bpp-phyl
2.2.0
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Substitution models defined as a mixture of nested substitution models. More...
#include <Bpp/Phyl/Model/MixtureOfASubstitutionModel.h>
Public Member Functions | |
MixtureOfASubstitutionModel (const Alphabet *alpha, SubstitutionModel *model, std::map< std::string, DiscreteDistribution *> parametersDistributionsList, int ffrom=-1, int tto=-1) throw (Exception) | |
MixtureOfASubstitutionModel (const MixtureOfASubstitutionModel &) | |
MixtureOfASubstitutionModel & | operator= (const MixtureOfASubstitutionModel &) |
virtual | ~MixtureOfASubstitutionModel () |
MixtureOfASubstitutionModel * | clone () const |
std::string | getName () const |
Get the name of the model. More... | |
void | updateMatrices () |
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More... | |
Vint | getSubmodelNumbers (std::string &desc) const |
void | setFreq (std::map< int, double > &) |
sets the eq frequencies of the first nested model, and adapts the parameters at best to it (surely there is a better way to manage this). More... | |
const DiscreteDistribution * | getDistribution (std::string &parName) const |
returns the DiscreteDistribution associated with a given parameter name. More... | |
int | from () const |
Numbers of the states between which the substitution rates of all the submodels must be equal. If they are set to -1, this constraint does not exist among the submodels. More... | |
int | to () const |
virtual size_t | getNumberOfModels () const |
returns the number of models in the mixture More... | |
virtual const SubstitutionModel * | getNModel (size_t i) const |
Returns a specific model from the mixture. More... | |
virtual SubstitutionModel * | getNModel (size_t i) |
double | getNRate (size_t i) const |
Returns the rate of a specific model from the mixture. More... | |
virtual void | setRate (double rate) |
Set the rate of the model and the submodels. More... | |
virtual void | setVRates (const Vdouble &vd) |
Sets the rates of the submodels to be proportional to a given vector, with the constraint that the mean rate of the mixture equals rate_. More... | |
virtual void | normalizeVRates () |
Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_. More... | |
const std::vector< double > & | getVRates () const |
Returns the vector of all the rates of the mixture. More... | |
virtual double | getNProbability (size_t i) const |
Returns the probability of a specific model from the mixture. More... | |
virtual const std::vector< double > & | getProbabilities () const |
Returns the vector of probabilities. More... | |
virtual void | setNProbability (size_t i, double prob) |
Sets the probability of a specific model from the mixture. More... | |
double | Qij (size_t i, size_t j) const |
This function can not be applied here, so it is defined to prevent wrong usage. More... | |
virtual size_t | getNumberOfStates () const |
From SubstitutionModel interface. More... | |
virtual const Matrix< double > & | getPij_t (double t) const |
virtual const Matrix< double > & | getdPij_dt (double t) const |
virtual const Matrix< double > & | getd2Pij_dt2 (double t) const |
virtual const std::vector< int > & | getAlphabetStates () const =0 |
const std::vector< int > & | getAlphabetStates () const |
virtual const StateMap & | getStateMap () const =0 |
const StateMap & | getStateMap () const |
virtual std::vector< size_t > | getModelStates (int code) const =0 |
Get the state in the model corresponding to a particular state in the alphabet. More... | |
virtual std::vector< size_t > | getModelStates (const std::string &code) const =0 |
Get the state in the model corresponding to a particular state in the alphabet. More... | |
std::vector< size_t > | getModelStates (int code) const |
Get the state in the model corresponding to a particular state in the alphabet. More... | |
std::vector< size_t > | getModelStates (const std::string &code) const |
Get the state in the model corresponding to a particular state in the alphabet. More... | |
virtual int | getAlphabetStateAsInt (size_t index) const =0 |
int | getAlphabetStateAsInt (size_t index) const |
virtual std::string | getAlphabetStateAsChar (size_t index) const =0 |
std::string | getAlphabetStateAsChar (size_t index) const |
virtual double | freq (size_t i) const =0 |
virtual double | freq (size_t i) const |
virtual double | Pij_t (size_t i, size_t j, double t) const =0 |
virtual double | Pij_t (size_t i, size_t j, double t) const |
virtual double | dPij_dt (size_t i, size_t j, double t) const =0 |
virtual double | dPij_dt (size_t i, size_t j, double t) const |
virtual double | d2Pij_dt2 (size_t i, size_t j, double t) const =0 |
virtual double | d2Pij_dt2 (size_t i, size_t j, double t) const |
virtual const Vdouble & | getFrequencies () const =0 |
virtual const Vdouble & | getFrequencies () const |
virtual const Matrix< double > & | getGenerator () const =0 |
const Matrix< double > & | getGenerator () const |
virtual const Matrix< double > & | getExchangeabilityMatrix () const =0 |
const Matrix< double > & | getExchangeabilityMatrix () const |
virtual double | Sij (size_t i, size_t j) const =0 |
double | Sij (size_t i, size_t j) const |
virtual void | enableEigenDecomposition (bool yn)=0 |
Set if eigenValues and Vectors must be computed. More... | |
virtual bool | enableEigenDecomposition ()=0 |
Tell if eigenValues and Vectors must be computed. More... | |
void | enableEigenDecomposition (bool yn) |
Set if eigenValues and Vectors must be computed. More... | |
bool | enableEigenDecomposition () |
Tell if eigenValues and Vectors must be computed. More... | |
virtual const Vdouble & | getEigenValues () const =0 |
const Vdouble & | getEigenValues () const |
virtual const Vdouble & | getIEigenValues () const =0 |
const Vdouble & | getIEigenValues () const |
virtual bool | isDiagonalizable () const =0 |
bool | isDiagonalizable () const |
virtual bool | isNonSingular () const =0 |
bool | isNonSingular () const |
virtual const Matrix< double > & | getRowLeftEigenVectors () const =0 |
const Matrix< double > & | getRowLeftEigenVectors () const |
virtual const Matrix< double > & | getColumnRightEigenVectors () const =0 |
const Matrix< double > & | getColumnRightEigenVectors () const |
virtual const Alphabet * | getAlphabet () const =0 |
const Alphabet * | getAlphabet () const |
virtual double | getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException) |
double | getInitValue (size_t i, int state) const throw (IndexOutOfBoundsException, BadIntException) |
virtual double | getScale () const =0 |
Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More... | |
double | getScale () const |
Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More... | |
virtual void | setScale (double scale)=0 |
Multiplies the current generator by the given scale. More... | |
void | setScale (double scale) |
Multiplies the current generator by the given scale. More... | |
virtual double | getRate () const =0 |
Get the rate. More... | |
virtual double | getRate () const |
Get the rate. More... | |
virtual void | addRateParameter ()=0 |
void | addRateParameter () |
virtual void | setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0 |
Set equilibrium frequencies equal to the frequencies estimated from the data. More... | |
void | setFreqFromData (const SequenceContainer &data, double pseudoCount=0) |
Set equilibrium frequencies equal to the frequencies estimated from the data. More... | |
virtual const FrequenciesSet * | getFrequenciesSet () const |
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More... | |
virtual void | fireParameterChanged (const ParameterList ¶meters) |
Tells the model that a parameter value has changed. More... | |
Protected Attributes | |
std::vector< SubstitutionModel * > | modelsContainer_ |
vector of pointers to SubstitutionModels. More... | |
std::vector< double > | vProbas_ |
vector of the probabilities of the models More... | |
std::vector< double > | vRates_ |
vector of the rates of the models. More... | |
const Alphabet * | alphabet_ |
The alphabet relevant to this model. More... | |
std::auto_ptr< StateMap > | stateMap_ |
The map of model states with alphabet states. More... | |
size_t | size_ |
The size of the generator, i.e. the number of states. More... | |
double | rate_ |
The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More... | |
RowMatrix< double > | generator_ |
The generator matrix of the model. More... | |
Vdouble | freq_ |
The vector of equilibrium frequencies. More... | |
RowMatrix< double > | exchangeability_ |
The exchangeability matrix of the model, defined as . When the model is reversible, this matrix is symetric. More... | |
RowMatrix< double > | pijt_ |
These ones are for bookkeeping: More... | |
RowMatrix< double > | dpijt_ |
RowMatrix< double > | d2pijt_ |
bool | eigenDecompose_ |
Tell if the eigen decomposition should be performed. More... | |
Vdouble | eigenValues_ |
The vector of eigen values. More... | |
Vdouble | iEigenValues_ |
The vector of the imaginary part of the eigen values. More... | |
bool | isDiagonalizable_ |
boolean value for diagonalizability in R of the generator_ More... | |
RowMatrix< double > | rightEigenVectors_ |
The matrix made of right eigen vectors (by column). More... | |
bool | isNonSingular_ |
boolean value for non-singularity of rightEigenVectors_ More... | |
RowMatrix< double > | leftEigenVectors_ |
The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More... | |
std::vector< RowMatrix< double > > | vPowGen_ |
vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More... | |
RowMatrix< double > | tmpMat_ |
For computational issues. More... | |
Private Attributes | |
std::map< std::string, DiscreteDistribution * > | distributionMap_ |
int | from_ |
int | to_ |
Substitution models defined as a mixture of nested substitution models.
All the nested models are of the same type (for example T92 or GY94), and their parameter values can follow discrete distributions.
In this kind of model, there is no generator.
There is a map with connection from parameter names to discrete distributions, and then a related vector of "simple" substitution models for all the combinations of parameter values.
For example: HKY85(kappa=Gamma(n=3,alpha=2,beta=5), theta=TruncExponential(n=4,lambda=0.2,tp=1), theta1=0.4, theta2=TruncExponential(n=5,lambda=0.6,tp=1))
defines 3*4*5=60 different HKY85 nested models with rate one.
Optionnal arguments are used to homogeneize the rates of the nested models. Default values sets all the rates to 1, and given values are the two letters (from_ & to_) between which the substitution rates are the same in all nested models.
For example: HKY85(kappa=Gamma(n=3,alpha=2,beta=5), theta=TruncExponential(n=4,lambda=0.2,tp=1), theta1=0.4, theta2=TruncExponential(n=5,lambda=0.6,tp=1), from=A, to=C)
defines 3*4*5=60 different HKY85 nested models with the same A->C substitution rate.
If a distribution parameter does not respect the constraints of this parameter, there is an Exception at the creation of the wrong model, if any.
When used through a MixedTreeLikelihood objets, all the models have a specific probability, defined through the probabilities of the several parameter distributions. The computing of the likelihoods and probabilities are the expectation of the "simple" models values.
Definition at line 103 of file MixtureOfASubstitutionModel.h.
MixtureOfASubstitutionModel::MixtureOfASubstitutionModel | ( | const Alphabet * | alpha, |
SubstitutionModel * | model, | ||
std::map< std::string, DiscreteDistribution *> | parametersDistributionsList, | ||
int | ffrom = -1 , |
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int | tto = -1 |
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throw | ( | Exception | |
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Definition at line 51 of file MixtureOfASubstitutionModel.cpp.
Referenced by clone().
MixtureOfASubstitutionModel::MixtureOfASubstitutionModel | ( | const MixtureOfASubstitutionModel & | msm | ) |
Definition at line 139 of file MixtureOfASubstitutionModel.cpp.
References distributionMap_.
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virtual |
Definition at line 174 of file MixtureOfASubstitutionModel.cpp.
References distributionMap_.
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virtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 433 of file AbstractSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::rate_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.
Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter().
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inlinevirtual |
Implements bpp::AbstractMixedSubstitutionModel.
Definition at line 123 of file MixtureOfASubstitutionModel.h.
References MixtureOfASubstitutionModel().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Reimplemented in bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, and bpp::BinarySubstitutionModel.
Definition at line 281 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::getd2Pij_dt2().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Reimplemented in bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, and bpp::BinarySubstitutionModel.
Definition at line 280 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::getdPij_dt().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::dPij_dt().
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inlinevirtualinherited |
Set if eigenValues and Vectors must be computed.
Implements bpp::SubstitutionModel.
Definition at line 289 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::eigenDecompose_.
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inlinevirtualinherited |
Tell if eigenValues and Vectors must be computed.
Implements bpp::SubstitutionModel.
Definition at line 291 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::eigenDecompose_.
Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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pure virtualinherited |
Set if eigenValues and Vectors must be computed.
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), and bpp::YpR::YpR().
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pure virtualinherited |
Tell if eigenValues and Vectors must be computed.
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
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inlinevirtualinherited |
Tells the model that a parameter value has changed.
This updates the matrices consequently.
Reimplemented in bpp::JCprot, bpp::YpR, bpp::RE08, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::DSO78, bpp::JTT92, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::LG08, bpp::CodonDistanceSubstitutionModel, bpp::gBGC, bpp::CodonRateFrequenciesSubstitutionModel, and bpp::CodonRateSubstitutionModel.
Definition at line 298 of file AbstractSubstitutionModel.h.
References bpp::SubstitutionModel::getName(), and bpp::AbstractSubstitutionModel::updateMatrices().
Referenced by bpp::CodonRateSubstitutionModel::fireParameterChanged(), bpp::CodonRateFrequenciesSubstitutionModel::fireParameterChanged(), bpp::gBGC::fireParameterChanged(), bpp::CodonDistanceSubstitutionModel::fireParameterChanged(), bpp::LG08::fireParameterChanged(), bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), and bpp::JCprot::fireParameterChanged().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), and bpp::AbstractBiblioSubstitutionModel::freq().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 275 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::freq_.
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inline |
Numbers of the states between which the substitution rates of all the submodels must be equal. If they are set to -1, this constraint does not exist among the submodels.
Definition at line 164 of file MixtureOfASubstitutionModel.h.
References from_.
Referenced by bpp::BppOSubstitutionModelFormat::writeMixed_().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 237 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::alphabet_.
Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::AbstractWordSubstitutionModel::extractAlph(), bpp::AbstractWordSubstitutionModel::getNumberOfStates(), and bpp::AbstractWordSubstitutionModel::operator=().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AAExteriorSubstitutionRegister::AAExteriorSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::AAInteriorSubstitutionRegister(), bpp::SubstitutionModelSet::addModel(), bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::AbstractBiblioSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::DnDsSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setCategories(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::DecompositionReward::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().
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inlinevirtualinherited |
index | The model state. |
Implements bpp::SubstitutionModel.
Definition at line 243 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::stateMap_.
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pure virtualinherited |
index | The model state. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsChar(), bpp::TwoTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().
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inlinevirtualinherited |
index | The model state. |
Implements bpp::SubstitutionModel.
Definition at line 245 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::stateMap_.
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pure virtualinherited |
index | The model state. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsInt(), bpp::TwoTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::CategorySubstitutionRegister::getCategory(), bpp::SiteSimulationResult::getSite(), bpp::CategorySubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::DecompositionReward::computeBMatrice_(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractBiblioSubstitutionModel::getAlphabetStates(), bpp::TwoTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::SubstitutionModelSet::getAlphabetStates(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::CategorySubstitutionRegister::setCategories(), bpp::NaiveSubstitutionCount::setSubstitutionModel(), and bpp::LabelSubstitutionCount::setSubstitutionModel().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 241 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::stateMap_.
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 273 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::rightEigenVectors_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().
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virtualinherited |
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 170 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::d2pijt_, bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, and bpp::AbstractMixedSubstitutionModel::vProbas_.
const DiscreteDistribution * MixtureOfASubstitutionModel::getDistribution | ( | std::string & | parName | ) | const |
returns the DiscreteDistribution associated with a given parameter name.
parName | name of the parameter |
Definition at line 184 of file MixtureOfASubstitutionModel.cpp.
References distributionMap_.
Referenced by bpp::BppOSubstitutionModelFormat::writeMixed_().
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virtualinherited |
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 144 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::dpijt_, bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, and bpp::AbstractMixedSubstitutionModel::vProbas_.
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 263 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::eigenValues_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 255 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::exchangeability_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::Coala::Coala(), bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 251 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::freq_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().
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inlinevirtualinherited |
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::AbstractCodonFrequenciesSubstitutionModel.
Definition at line 479 of file SubstitutionModel.h.
Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().
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inlinevirtualinherited |
See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.
Implements bpp::SubstitutionModel.
Definition at line 253 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::generator_.
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pure virtualinherited |
See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 265 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::iEigenValues_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().
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virtualinherited |
This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.
i | the index of the state in the model. |
state | An observed state in the sequence/site. |
IndexOutOfBoundsException | if array position is out of range. |
BadIntException | if states are not allowed in the associated alphabet. |
Implements bpp::SubstitutionModel.
Reimplemented in bpp::RE08.
Definition at line 349 of file AbstractSubstitutionModel.cpp.
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pure virtualinherited |
This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.
i | the index of the state in the model. |
state | An observed state in the sequence/site. |
IndexOutOfBoundsException | if array position is out of range. |
BadIntException | if states are not allowed in the associated alphabet. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().
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pure virtualinherited |
Get the state in the model corresponding to a particular state in the alphabet.
code | The alphabet state to check. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::SubstitutionModelSet::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().
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pure virtualinherited |
Get the state in the model corresponding to a particular state in the alphabet.
code | The alphabet state to check. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
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inlinevirtualinherited |
Get the state in the model corresponding to a particular state in the alphabet.
code | The alphabet state to check. |
Implements bpp::SubstitutionModel.
Definition at line 247 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::stateMap_.
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inlinevirtualinherited |
Get the state in the model corresponding to a particular state in the alphabet.
code | The alphabet state to check. |
Implements bpp::SubstitutionModel.
Definition at line 249 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::stateMap_.
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inlinevirtual |
Get the name of the model.
Implements bpp::SubstitutionModel.
Definition at line 126 of file MixtureOfASubstitutionModel.h.
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inlinevirtualinherited |
Returns a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 122 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_.
Referenced by bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().
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inlinevirtualinherited |
Implements bpp::MixedSubstitutionModel.
Definition at line 127 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_.
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inlinevirtualinherited |
Returns the probability of a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 179 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::vProbas_.
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inlinevirtualinherited |
Returns the rate of a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 135 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::vRates_.
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inlinevirtualinherited |
returns the number of models in the mixture
Implements bpp::MixedSubstitutionModel.
Definition at line 114 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_.
Referenced by bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), and bpp::BppOSubstitutionModelFormat::writeMixed_().
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virtualinherited |
From SubstitutionModel interface.
Implements bpp::SubstitutionModel.
Definition at line 113 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_.
Referenced by bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getPij_t(), updateMatrices(), and bpp::MixtureOfSubstitutionModels::updateMatrices().
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virtualinherited |
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 118 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractSubstitutionModel::pijt_, and bpp::AbstractMixedSubstitutionModel::vProbas_.
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inlinevirtualinherited |
Returns the vector of probabilities.
Implements bpp::MixedSubstitutionModel.
Definition at line 189 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::vProbas_.
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virtualinherited |
Get the rate.
Implements bpp::SubstitutionModel.
Definition at line 415 of file AbstractSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::rate_.
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pure virtualinherited |
Get the rate.
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.
Referenced by bpp::AbstractBiblioSubstitutionModel::getRate(), and bpp::MarkovModulatedSubstitutionModel::getRate().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 271 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::leftEigenVectors_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().
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virtualinherited |
Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
Implements bpp::SubstitutionModel.
Definition at line 400 of file AbstractSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::freq_, and bpp::AbstractSubstitutionModel::generator_.
Referenced by bpp::AbstractReversibleSubstitutionModel::updateMatrices().
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pure virtualinherited |
Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getStateMap(), bpp::SubstitutionModelSet::getStateMap(), and bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 239 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::stateMap_.
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virtual |
Implements bpp::MixedSubstitutionModel.
Definition at line 279 of file MixtureOfASubstitutionModel.cpp.
References distributionMap_, and bpp::AbstractMixedSubstitutionModel::modelsContainer_.
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inlinevirtualinherited |
Returns the vector of all the rates of the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 170 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::vRates_.
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 267 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::isDiagonalizable_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::isDiagonalizable().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 269 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::isNonSingular_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::isNonSingular().
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virtualinherited |
Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.
Implements bpp::MixedSubstitutionModel.
Definition at line 229 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractMixedSubstitutionModel::vProbas_, and bpp::AbstractMixedSubstitutionModel::vRates_.
Referenced by bpp::AbstractMixedSubstitutionModel::setVRates().
MixtureOfASubstitutionModel & MixtureOfASubstitutionModel::operator= | ( | const MixtureOfASubstitutionModel & | msm | ) |
Definition at line 154 of file MixtureOfASubstitutionModel.cpp.
References distributionMap_, from_, bpp::AbstractMixedSubstitutionModel::operator=(), and to_.
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), and bpp::AbstractBiblioSubstitutionModel::Pij_t().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Reimplemented in bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, and bpp::BinarySubstitutionModel.
Definition at line 279 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::getPij_t().
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inlinevirtualinherited |
This function can not be applied here, so it is defined to prevent wrong usage.
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 207 of file AbstractMixedSubstitutionModel.h.
Referenced by updateMatrices().
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virtual |
sets the eq frequencies of the first nested model, and adapts the parameters at best to it (surely there is a better way to manage this).
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 273 of file MixtureOfASubstitutionModel.cpp.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_.
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virtualinherited |
Set equilibrium frequencies equal to the frequencies estimated from the data.
data | The sequences to use. |
pseudoCount | A quantity to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as
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Implements bpp::SubstitutionModel.
Reimplemented in bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, and bpp::Coala.
Definition at line 366 of file AbstractSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::setFreq(), and bpp::AbstractSubstitutionModel::size_.
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pure virtualinherited |
Set equilibrium frequencies equal to the frequencies estimated from the data.
data | The sequences to use. |
pseudoCount | A quantity to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as
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Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, and bpp::Coala.
Referenced by bpp::BppOSubstitutionModelFormat::read(), bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), and bpp::MarkovModulatedSubstitutionModel::setFreqFromData().
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inlinevirtualinherited |
Sets the probability of a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 197 of file AbstractMixedSubstitutionModel.h.
References bpp::AbstractMixedSubstitutionModel::vProbas_.
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virtualinherited |
Set the rate of the model and the submodels.
rate | must be positive. |
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 196 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractSubstitutionModel::rate_, bpp::AbstractSubstitutionModel::setRate(), bpp::AbstractMixedSubstitutionModel::vProbas_, and bpp::AbstractMixedSubstitutionModel::vRates_.
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virtualinherited |
Multiplies the current generator by the given scale.
scale | the scale by which the generator is multiplied. |
Implements bpp::SubstitutionModel.
Definition at line 409 of file AbstractSubstitutionModel.cpp.
References bpp::AbstractSubstitutionModel::generator_.
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pure virtualinherited |
Multiplies the current generator by the given scale.
scale | the scale by which the generator is multiplied. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().
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virtualinherited |
Sets the rates of the submodels to be proportional to a given vector, with the constraint that the mean rate of the mixture equals rate_.
vd | a vector of positive values such that the rates of the respective submodels are in the same proportions (ie this vector does not need to be normalized). |
Implements bpp::MixedSubstitutionModel.
Reimplemented in bpp::MixtureOfSubstitutionModels.
Definition at line 216 of file AbstractMixedSubstitutionModel.cpp.
References bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractMixedSubstitutionModel::normalizeVRates(), and bpp::AbstractMixedSubstitutionModel::vRates_.
Referenced by bpp::MixtureOfSubstitutionModels::setVRates(), and updateMatrices().
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inlinevirtualinherited |
By definition Sij(i,j) = Sij(j,i).
Implements bpp::SubstitutionModel.
Definition at line 257 of file AbstractSubstitutionModel.h.
References bpp::AbstractSubstitutionModel::exchangeability_.
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pure virtualinherited |
By definition Sij(i,j) = Sij(j,i).
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::Sij().
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inline |
Definition at line 165 of file MixtureOfASubstitutionModel.h.
References to_.
Referenced by bpp::BppOSubstitutionModelFormat::writeMixed_().
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virtual |
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.
The generator_ matrix and freq_ vector must be initialized.
Eigen values and vectors are computed from the generator and assigned to the eigenValues_ for the real part, iEigenValues_ for the imaginary part, rightEigenVectors_ and leftEigenVectors_ variables. isDiagonalizable_ checks if the generator_ is diagonalizable in R.
The optional rate parameter is not taken into account in this method to prevent unnecessary computation.
Reimplemented from bpp::AbstractSubstitutionModel.
Definition at line 192 of file MixtureOfASubstitutionModel.cpp.
References distributionMap_, bpp::AbstractSubstitutionModel::freq_, from_, bpp::AbstractMixedSubstitutionModel::getNModel(), bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::modelsContainer_, bpp::AbstractMixedSubstitutionModel::Qij(), bpp::AbstractMixedSubstitutionModel::setVRates(), to_, and bpp::AbstractMixedSubstitutionModel::vProbas_.
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protectedinherited |
The alphabet relevant to this model.
Definition at line 86 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractSubstitutionModel::getAlphabet(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), and bpp::AbstractWordSubstitutionModel::~AbstractWordSubstitutionModel().
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mutableprotectedinherited |
Definition at line 129 of file AbstractSubstitutionModel.h.
Referenced by bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), and bpp::AbstractSubstitutionModel::operator=().
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private |
Definition at line 107 of file MixtureOfASubstitutionModel.h.
Referenced by getDistribution(), getSubmodelNumbers(), MixtureOfASubstitutionModel(), operator=(), updateMatrices(), and ~MixtureOfASubstitutionModel().
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mutableprotectedinherited |
Definition at line 128 of file AbstractSubstitutionModel.h.
Referenced by bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractSubstitutionModel::operator=().
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protectedinherited |
Tell if the eigen decomposition should be performed.
Definition at line 134 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractSubstitutionModel::operator=().
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protectedinherited |
The vector of eigen values.
Definition at line 139 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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protectedinherited |
The exchangeability matrix of the model, defined as . When the model is reversible, this matrix is symetric.
Definition at line 122 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::Coala::Coala(), bpp::LGL08_CAT::EmbeddedModel::EmbeddedModel(), bpp::AbstractSubstitutionModel::getExchangeabilityMatrix(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::Coala::readFromFile(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::Sij(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::SSR::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().
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protectedinherited |
The vector of equilibrium frequencies.
Definition at line 113 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::Coala::computeEquilibriumFrequencies(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::DSO78::DSO78(), bpp::LG08::fireParameterChanged(), bpp::DSO78::fireParameterChanged(), bpp::JTT92::fireParameterChanged(), bpp::WAG01::fireParameterChanged(), bpp::UserProteinSubstitutionModel::fireParameterChanged(), bpp::JCprot::fireParameterChanged(), bpp::AbstractSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getFrequencies(), bpp::RN95s::getPij_t(), bpp::RE08::getPij_t(), bpp::RN95::getPij_t(), bpp::AbstractSubstitutionModel::getScale(), bpp::JCprot::JCprot(), bpp::JTT92::JTT92(), bpp::LG08::LG08(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::RE08::Pij_t(), bpp::RN95::Pij_t(), bpp::RE08::RE08(), bpp::UserProteinSubstitutionModel::readFromFile(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::L95::updateMatrices(), bpp::SSR::updateMatrices(), updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), bpp::YpR::updateMatrices(), bpp::GTR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::TN93::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), bpp::AbstractReversibleSubstitutionModel::updateMatrices(), bpp::UserProteinSubstitutionModel::UserProteinSubstitutionModel(), and bpp::WAG01::WAG01().
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private |
Definition at line 108 of file MixtureOfASubstitutionModel.h.
Referenced by from(), operator=(), and updateMatrices().
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protectedinherited |
The generator matrix of the model.
Definition at line 108 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractSubstitutionModel::getGenerator(), bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::Qij(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::L95::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::RE08::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().
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protectedinherited |
The vector of the imaginary part of the eigen values.
Definition at line 144 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getIEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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protectedinherited |
boolean value for diagonalizability in R of the generator_
Definition at line 150 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isDiagonalizable(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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protectedinherited |
boolean value for non-singularity of rightEigenVectors_
Definition at line 160 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isNonSingular(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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protectedinherited |
The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.
Definition at line 166 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRowLeftEigenVectors(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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protectedinherited |
vector of pointers to SubstitutionModels.
Beware: these SubstitutionModels are owned by the object, so will be deleted at destruction
Definition at line 78 of file AbstractMixedSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getNModel(), bpp::AbstractMixedSubstitutionModel::getNumberOfModels(), bpp::AbstractMixedSubstitutionModel::getNumberOfStates(), bpp::AbstractMixedSubstitutionModel::getPij_t(), getSubmodelNumbers(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractMixedSubstitutionModel::operator=(), setFreq(), bpp::MixtureOfSubstitutionModels::setFreq(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractMixedSubstitutionModel::setVRates(), bpp::MixtureOfSubstitutionModels::setVRates(), updateMatrices(), bpp::MixtureOfSubstitutionModels::updateMatrices(), and bpp::AbstractMixedSubstitutionModel::~AbstractMixedSubstitutionModel().
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These ones are for bookkeeping:
Definition at line 127 of file AbstractSubstitutionModel.h.
Referenced by bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractMixedSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), and bpp::AbstractSubstitutionModel::operator=().
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The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized.
Definition at line 103 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractSubstitutionModel::addRateParameter(), bpp::RN95s::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::RN95::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::RN95s::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::TN93::dPij_dt(), bpp::RN95::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::F84::dPij_dt(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::RN95s::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::RN95::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::RN95s::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::RN95::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::RN95s::getPij_t(), bpp::JCnuc::getPij_t(), bpp::TN93::getPij_t(), bpp::RN95::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::JCprot::getPij_t(), bpp::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getRate(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractSubstitutionModel::operator=(), bpp::RN95s::Pij_t(), bpp::JCnuc::Pij_t(), bpp::TN93::Pij_t(), bpp::RN95::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::JCprot::Pij_t(), bpp::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractSubstitutionModel::setRate(), and bpp::BinarySubstitutionModel::updateMatrices().
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The matrix made of right eigen vectors (by column).
Definition at line 155 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::getColumnRightEigenVectors(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::RE08(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::BinarySubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::TN93::updateMatrices(), bpp::RN95::updateMatrices(), bpp::JCnuc::updateMatrices(), bpp::K80::updateMatrices(), bpp::T92::updateMatrices(), bpp::HKY85::updateMatrices(), bpp::F84::updateMatrices(), bpp::JCprot::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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The size of the generator, i.e. the number of states.
Definition at line 96 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::JCnuc::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::RE08::getNumberOfStates(), bpp::JCnuc::getPij_t(), bpp::RE08::getPij_t(), bpp::JCprot::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setFreq(), bpp::LG08::setFreqFromData(), bpp::DSO78::setFreqFromData(), bpp::JTT92::setFreqFromData(), bpp::WAG01::setFreqFromData(), bpp::UserProteinSubstitutionModel::setFreqFromData(), bpp::JCprot::setFreqFromData(), bpp::AbstractSubstitutionModel::setFreqFromData(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), bpp::RE08::updateMatrices(), bpp::AbstractSubstitutionModel::updateMatrices(), and bpp::AbstractReversibleSubstitutionModel::updateMatrices().
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The map of model states with alphabet states.
Definition at line 91 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractSubstitutionModel::getAlphabetStateAsChar(), bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(), bpp::AbstractSubstitutionModel::getAlphabetStates(), bpp::AbstractSubstitutionModel::getModelStates(), bpp::AbstractSubstitutionModel::getStateMap(), and bpp::AbstractSubstitutionModel::operator=().
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mutableprotectedinherited |
For computational issues.
Definition at line 177 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), and bpp::YpR::updateMatrices().
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Definition at line 108 of file MixtureOfASubstitutionModel.h.
Referenced by operator=(), to(), and updateMatrices().
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vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).
Definition at line 172 of file AbstractSubstitutionModel.h.
Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::gBGC::updateMatrices(), bpp::RN95s::updateMatrices(), bpp::YpR::updateMatrices(), bpp::RN95::updateMatrices(), and bpp::AbstractSubstitutionModel::updateMatrices().
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vector of the probabilities of the models
Definition at line 83 of file AbstractMixedSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedSubstitutionModel::getdPij_dt(), bpp::AbstractMixedSubstitutionModel::getNProbability(), bpp::AbstractMixedSubstitutionModel::getPij_t(), bpp::AbstractMixedSubstitutionModel::getProbabilities(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractMixedSubstitutionModel::operator=(), bpp::AbstractMixedSubstitutionModel::setNProbability(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::MixtureOfSubstitutionModels::setVRates(), updateMatrices(), and bpp::MixtureOfSubstitutionModels::updateMatrices().
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vector of the rates of the models.
For the computation of the transition probabilities, the rates are included in the submodels while updating the mixture, so there is no need to multiply here the transition times with the rates.
The mean (on the distribution of the models) of the elements of this vector equals the overall rate of the mixture model, that is rate_;
Definition at line 97 of file AbstractMixedSubstitutionModel.h.
Referenced by bpp::AbstractMixedSubstitutionModel::AbstractMixedSubstitutionModel(), bpp::AbstractMixedSubstitutionModel::getNRate(), bpp::AbstractMixedSubstitutionModel::getVRates(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::AbstractMixedSubstitutionModel::normalizeVRates(), bpp::AbstractMixedSubstitutionModel::operator=(), bpp::AbstractMixedSubstitutionModel::setRate(), bpp::AbstractMixedSubstitutionModel::setVRates(), bpp::MixtureOfSubstitutionModels::setVRates(), and bpp::MixtureOfSubstitutionModels::updateMatrices().