bpp-phyl3 3.0.0
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bpp::NucleotideFrequencySetInterface Class Referenceabstract

Parametrize a set of state frequencies for nucleotides. More...

#include <Bpp/Phyl/Model/FrequencySet/NucleotideFrequencySet.h>

+ Inheritance diagram for bpp::NucleotideFrequencySetInterface:
+ Collaboration diagram for bpp::NucleotideFrequencySetInterface:

Public Member Functions

NucleotideFrequencySetInterfaceclone () const override=0
 
virtual std::shared_ptr< const NucleicAlphabetgetNucleicAlphabet () const =0
 
virtual std::shared_ptr< const AlphabetgetAlphabet () const =0
 
virtual const Alphabetalphabet () const =0
 
virtual const StateMapInterfacestateMap () const =0
 
virtual std::shared_ptr< const StateMapInterfacegetStateMap () const =0
 
virtual const VdoublegetFrequencies () const =0
 
virtual const std::map< int, double > getAlphabetStatesFrequencies () const =0
 
virtual void setFrequencies (const std::vector< double > &frequencies)=0
 Set the parameters in order to match a given set of frequencies. More...
 
virtual void setFrequenciesFromAlphabetStatesFrequencies (const std::map< int, double > &frequencies)=0
 Set the Frequencies from the one of the map which keys match with a letter of the Alphabet. The frequencies are normalized so that the matching values sum 1. More...
 
virtual std::string getName () const =0
 
virtual size_t getNumberOfFrequencies () const =0
 
virtual size_t getNumberOfIndependentParameters () const=0
 
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
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual const ParameterListgetIndependentParameters () const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual bool hasParameter (const std::string &name) const=0
 
virtual const ParameterListgetParameters () const=0
 
virtual const Parameterparameter (const std::string &name) const=0
 
virtual double getParameterValue (const std::string &name) const=0
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
virtual void setParameterValue (const std::string &name, double value)=0
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
virtual void removeConstraint (const std::string &name)=0
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
virtual size_t getNumberOfParameters () const=0
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 

Static Public Attributes

static std::shared_ptr< IntervalConstraintFREQUENCE_CONSTRAINT_SMALL
 
static std::shared_ptr< IntervalConstraintFREQUENCE_CONSTRAINT_MILLI
 
static std::shared_ptr< IntervalConstraintFREQUENCE_CONSTRAINT_CENTI
 

Protected Member Functions

virtual ParameterListgetParameters_ ()=0
 

Detailed Description

Parametrize a set of state frequencies for nucleotides.

Definition at line 17 of file NucleotideFrequencySet.h.

Member Function Documentation

◆ alphabet()

virtual const Alphabet & bpp::FrequencySetInterface::alphabet ( ) const
pure virtualinherited
Returns
The alphabet associated to this set.

Implemented in bpp::AbstractFrequencySet.

◆ clone()

NucleotideFrequencySetInterface * bpp::NucleotideFrequencySetInterface::clone ( ) const
overridepure virtual

◆ getAlphabet()

◆ getAlphabetStatesFrequencies()

virtual const std::map< int, double > bpp::FrequencySetInterface::getAlphabetStatesFrequencies ( ) const
pure virtualinherited
Returns
The frequencies of each alphabet states according to this model.

Implemented in bpp::AbstractFrequencySet.

◆ getFrequencies()

◆ getName()

virtual std::string bpp::FrequencySetInterface::getName ( ) const
pure virtualinherited

◆ getNucleicAlphabet()

virtual std::shared_ptr< const NucleicAlphabet > bpp::NucleotideFrequencySetInterface::getNucleicAlphabet ( ) const
pure virtual

◆ getNumberOfFrequencies()

virtual size_t bpp::FrequencySetInterface::getNumberOfFrequencies ( ) const
pure virtualinherited
Returns
The number of frequencies in the set. This is equivalent to getStateMap().getNumberOfModelStates().

Implemented in bpp::AbstractFrequencySet.

◆ getStateMap()

virtual std::shared_ptr< const StateMapInterface > bpp::FrequencySetInterface::getStateMap ( ) const
pure virtualinherited
Returns
A shared_ptr toward the mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequencySet.

◆ setFrequencies()

virtual void bpp::FrequencySetInterface::setFrequencies ( const std::vector< double > &  frequencies)
pure virtualinherited

◆ setFrequenciesFromAlphabetStatesFrequencies()

virtual void bpp::FrequencySetInterface::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > &  frequencies)
pure virtualinherited

Set the Frequencies from the one of the map which keys match with a letter of the Alphabet. The frequencies are normalized so that the matching values sum 1.

Parameters
frequenciesThe set of frequencies to match.

Implemented in bpp::AbstractFrequencySet.

Referenced by bpp::BppOFrequencySetFormat::initialize_().

◆ stateMap()

virtual const StateMapInterface & bpp::FrequencySetInterface::stateMap ( ) const
pure virtualinherited
Returns
The mapping of model states with alphabet states.

Implemented in bpp::AbstractFrequencySet.

Member Data Documentation

◆ FREQUENCE_CONSTRAINT_CENTI

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_CENTI
staticinherited

◆ FREQUENCE_CONSTRAINT_MILLI

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_MILLI
staticinherited

Definition at line 91 of file FrequencySet.h.

◆ FREQUENCE_CONSTRAINT_SMALL

std::shared_ptr< IntervalConstraint > FrequencySetInterface::FREQUENCE_CONSTRAINT_SMALL
staticinherited

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