bpp-phyl
2.2.0
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#include <Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h>
Public Member Functions | |
AbstractWordFrequenciesSet (StateMap *stateMap, const std::string &prefix="", const std::string &name="") | |
AbstractWordFrequenciesSet * | clone () const =0 |
AbstractWordFrequenciesSet (const AbstractWordFrequenciesSet &af) | |
AbstractWordFrequenciesSet & | operator= (const AbstractWordFrequenciesSet &af) |
const WordAlphabet * | getAlphabet () const |
virtual | ~AbstractWordFrequenciesSet () |
size_t | getLength () const |
virtual const FrequenciesSet & | getFrequenciesSetForLetter (size_t i) const =0 |
virtual const StateMap & | getStateMap () const =0 |
virtual const std::vector< double > | getFrequencies () 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 |
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 | |
size_t | getSizeFromVector (const std::vector< FrequenciesSet *> &freqVector) |
std::vector< double > & | getFrequencies_ () |
double & | getFreq_ (size_t i) |
const double & | getFreq_ (size_t i) const |
void | setFrequencies_ (const std::vector< double > &frequencies) |
Definition at line 91 of file WordFrequenciesSet.h.
AbstractWordFrequenciesSet::AbstractWordFrequenciesSet | ( | StateMap * | stateMap, |
const std::string & | prefix = "" , |
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const std::string & | name = "" |
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Definition at line 61 of file WordFrequenciesSet.cpp.
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inline |
Definition at line 108 of file WordFrequenciesSet.h.
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virtual |
Definition at line 70 of file WordFrequenciesSet.cpp.
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pure virtual |
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inlinevirtual |
Reimplemented from bpp::AbstractFrequenciesSet.
Definition at line 118 of file WordFrequenciesSet.h.
References bpp::AbstractFrequenciesSet::getAlphabet().
Referenced by bpp::CodonFromIndependentFrequenciesSet::getAlphabet(), bpp::CodonFromUniqueFrequenciesSet::getAlphabet(), getLength(), bpp::WordFromIndependentFrequenciesSet::setFrequencies(), bpp::WordFromUniqueFrequenciesSet::setFrequencies(), bpp::WordFromIndependentFrequenciesSet::updateFrequencies(), and bpp::WordFromUniqueFrequenciesSet::updateFrequencies().
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pure virtualinherited |
Implemented in bpp::AbstractFrequenciesSet.
Referenced by bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel::setFreq().
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virtualinherited |
Implements bpp::FrequenciesSet.
Definition at line 79 of file FrequenciesSet.cpp.
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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().
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inlineprotectedinherited |
Definition at line 204 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::freq_.
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pure virtualinherited |
Implemented in bpp::AbstractFrequenciesSet.
Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet(), bpp::WordFromUniqueFrequenciesSet::updateFrequencies(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), bpp::WAG01::WAG01(), and bpp::BppOFrequenciesSetFormat::write().
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inlinevirtualinherited |
Implements bpp::FrequenciesSet.
Definition at line 174 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::freq_.
Referenced by bpp::MvaFrequenciesSet::updateFrequencies().
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inlineprotectedinherited |
Definition at line 202 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::freq_.
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pure virtualinherited |
@ brief Returns the n-th FrequenciesSet&
Implemented in bpp::WordFromUniqueFrequenciesSet, and bpp::WordFromIndependentFrequenciesSet.
Referenced by bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::getCodonsMulRate().
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virtual |
@ brief Return the length of the words
Implements bpp::WordFrequenciesSet.
Reimplemented in bpp::WordFromUniqueFrequenciesSet, and bpp::WordFromIndependentFrequenciesSet.
Definition at line 65 of file WordFrequenciesSet.cpp.
References getAlphabet().
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pure virtualinherited |
Implemented in bpp::AbstractFrequenciesSet.
Referenced by bpp::AbstractCodonFrequenciesSubstitutionModel::AbstractCodonFrequenciesSubstitutionModel(), bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel(), bpp::WordFromUniqueFrequenciesSet::getDescription(), bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(), bpp::BppOFrequenciesSetFormat::read(), and bpp::BppOFrequenciesSetFormat::write().
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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().
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pure virtualinherited |
Implemented in bpp::AbstractFrequenciesSet.
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inlinevirtualinherited |
Implements bpp::FrequenciesSet.
Definition at line 189 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::freq_.
Referenced by bpp::FixedFrequenciesSet::setFrequencies().
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protectedvirtual |
Implements bpp::WordFrequenciesSet.
Definition at line 48 of file WordFrequenciesSet.cpp.
Referenced by bpp::WordFromIndependentFrequenciesSet::WordFromIndependentFrequenciesSet().
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pure virtualinherited |
Implemented in bpp::AbstractFrequenciesSet.
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inlinevirtualinherited |
Implements bpp::FrequenciesSet.
Definition at line 172 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::stateMap_.
Referenced by bpp::FullPerAACodonFrequenciesSet::updateFrequencies().
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inlineinherited |
Definition at line 193 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::freq_.
Referenced by bpp::FullPerAACodonFrequenciesSet::updateFrequencies().
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inline |
Definition at line 111 of file WordFrequenciesSet.h.
References bpp::AbstractFrequenciesSet::operator=().
Referenced by bpp::WordFromIndependentFrequenciesSet::operator=(), and bpp::WordFromUniqueFrequenciesSet::operator=().
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pure virtualinherited |
Set the parameters in order to match a given set of frequencies.
frequencies | The set of frequencies to match. |
DimensionException | If the number of frequencies does not match the size of the alphabet. |
Exception | If 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().
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inlineprotectedinherited |
Definition at line 205 of file FrequenciesSet.h.
References bpp::AbstractFrequenciesSet::freq_.
Referenced by bpp::MarkovModulatedFrequenciesSet::fireParameterChanged(), bpp::MarkovModulatedFrequenciesSet::MarkovModulatedFrequenciesSet(), bpp::FullNucleotideFrequenciesSet::setFrequencies(), bpp::FixedFrequenciesSet::setFrequencies(), and bpp::MvaFrequenciesSet::updateFrequencies().
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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.
frequencies | The set of frequencies to match. |
Implemented in bpp::AbstractFrequenciesSet.
Referenced by bpp::BppOFrequenciesSetFormat::initialize_(), bpp::AbstractCodonFitnessSubstitutionModel::setFreq(), bpp::AbstractCodonFrequenciesSubstitutionModel::setFreq(), and bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::setFreq().
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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.
frequencies | The set of frequencies to match. |
Implements bpp::FrequenciesSet.
Definition at line 58 of file FrequenciesSet.cpp.
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staticinherited |
Definition at line 118 of file FrequenciesSet.h.
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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().