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

FrequenciesSet to be used with a Markov-modulated substitution model. More...

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

+ Inheritance diagram for bpp::MarkovModulatedFrequenciesSet:
+ Collaboration diagram for bpp::MarkovModulatedFrequenciesSet:

Public Member Functions

 MarkovModulatedFrequenciesSet (FrequenciesSet *freqSet, const std::vector< double > &rateFreqs)
 
 MarkovModulatedFrequenciesSet (const MarkovModulatedFrequenciesSet &mmfs)
 
MarkovModulatedFrequenciesSet & operator= (const MarkovModulatedFrequenciesSet &mmfs)
 
MarkovModulatedFrequenciesSet * clone () const
 
virtual ~MarkovModulatedFrequenciesSet ()
 
void setFrequencies (const std::vector< double > &frequencies)
 Set the parameters in order to match a given set of frequencies. More...
 
void fireParameterChanged (const ParameterList &pl)
 
const FrequenciesSet & getStatesFrequenciesSet () const
 
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

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

Private Attributes

FrequenciesSet * freqSet_
 
std::vector< double > rateFreqs_
 

Detailed Description

FrequenciesSet to be used with a Markov-modulated substitution model.

This implementation uses one parameter per character state frequency. The rate states are assumed to be fixed and are passed as an argument to the constructor, together with a 'regular' FrequenciesSet. The number of parameters hence do not depends on the number of rates used.

Definition at line 260 of file FrequenciesSet.h.

Constructor & Destructor Documentation

◆ MarkovModulatedFrequenciesSet() [1/2]

MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet ( FrequenciesSet *  freqSet,
const std::vector< double > &  rateFreqs 
)

Definition at line 177 of file FrequenciesSet.cpp.

References freqSet_, bpp::FrequenciesSet::getFrequencies(), and bpp::AbstractFrequenciesSet::setFrequencies_().

Referenced by clone().

◆ MarkovModulatedFrequenciesSet() [2/2]

bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet ( const MarkovModulatedFrequenciesSet &  mmfs)
inline

Definition at line 270 of file FrequenciesSet.h.

◆ ~MarkovModulatedFrequenciesSet()

virtual bpp::MarkovModulatedFrequenciesSet::~MarkovModulatedFrequenciesSet ( )
inlinevirtual

Definition at line 286 of file FrequenciesSet.h.

References freqSet_.

Member Function Documentation

◆ clone()

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

Implements bpp::AbstractFrequenciesSet.

Definition at line 284 of file FrequenciesSet.h.

References MarkovModulatedFrequenciesSet().

◆ fireParameterChanged()

void bpp::MarkovModulatedFrequenciesSet::fireParameterChanged ( const ParameterList &  pl)
inline

Definition at line 295 of file FrequenciesSet.h.

References freqSet_, bpp::FrequenciesSet::getFrequencies(), rateFreqs_, and bpp::AbstractFrequenciesSet::setFrequencies_().

◆ 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(), bpp::FixedFrequenciesSet::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 bpp::FixedFrequenciesSet::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().

◆ getStatesFrequenciesSet()

const FrequenciesSet& bpp::MarkovModulatedFrequenciesSet::getStatesFrequenciesSet ( ) const
inline

Definition at line 301 of file FrequenciesSet.h.

References freqSet_.

◆ normalize()

void bpp::AbstractFrequenciesSet::normalize ( )
inlineinherited

Definition at line 193 of file FrequenciesSet.h.

References bpp::AbstractFrequenciesSet::freq_.

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

◆ operator=()

MarkovModulatedFrequenciesSet& bpp::MarkovModulatedFrequenciesSet::operator= ( const MarkovModulatedFrequenciesSet &  mmfs)
inline

Definition at line 276 of file FrequenciesSet.h.

References bpp::FrequenciesSet::clone(), freqSet_, bpp::AbstractFrequenciesSet::operator=(), and rateFreqs_.

◆ setFrequencies()

void bpp::MarkovModulatedFrequenciesSet::setFrequencies ( const std::vector< double > &  frequencies)
inlinevirtual

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 289 of file FrequenciesSet.h.

References freqSet_, and bpp::FrequenciesSet::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 fireParameterChanged(), MarkovModulatedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::setFrequencies(), bpp::FixedFrequenciesSet::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

◆ freqSet_

FrequenciesSet* bpp::MarkovModulatedFrequenciesSet::freqSet_
private

Definition at line 264 of file FrequenciesSet.h.

Referenced by fireParameterChanged(), getStatesFrequenciesSet(), MarkovModulatedFrequenciesSet(), operator=(), setFrequencies(), and ~MarkovModulatedFrequenciesSet().

◆ 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().

◆ rateFreqs_

std::vector<double> bpp::MarkovModulatedFrequenciesSet::rateFreqs_
private

Definition at line 265 of file FrequenciesSet.h.

Referenced by fireParameterChanged(), and operator=().

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