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

Basic implementation of the FrequenciesSet interface. More...

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

+ Inheritance diagram for bpp::AbstractFrequenciesSet:
+ Collaboration diagram for bpp::AbstractFrequenciesSet:

Public Member Functions

 AbstractFrequenciesSet (StateMap *stateMap, const std::string &prefix, const std::string &name)
 
AbstractFrequenciesSet * clone () const =0
 
 AbstractFrequenciesSet (const AbstractFrequenciesSet &af)
 
AbstractFrequenciesSet & operator= (const AbstractFrequenciesSet &af)
 
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 ()
 
virtual void setFrequencies (const std::vector< double > &frequencies)=0
 Set the parameters in order to match a given set of frequencies. More...
 

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

const Alphabet * alphabet_
 
std::auto_ptr< StateMap > stateMap_
 
std::vector< double > freq_
 
std::string name_
 

Detailed Description

Basic implementation of the FrequenciesSet interface.

Definition at line 125 of file FrequenciesSet.h.

Constructor & Destructor Documentation

◆ AbstractFrequenciesSet() [1/2]

bpp::AbstractFrequenciesSet::AbstractFrequenciesSet ( StateMap *  stateMap,
const std::string &  prefix,
const std::string &  name 
)
inline

Definition at line 136 of file FrequenciesSet.h.

◆ AbstractFrequenciesSet() [2/2]

bpp::AbstractFrequenciesSet::AbstractFrequenciesSet ( const AbstractFrequenciesSet &  af)
inline

Definition at line 151 of file FrequenciesSet.h.

Member Function Documentation

◆ clone()

AbstractFrequenciesSet* bpp::AbstractFrequenciesSet::clone ( ) const
pure virtual

Implements bpp::FrequenciesSet.

Implemented in bpp::CodonFromUniqueFrequenciesSet, bpp::CodonFromIndependentFrequenciesSet, bpp::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::FullFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::FixedNucleotideFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::FixedProteinFrequenciesSet, bpp::AbstractWordFrequenciesSet, bpp::GCFrequenciesSet, bpp::FullProteinFrequenciesSet, and bpp::MvaFrequenciesSet.

◆ getAlphabet()

const Alphabet* bpp::AbstractFrequenciesSet::getAlphabet ( ) const
inlinevirtual
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 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
virtual
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)
inlineprotected

Definition at line 203 of file FrequenciesSet.h.

References 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
inlineprotected

Definition at line 204 of file FrequenciesSet.h.

References freq_.

◆ getFrequencies()

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

Implements bpp::FrequenciesSet.

Definition at line 174 of file FrequenciesSet.h.

References freq_.

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

◆ getFrequencies_()

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

Definition at line 202 of file FrequenciesSet.h.

References freq_.

◆ getName()

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

Implements bpp::FrequenciesSet.

Definition at line 191 of file FrequenciesSet.h.

References name_.

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

◆ getNumberOfFrequencies()

size_t bpp::AbstractFrequenciesSet::getNumberOfFrequencies ( ) const
inlinevirtual
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 freq_.

Referenced by bpp::FixedFrequenciesSet::setFrequencies().

◆ getStateMap()

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

Implements bpp::FrequenciesSet.

Definition at line 172 of file FrequenciesSet.h.

References stateMap_.

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

◆ normalize()

void bpp::AbstractFrequenciesSet::normalize ( )
inline

Definition at line 193 of file FrequenciesSet.h.

References freq_.

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

◆ operator=()

AbstractFrequenciesSet& bpp::AbstractFrequenciesSet::operator= ( const AbstractFrequenciesSet &  af)
inline

Definition at line 159 of file FrequenciesSet.h.

References alphabet_, freq_, name_, and stateMap_.

Referenced by bpp::MvaFrequenciesSet::operator=(), bpp::AbstractWordFrequenciesSet::operator=(), bpp::FullCodonFrequenciesSet::operator=(), bpp::FixedCodonFrequenciesSet::operator=(), bpp::MarkovModulatedFrequenciesSet::operator=(), and bpp::FullPerAACodonFrequenciesSet::operator=().

◆ setFrequencies()

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

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.

Implemented in bpp::FixedFrequenciesSet, bpp::FullPerAACodonFrequenciesSet, bpp::MarkovModulatedFrequenciesSet, bpp::FullFrequenciesSet, bpp::FixedCodonFrequenciesSet, bpp::WordFromUniqueFrequenciesSet, bpp::WordFromIndependentFrequenciesSet, bpp::FullNucleotideFrequenciesSet, bpp::FullCodonFrequenciesSet, bpp::MvaFrequenciesSet, and bpp::GCFrequenciesSet.

Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::BppOFrequenciesSetFormat::initialize_(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::LG08::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::WordFromUniqueFrequenciesSet::setFrequencies(), bpp::MarkovModulatedFrequenciesSet::setFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().

◆ setFrequencies_()

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

Definition at line 205 of file FrequenciesSet.h.

References freq_.

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

◆ setFrequenciesFromAlphabetStatesFrequencies()

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

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

◆ alphabet_

const Alphabet* bpp::AbstractFrequenciesSet::alphabet_
private

Definition at line 130 of file FrequenciesSet.h.

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

◆ freq_

std::vector<double> bpp::AbstractFrequenciesSet::freq_
private

Definition at line 132 of file FrequenciesSet.h.

Referenced by getFreq_(), getFrequencies(), getFrequencies_(), getNumberOfFrequencies(), normalize(), operator=(), and setFrequencies_().

◆ 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().

◆ name_

std::string bpp::AbstractFrequenciesSet::name_
private

Definition at line 133 of file FrequenciesSet.h.

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

◆ stateMap_

std::auto_ptr<StateMap> bpp::AbstractFrequenciesSet::stateMap_
private

Definition at line 131 of file FrequenciesSet.h.

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

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