.
Referenced by computeLikelihood(), LogsumHmmLikelihood(), and setBreakPoints().
void LogsumHmmLikelihood::computeLikelihood | ( | ) |
Definition at line 130 of file LogsumHmmLikelihood.cpp.
References computeForward_().
Referenced by fireParameterChanged().
|
inlinevirtualinherited |
Get the value of the second order derivative of the function according to a given set of parameters.
variable | The name of the ![]() ![]() |
parameters | The parameter set to pass to the function. |
Exception | If an error occured. |
Definition at line 228 of file Functions.h.
References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().
|
inlinevirtualinherited |
Get the value of the cross derivative of the function according to a given set of parameters.
variable1 | The name of the ![]() ![]() |
variable2 | The name of the ![]() ![]() |
parameters | The parameter set to pass to the function. |
Exception | If an error occured. |
Definition at line 255 of file Functions.h.
References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 163 of file AbstractParametrizable.h.
References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().
Referenced by bpp::AbstractParameterAliasable::deleteParameter_().
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 170 of file AbstractParametrizable.h.
References bpp::ParameterList::deleteParameter(), and bpp::AbstractParametrizable::parameters_.
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 175 of file AbstractParametrizable.h.
References bpp::ParameterList::deleteParameters(), and bpp::AbstractParametrizable::parameters_.
|
inlinevirtualinherited |
Get the value of the first derivative of the function according to a given set of parameters.
variable | The name of the ![]() ![]() |
parameters | The parameter set to pass to the function. |
Exception | If an error occured. |
Definition at line 173 of file Functions.h.
References bpp::DerivableFirstOrder::getFirstOrderDerivative(), and bpp::Function::setParameters().
|
inlinevirtualinherited |
Tell if derivatives must be computed.
Implements bpp::DerivableFirstOrder.
Definition at line 162 of file HmmLikelihood.h.
|
inlinevirtualinherited |
Tell if derivatives must be computed.
yn | yes/no |
Implements bpp::DerivableFirstOrder.
Definition at line 160 of file HmmLikelihood.h.
|
inlinevirtualinherited |
Tell if derivatives must be computed.
Implements bpp::DerivableSecondOrder.
Definition at line 183 of file HmmLikelihood.h.
|
inlinevirtualinherited |
Tell if derivatives must be computed.
yn | yes/no |
Implements bpp::DerivableSecondOrder.
Definition at line 181 of file HmmLikelihood.h.
|
inlinevirtualinherited |
Get the value of the function according to a given set of parameters.
parameters | The parameter set to pass to the function. |
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::BrentOneDimension::doInit(), bpp::DownhillSimplexMethod::doInit(), bpp::GoldenSectionSearch::doInit(), bpp::NewtonBacktrackOneDimension::doInit(), bpp::NewtonOneDimension::doInit(), bpp::PowellMultiDimensions::doInit(), bpp::BfgsMultiDimensions::doStep(), bpp::BrentOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::NewtonOneDimension::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::FunctionWrapper::f(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::PowellMultiDimensions::optimize(), bpp::AbstractOptimizer::step(), bpp::DownhillSimplexMethod::tryExtrapolation(), and bpp::NumTools::uniRoot().
|
virtual |
Notify the class when one or several parameters have changed.
parameters | A ParameterList object with parameters that changed. |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 110 of file LogsumHmmLikelihood.cpp.
References backLogLikelihoodUpToDate_, computeLikelihood(), bpp::AbstractHmmLikelihood::d2Variable_, bpp::AbstractHmmLikelihood::dVariable_, emissionProbabilities_, bpp::Parametrizable::getParameters(), hiddenAlphabet_, bpp::Parametrizable::matchParametersValues(), bpp::Parametrizable::setParametersValues(), and transitionMatrix_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 256 of file LogsumHmmLikelihood.h.
References breakPoints_.
|
inlinevirtualinherited |
Implements bpp::HmmLikelihood.
Definition at line 187 of file HmmLikelihood.h.
References bpp::AbstractHmmLikelihood::d2LogLik_.
|
virtual |
Implements bpp::HmmLikelihood.
Definition at line 639 of file LogsumHmmLikelihood.cpp.
References partialD2LogLikelihoods_.
|
inlinevirtualinherited |
Implements bpp::HmmLikelihood.
Definition at line 166 of file HmmLikelihood.h.
References bpp::AbstractHmmLikelihood::dLogLik_.
|
virtual |
Implements bpp::HmmLikelihood.
Definition at line 515 of file LogsumHmmLikelihood.cpp.
References partialDLogLikelihoods_.
|
virtualinherited |
Get the derivative of the function at the current point.
variable | The name of the ![]() ![]() |
Exception | If no point is specified or if an error occured. |
Implements bpp::DerivableFirstOrder.
Definition at line 70 of file HmmLikelihood.cpp.
References bpp::HmmEmissionProbabilities::computeDEmissionProbabilities(), bpp::HmmLikelihood::computeDLikelihood_(), bpp::AbstractHmmLikelihood::dLogLik_, bpp::AbstractHmmLikelihood::dVariable_, and bpp::HmmLikelihood::getHmmEmissionProbabilities().
Referenced by computeD2Forward_().
|
virtual |
Implements bpp::HmmLikelihood.
Definition at line 377 of file LogsumHmmLikelihood.cpp.
References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, computeBackward_(), logLikelihood_, nbSites_, nbStates_, and partialLogLikelihoods_.
Referenced by getLikelihoodForEachSite().
|
virtual |
Implements bpp::HmmLikelihood.
Definition at line 351 of file LogsumHmmLikelihood.cpp.
References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, computeBackward_(), logLikelihood_, nbStates_, and partialLogLikelihoods_.
Referenced by getLikelihoodForASite().
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 247 of file LogsumHmmLikelihood.h.
References emissionProbabilities_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 246 of file LogsumHmmLikelihood.h.
References emissionProbabilities_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 241 of file LogsumHmmLikelihood.h.
References hiddenAlphabet_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 240 of file LogsumHmmLikelihood.h.
References hiddenAlphabet_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 244 of file LogsumHmmLikelihood.h.
References transitionMatrix_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 243 of file LogsumHmmLikelihood.h.
References transitionMatrix_.
|
virtual |
Get the likelihood for a site, and its derivatives.
site | The site index to analyse. |
Implements bpp::HmmLikelihood.
Definition at line 318 of file LogsumHmmLikelihood.cpp.
References getHiddenStatesPosteriorProbabilitiesForASite(), and nbStates_.
|
virtual |
Get the likelihood for each site.
Implements bpp::HmmLikelihood.
Definition at line 330 of file LogsumHmmLikelihood.cpp.
References getHiddenStatesPosteriorProbabilities(), nbSites_, and nbStates_.
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 265 of file LogsumHmmLikelihood.h.
References logLik_.
|
inlinevirtualinherited |
Implements bpp::Parametrizable.
Definition at line 125 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::prefix_.
Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::hasIndependentParameter(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
|
pure virtualinherited |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getNamespace().
|
inlinevirtualinherited |
Get the number of parameters.
Implements bpp::Parametrizable.
Definition at line 121 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().
Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractParameterAliasable::operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().
|
pure virtualinherited |
Get the number of parameters.
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
|
inlinevirtualinherited |
Get the parameter with specified name.
name | The name of the parameter to look for. |
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::AbstractParameterAliasable::getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::TestFunction::getValue().
|
pure virtualinherited |
Get the parameter with specified name.
name | The name of the parameter to look for. |
ParameterNotFoundException | if no parameter with this name is found. |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameter().
|
inlineprotectedinherited |
name | The name of the parameter. |
ParameterNotFoundException | If no parameter with that name is found in the list. |
Definition at line 190 of file AbstractParametrizable.h.
References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.
Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ConstantDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), and bpp::AbstractParameterAliasable::unaliasParameters().
|
inlineprotectedinherited |
Definition at line 216 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().
|
inlineprotectedinherited |
Definition at line 223 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().
|
virtualinherited |
Resolves a parameter name according to the current namespace.
Implements bpp::Parametrizable.
Definition at line 65 of file AbstractParametrizable.cpp.
References bpp::TextTools::startsWith().
Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), and bpp::AbstractParameterAliasable::shareParameters_().
|
pure virtualinherited |
Resolves a parameter name according to the current namespace.
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), and bpp::BppOParametrizableFormat::write().
|
inlinevirtualinherited |
Get all parameters available.
Implements bpp::Parametrizable.
Definition at line 77 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_.
Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::ParametrizableCollection< N >::removeObject().
|
pure virtualinherited |
Get all parameters available.
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.
Referenced by bpp::NewtonOneDimension::doStep(), fireParameterChanged(), bpp::FunctionWrapper::getParameters(), LogsumHmmLikelihood(), bpp::AbstractNumericalDerivative::setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().
|
inlineprotectedvirtualinherited |
Get all parameters available.
Implements bpp::Parametrizable.
Definition at line 231 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_.
Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), and bpp::AbstractParameterAliasable::operator=().
|
protectedpure virtualinherited |
Get all parameters available.
Implemented in bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameters_().
|
inlinevirtualinherited |
Get the value for parameter of name 'name'.
name | The name of the parameter. |
Implements bpp::Parametrizable.
Definition at line 89 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::getParameter(), and bpp::Parameter::getValue().
Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ConstantDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().
|
pure virtualinherited |
Get the value for parameter of name 'name'.
name | The name of the parameter. |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameterValue().
|
inlineprotectedinherited |
name | The name of the parameter, including its namespace. |
ParameterNotFoundException | If no parameter with that name is found in the list. |
Definition at line 202 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::getParameter_().
|
inlineprotectedinherited |
name | The name of the parameter, including its namespace. |
ParameterNotFoundException | If no parameter with that name is found in the list. |
Definition at line 211 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::getParameter().
|
virtualinherited |
Get the second order derivative of the function at the current point.
variable | The name of the ![]() ![]() |
Exception | If no point is specified or if an error occured. |
Implements bpp::DerivableSecondOrder.
Definition at line 82 of file HmmLikelihood.cpp.
References bpp::HmmEmissionProbabilities::computeD2EmissionProbabilities(), bpp::HmmLikelihood::computeD2Likelihood_(), bpp::AbstractHmmLikelihood::d2LogLik_, bpp::AbstractHmmLikelihood::d2Variable_, and bpp::HmmLikelihood::getHmmEmissionProbabilities().
|
inlinevirtualinherited |
Get the value of the cross derivative of the function according to a given set of parameters.
variable1 | The name of the ![]() ![]() |
variable2 | The name of the ![]() ![]() |
Exception | If an error occured. |
Implements bpp::DerivableSecondOrder.
Definition at line 192 of file HmmLikelihood.h.
|
inlineinherited |
Definition at line 84 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.
Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().
|
inlineprotectedinherited |
Definition at line 242 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.
|
inlineprotectedinherited |
Definition at line 237 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.
|
inlinevirtual |
Get the value of the function at the current point.
Exception | If no point is specified or if an error occured. |
Implements bpp::Function.
Definition at line 263 of file LogsumHmmLikelihood.h.
References logLik_.
|
inlinevirtualinherited |
Tell if there is a parameter with specified name.
name | The name of the parameter to look for. |
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::AbstractParameterAliasable::aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AbstractParametrizable::getParameter_(), and bpp::AbstractParameterAliasable::unaliasParameters().
|
pure virtualinherited |
Tell if there is a parameter with specified name.
name | The name of the parameter to look for. |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::hasParameter().
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 158 of file AbstractParametrizable.h.
References bpp::ParameterList::includeParameters(), and bpp::AbstractParametrizable::parameters_.
Referenced by bpp::AbstractParameterAliasable::includeParameters_().
|
inlinevirtualinherited |
Update the parameters from parameters.
Only common parameters with parameters will be updated.
parameters | A list of parameters. |
ConstraintException | If a value in parameters does not match the constraint in the corresponding parameter in the list. |
Implements bpp::Parametrizable.
Definition at line 112 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareSubList().
Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::TestFunction::setParameters(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().
|
pure virtualinherited |
Update the parameters from parameters.
Only common parameters with parameters will be updated.
parameters | A list of parameters. |
ConstraintException | If a value in parameters does not match the constraint in the corresponding parameter in the list. |
Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.
Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().
|
inline |
Definition at line 187 of file LogsumHmmLikelihood.h.
References backLogLikelihood_, backLogLikelihoodUpToDate_, breakPoints_, bpp::Clonable::clone(), bpp::HmmEmissionProbabilities::clone(), d2LogLikelihood_, dLogLikelihood_, emissionProbabilities_, hiddenAlphabet_, logLik_, logLikelihood_, nbSites_, nbStates_, bpp::AbstractHmmLikelihood::operator=(), ownsPointers_, partialD2LogLikelihoods_, partialDLogLikelihoods_, partialLogLikelihoods_, bpp::HmmEmissionProbabilities::setHmmStateAlphabet(), bpp::HmmTransitionMatrix::setHmmStateAlphabet(), and transitionMatrix_.
|
inlineprotectedinherited |
Definition at line 180 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::reset().
Referenced by bpp::AbstractParameterAliasable::resetParameters_().
|
inlinevirtualinherited |
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 | A list with all parameters. |
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 94 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setAllParametersValues().
|
pure virtualinherited |
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 | A list with all parameters. |
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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.
Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().
|
inlinevirtual |
Implements bpp::HmmLikelihood.
Definition at line 249 of file LogsumHmmLikelihood.h.
References backLogLikelihoodUpToDate_, breakPoints_, and computeForward_().
|
virtual |
Set the namespace for the parameter names.
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. |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 101 of file LogsumHmmLikelihood.cpp.
References emissionProbabilities_, hiddenAlphabet_, bpp::AbstractParametrizable::setNamespace(), bpp::Parametrizable::setNamespace(), and transitionMatrix_.
|
inlinevirtual |
Set the point where the function must be computed.
parameters | The parameter set to pass to the function. |
Implements bpp::Function.
Definition at line 258 of file LogsumHmmLikelihood.h.
References bpp::AbstractParametrizable::setParametersValues().
|
inlinevirtualinherited |
Update the parameters from parameters.
parameters must be a subset of all parameters available.
parameters | A list containing all parameters to update. |
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 106 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setParametersValues().
Referenced by setParameters(), bpp::LowMemoryRescaledHmmLikelihood::setParameters(), and bpp::RescaledHmmLikelihood::setParameters().
|
pure virtualinherited |
Update the parameters from parameters.
parameters must be a subset of all parameters available.
parameters | A list containing all parameters to update. |
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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.
Referenced by fireParameterChanged(), bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().
|
inlinevirtualinherited |
Set the value of parameter with name name to be equal to value.
name | the name of the parameter to set. |
value | The value of the parameter. |
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 100 of file AbstractParametrizable.h.
References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, and bpp::ParameterList::setParameterValue().
|
pure virtualinherited |
Set the value of parameter with name name to be equal to value.
name | the name of the parameter to set. |
value | The value of the parameter. |
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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.
Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 148 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareParameter().
Referenced by bpp::AbstractParameterAliasable::shareParameter_().
|
inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 153 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareParameters().
Referenced by bpp::AbstractParameterAliasable::shareParameters_().
|
mutableprotected |
backward logLikelihood
backLogLikelihood_[i][j] corresponds to log(Pr(x_i+1...x_n | yi=j)), where the x are the observed states, and y the hidden states.
Definition at line 121 of file LogsumHmmLikelihood.h.
Referenced by computeBackward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), and operator=().
|
mutableprotected |
Definition at line 122 of file LogsumHmmLikelihood.h.
Referenced by computeBackward_(), fireParameterChanged(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), operator=(), and setBreakPoints().
|
protected |
Definition at line 124 of file LogsumHmmLikelihood.h.
Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getBreakPoints(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), operator=(), and setBreakPoints().
|
mutableprotectedinherited |
Definition at line 145 of file HmmLikelihood.h.
Referenced by computeD2Forward_(), bpp::RescaledHmmLikelihood::computeD2Forward_(), bpp::AbstractHmmLikelihood::getD2LogLikelihood(), bpp::AbstractHmmLikelihood::getSecondOrderDerivative(), and bpp::AbstractHmmLikelihood::operator=().
|
mutableprotected |
Definition at line 111 of file LogsumHmmLikelihood.h.
Referenced by computeD2Forward_(), and operator=().
|
mutableprotectedinherited |
Definition at line 146 of file HmmLikelihood.h.
Referenced by computeD2Forward_(), fireParameterChanged(), bpp::AbstractHmmLikelihood::getSecondOrderDerivative(), and bpp::AbstractHmmLikelihood::operator=().
|
mutableprotectedinherited |
Definition at line 142 of file HmmLikelihood.h.
Referenced by bpp::RescaledHmmLikelihood::computeD2Forward_(), computeDForward_(), bpp::RescaledHmmLikelihood::computeDForward_(), bpp::AbstractHmmLikelihood::getDLogLikelihood(), bpp::AbstractHmmLikelihood::getFirstOrderDerivative(), and bpp::AbstractHmmLikelihood::operator=().
|
mutableprotected |
The DLogLikelihood arrays.
dLogLikelihood_[i][j] corresponds to d(log(Pr(x1...xi, yi=j))), where the x are the observed states, and y the hidden states.
d2LogLikelihood_[i][j] corresponds to d2(log(Pr(x1...xi, yi=j))), where the x are the observed states, and y the hidden states.
Definition at line 108 of file LogsumHmmLikelihood.h.
Referenced by computeD2Forward_(), computeDForward_(), and operator=().
|
mutableprotectedinherited |
Definition at line 143 of file HmmLikelihood.h.
Referenced by fireParameterChanged(), bpp::AbstractHmmLikelihood::getFirstOrderDerivative(), and bpp::AbstractHmmLikelihood::operator=().
|
protected |
Definition at line 78 of file LogsumHmmLikelihood.h.
Referenced by computeD2Forward_(), computeDForward_(), fireParameterChanged(), getHmmEmissionProbabilities(), LogsumHmmLikelihood(), operator=(), setNamespace(), and ~LogsumHmmLikelihood().
|
protected |
The alphabet describing the hidden states.
Definition at line 76 of file LogsumHmmLikelihood.h.
Referenced by fireParameterChanged(), getHmmStateAlphabet(), LogsumHmmLikelihood(), operator=(), setNamespace(), and ~LogsumHmmLikelihood().
|
protected |
Definition at line 95 of file LogsumHmmLikelihood.h.
Referenced by computeForward_(), getLogLikelihood(), getValue(), and operator=().
|
protected |
The likelihood array.
logLikelihood_[i * nbStates_ + j] corresponds to log(Pr(x1...xi, yi=j)), where the x are the observed states, and y the hidden states.
Definition at line 93 of file LogsumHmmLikelihood.h.
Referenced by computeD2Forward_(), computeDForward_(), computeForward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), LogsumHmmLikelihood(), and operator=().
|
protected |
Definition at line 126 of file LogsumHmmLikelihood.h.
Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getHiddenStatesPosteriorProbabilities(), getLikelihoodForEachSite(), LogsumHmmLikelihood(), and operator=().
|
protected |
Definition at line 126 of file LogsumHmmLikelihood.h.
Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), getLikelihoodForASite(), getLikelihoodForEachSite(), LogsumHmmLikelihood(), and operator=().
|
protected |
Owns previous objects.
Definition at line 85 of file LogsumHmmLikelihood.h.
Referenced by LogsumHmmLikelihood(), operator=(), and ~LogsumHmmLikelihood().
|
privateinherited |
Definition at line 66 of file AbstractParametrizable.h.
Referenced by bpp::AbstractParametrizable::addParameter_(), bpp::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::deleteParameter_(), bpp::AbstractParametrizable::deleteParameters_(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::includeParameters_(), bpp::AbstractParametrizable::matchParametersValues(), bpp::AbstractParametrizable::resetParameters_(), bpp::AbstractParametrizable::setAllParametersValues(), bpp::AbstractParametrizable::setParametersValues(), bpp::AbstractParametrizable::setParameterValue(), bpp::AbstractParametrizable::shareParameter_(), and bpp::AbstractParametrizable::shareParameters_().
|
mutableprotected |
Definition at line 112 of file LogsumHmmLikelihood.h.
Referenced by computeD2Forward_(), getD2LogLikelihoodForASite(), and operator=().
|
mutableprotected |
Definition at line 109 of file LogsumHmmLikelihood.h.
Referenced by computeD2Forward_(), computeDForward_(), getDLogLikelihoodForASite(), and operator=().
|
protected |
Definition at line 94 of file LogsumHmmLikelihood.h.
Referenced by computeForward_(), getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), and operator=().
|
privateinherited |
Definition at line 67 of file AbstractParametrizable.h.
Referenced by bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), and bpp::AbstractParametrizable::setParameterValue().
|
protected |
Definition at line 77 of file LogsumHmmLikelihood.h.
Referenced by computeBackward_(), computeD2Forward_(), computeDForward_(), computeForward_(), fireParameterChanged(), getHmmTransitionMatrix(), LogsumHmmLikelihood(), operator=(), setNamespace(), and ~LogsumHmmLikelihood().