bpp-phyl  2.2.0
Public Member Functions | Static Public Attributes | Protected Member Functions | List of all members
bpp::FixedFrequenciesSet Class Reference

FrequenciesSet useful for homogeneous and stationary models. More...

#include <Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h>

+ Inheritance diagram for bpp::FixedFrequenciesSet:
+ Collaboration diagram for bpp::FixedFrequenciesSet:

Public Member Functions

 FixedFrequenciesSet (StateMap *stateMap, const std::vector< double > &initFreqs, const std::string &name="Fixed") throw (Exception)
 Construction with user-defined frequencies on the states of the model. More...
 
 FixedFrequenciesSet (StateMap *stateMap, const std::string &name="Fixed")
 Construction with uniform frequencies on the states of the model. More...
 
FixedFrequenciesSet * clone () const
 
void setFrequencies (const std::vector< double > &frequencies)
 Set the parameters in order to match a given set of frequencies. More...
 
const Alphabet * getAlphabet () const
 
const StateMap & getStateMap () const
 
const std::vector< double > getFrequencies () const
 
const std::map< int, double > getAlphabetStatesFrequencies () const
 
void setFrequenciesFromAlphabetStatesFrequencies (const std::map< int, double > &frequencies)
 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...
 
size_t getNumberOfFrequencies () const
 
std::string getName () const
 
void normalize ()
 

Static Public Attributes

static IntervalConstraint FREQUENCE_CONSTRAINT_SMALL
 
static IntervalConstraint FREQUENCE_CONSTRAINT_MILLI
 

Protected Member Functions

void fireParameterChanged (const ParameterList &parameters)
 
std::vector< double > & getFrequencies_ ()
 
double & getFreq_ (size_t i)
 
const double & getFreq_ (size_t i) const
 
void setFrequencies_ (const std::vector< double > &frequencies)
 

Detailed Description

FrequenciesSet useful for homogeneous and stationary models.

This set contains no parameter.

Definition at line 311 of file FrequenciesSet.h.

Constructor & Destructor Documentation

◆ FixedFrequenciesSet() [1/2]

FixedFrequenciesSet::FixedFrequenciesSet ( StateMap *  stateMap,
const std::vector< double > &  initFreqs,
const std::string &  name = "Fixed" 
)
throw (Exception
)

Construction with user-defined frequencies on the states of the model.

Parameters
stateMapThe model states for which frequencies should be built.
initFreqsThe frequencies to use. The size of the vector should match the number of model states.
nameThe name of the set.
Exceptions
ExceptionIn case the number of frequencies does not match the number of model states.

Definition at line 145 of file FrequenciesSet.cpp.

Referenced by clone().

◆ FixedFrequenciesSet() [2/2]

FixedFrequenciesSet::FixedFrequenciesSet ( StateMap *  stateMap,
const std::string &  name = "Fixed" 
)

Construction with uniform frequencies on the states of the model.

Parameters
stateMapThe model states for which frequencies should be built.
nameThe name of the set.

Definition at line 153 of file FrequenciesSet.cpp.

References bpp::AbstractFrequenciesSet::getFreq_(), and bpp::StateMap::getNumberOfModelStates().

Member Function Documentation

◆ clone()

FixedFrequenciesSet* bpp::FixedFrequenciesSet::clone ( ) const
inlinevirtual

Implements bpp::AbstractFrequenciesSet.

Reimplemented in bpp::FixedNucleotideFrequenciesSet, and bpp::FixedProteinFrequenciesSet.

Definition at line 334 of file FrequenciesSet.h.

References FixedFrequenciesSet().

◆ fireParameterChanged()

void bpp::FixedFrequenciesSet::fireParameterChanged ( const ParameterList &  parameters)
inlineprotected

Definition at line 340 of file FrequenciesSet.h.

◆ getAlphabet()

const Alphabet* bpp::AbstractFrequenciesSet::getAlphabet ( ) const
inlinevirtualinherited
Returns
The alphabet associated to this set.

Implements bpp::FrequenciesSet.

Reimplemented in bpp::FixedNucleotideFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FixedProteinFrequenciesSet, bpp::AbstractWordFrequenciesSet, bpp::MvaFrequenciesSet, bpp::GCFrequenciesSet, and bpp::FullProteinFrequenciesSet.

Definition at line 170 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::alphabet_.

Referenced by bpp::FullProteinFrequenciesSet::getAlphabet(), bpp::GCFrequenciesSet::getAlphabet(), bpp::MvaFrequenciesSet::getAlphabet(), bpp::AbstractWordFrequenciesSet::getAlphabet(), bpp::FixedProteinFrequenciesSet::getAlphabet(), bpp::FullNucleotideFrequenciesSet::getAlphabet(), bpp::FullCodonFrequenciesSet::getAlphabet(), bpp::FixedNucleotideFrequenciesSet::getAlphabet(), bpp::FixedCodonFrequenciesSet::getAlphabet(), bpp::FullPerAACodonFrequenciesSet::getAlphabet(), and bpp::FullFrequenciesSet::updateFreq_().

◆ getAlphabetStatesFrequencies()

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

Implements bpp::FrequenciesSet.

Definition at line 79 of file FrequenciesSet.cpp.

◆ getFreq_() [1/2]

double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t  i)
inlineprotectedinherited

Definition at line 203 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::GCFrequenciesSet::fireParameterChanged(), bpp::FullNucleotideFrequenciesSet::fireParameterChanged(), bpp::FixedCodonFrequenciesSet::FixedCodonFrequenciesSet(), FixedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::GCFrequenciesSet::GCFrequenciesSet(), bpp::GCFrequenciesSet::setFrequencies(), bpp::FixedCodonFrequenciesSet::setFrequencies(), bpp::FullCodonFrequenciesSet::updateFreq_(), bpp::FullFrequenciesSet::updateFreq_(), bpp::MvaFrequenciesSet::updateFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::FullPerAACodonFrequenciesSet::updateFrequencies(), bpp::CodonFromIndependentFrequenciesSet::updateFrequencies(), and bpp::CodonFromUniqueFrequenciesSet::updateFrequencies().

◆ getFreq_() [2/2]

const double& bpp::AbstractFrequenciesSet::getFreq_ ( size_t  i) const
inlineprotectedinherited

Definition at line 204 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getFrequencies()

const std::vector<double> bpp::AbstractFrequenciesSet::getFrequencies ( ) const
inlinevirtualinherited
Returns
The frequencies values of the set.

Implements bpp::FrequenciesSet.

Definition at line 174 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::MvaFrequenciesSet::updateFrequencies().

◆ getFrequencies_()

std::vector<double>& bpp::AbstractFrequenciesSet::getFrequencies_ ( )
inlineprotectedinherited

Definition at line 202 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

◆ getName()

std::string bpp::AbstractFrequenciesSet::getName ( ) const
inlinevirtualinherited

Implements bpp::FrequenciesSet.

Definition at line 191 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::name_.

Referenced by bpp::WordFromIndependentFrequenciesSet::getDescription(), and bpp::WordFromUniqueFrequenciesSet::getDescription().

◆ getNumberOfFrequencies()

size_t bpp::AbstractFrequenciesSet::getNumberOfFrequencies ( ) const
inlinevirtualinherited
Returns
The number of frequencies in the set. This is equivalent to getStateMap().getNumberOfModelStates().

Implements bpp::FrequenciesSet.

Definition at line 189 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by setFrequencies().

◆ getStateMap()

const StateMap& bpp::AbstractFrequenciesSet::getStateMap ( ) const
inlinevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::FrequenciesSet.

Definition at line 172 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::stateMap_.

Referenced by bpp::FullPerAACodonFrequenciesSet::updateFrequencies().

◆ normalize()

void bpp::AbstractFrequenciesSet::normalize ( )
inlineinherited

Definition at line 193 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::FullPerAACodonFrequenciesSet::updateFrequencies().

◆ setFrequencies()

void FixedFrequenciesSet::setFrequencies ( const std::vector< double > &  frequencies)
virtual

Set the parameters in order to match a given set of frequencies.

Parameters
frequenciesThe set of frequencies to match.
Exceptions
DimensionExceptionIf the number of frequencies does not match the size of the alphabet.
ExceptionIf the frequencies do not sum to 1.

Implements bpp::FrequenciesSet.

Definition at line 163 of file FrequenciesSet.cpp.

References bpp::AbstractFrequenciesSet::getNumberOfFrequencies(), and bpp::AbstractFrequenciesSet::setFrequencies_().

◆ setFrequencies_()

void bpp::AbstractFrequenciesSet::setFrequencies_ ( const std::vector< double > &  frequencies)
inlineprotectedinherited

Definition at line 205 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

Referenced by bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::setFrequencies(), setFrequencies(), and bpp::MvaFrequenciesSet::updateFrequencies().

◆ setFrequenciesFromAlphabetStatesFrequencies()

void AbstractFrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies ( const std::map< int, double > &  frequencies)
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.

In this implementation, all model states with the same alphabet state are given the same frequency.

Parameters
frequenciesThe set of frequencies to match.

Implements bpp::FrequenciesSet.

Definition at line 58 of file FrequenciesSet.cpp.

Member Data Documentation

◆ FREQUENCE_CONSTRAINT_MILLI

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_MILLI
staticinherited

Definition at line 118 of file FrequenciesSet.h.

◆ FREQUENCE_CONSTRAINT_SMALL

IntervalConstraint FrequenciesSet::FREQUENCE_CONSTRAINT_SMALL
staticinherited

Definition at line 117 of file FrequenciesSet.h.

Referenced by bpp::F84::F84(), bpp::FullNucleotideFrequenciesSet::FullNucleotideFrequenciesSet(), bpp::GTR::GTR(), bpp::HKY85::HKY85(), bpp::T92::T92(), and bpp::TN93::TN93().

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