bpp-phyl
2.2.0
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The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
#include <Bpp/Phyl/Model/Codon/YNGKP_M1.h>
Public Member Functions | |
YNGKP_M1 (const GeneticCode *gc, FrequenciesSet *codonFreqs) | |
virtual | ~YNGKP_M1 () |
YNGKP_M1 * | clone () const |
YNGKP_M1 (const YNGKP_M1 &) | |
YNGKP_M1 & | operator= (const YNGKP_M1 &) |
const SubstitutionModel & | getModel () const |
const MixedSubstitutionModel & | getMixedModel () const |
std::string | getName () const |
Get the name of the model. More... | |
const SubstitutionModel * | getNModel (size_t i) const |
Returns a specific model from the mixture. More... | |
SubstitutionModel * | getNModel (size_t i) |
double | getNProbability (size_t i) const |
Returns the probability of a specific model from the mixture. More... | |
const std::vector< double > & | getProbabilities () const |
Returns the vector of the probabilities of the submodels of the mixture. More... | |
void | setNProbability (size_t i, double prob) |
Sets the probabilities of the submodels of the mixture. More... | |
size_t | getNumberOfModels () const |
Returns the number of submodels. More... | |
void | setVRates (const Vdouble &vd) |
sets the rates of the submodels. More... | |
void | normalizeVRates () |
normalizes the rates of the submodels. More... | |
const std::vector< double > & | getVRates () const |
Returns the vector of all the rates of the mixture. More... | |
double | getNRate (size_t i) const |
Returns the rate of a specific model from the mixture. More... | |
Vint | getSubmodelNumbers (std::string &desc) 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 i) const |
virtual std::string | getAlphabetStateAsChar (size_t index) const =0 |
std::string | getAlphabetStateAsChar (size_t i) const |
virtual double | freq (size_t i) const =0 |
virtual double | freq (size_t i) const |
virtual double | Qij (size_t i, size_t j) const =0 |
virtual double | Qij (size_t i, size_t j) 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 const Matrix< double > & | getPij_t (double t) const =0 |
const Matrix< double > & | getPij_t (double t) const |
virtual const Matrix< double > & | getdPij_dt (double t) const =0 |
const Matrix< double > & | getdPij_dt (double t) const |
virtual const Matrix< double > & | getd2Pij_dt2 (double t) const =0 |
const Matrix< double > & | getd2Pij_dt2 (double t) 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 size_t | getNumberOfStates () const =0 |
Get the number of states. More... | |
size_t | getNumberOfStates () const |
Get the number of states. More... | |
virtual double | getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException) |
double | getInitValue (size_t i, int state) const throw (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... | |
double | getRate () const |
Get the rate. More... | |
virtual void | setRate (double rate)=0 |
Set the rate of the model (must be positive). More... | |
void | setRate (double rate) |
Set the rate of the model (must be positive). 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 void | setFreq (std::map< int, double > &frequencies) |
Set equilibrium frequencies. More... | |
void | setFreq (std::map< int, double > &frequ) |
Set equilibrium frequencies. More... | |
virtual void | fireParameterChanged (const ParameterList ¶meters) |
Tells the model that a parameter value has changed. More... | |
Protected Member Functions | |
void | updateMatrices () |
Protected Attributes | |
std::map< std::string, std::string > | mapParNamesFromPmodel_ |
Tools to make the link between the Parameters of the object and those of pmixmodel_. More... | |
ParameterList | lParPmodel_ |
Private Member Functions | |
SubstitutionModel & | getModel () |
MixedSubstitutionModel & | getMixedModel () |
const FrequenciesSet * | getFrequenciesSet () const |
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More... | |
Private Attributes | |
std::auto_ptr< MixtureOfASubstitutionModel > | pmixmodel_ |
size_t | synfrom_ |
indexes of 2 codons states between which the substitution is synonymous, to set a basis to the homogeneization of the rates. More... | |
size_t | synto_ |
The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004).
This model is a mixture of models as described in YN98 class, the mixture being defined on the selection parameter to allow it to vary among sites. A site is either negatively selected (with probability ), or neutral ( ) with probability .
The synonymous rates must be the same between both models, so the overall rates of the models are modified to respect this constraint and such that the mean rate of the mixed model equals one.
This model includes 3 parameters ( , and ). The codon frequencies are either observed or infered.
References:
Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000) Genetics 155:431-449.
Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. (2004) Genetics 168:1041–1051.
Definition at line 79 of file YNGKP_M1.h.
YNGKP_M1::YNGKP_M1 | ( | const GeneticCode * | gc, |
FrequenciesSet * | codonFreqs | ||
) |
Definition at line 51 of file YNGKP_M1.cpp.
References bpp::AbstractBiblioSubstitutionModel::getAlphabetStates(), getFrequenciesSet(), bpp::AbstractBiblioSubstitutionModel::lParPmodel_, bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, pmixmodel_, synfrom_, synto_, and updateMatrices().
Referenced by clone().
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virtual |
Definition at line 142 of file YNGKP_M1.cpp.
YNGKP_M1::YNGKP_M1 | ( | const YNGKP_M1 & | mod2 | ) |
Definition at line 125 of file YNGKP_M1.cpp.
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virtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 84 of file AbstractBiblioSubstitutionModel.cpp.
References bpp::SubstitutionModel::addRateParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractBiblioSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::lParPmodel_, and bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_.
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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::AbstractBiblioMixedSubstitutionModel.
Definition at line 99 of file YNGKP_M1.h.
References YNGKP_M1().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 112 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::d2Pij_dt2(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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.
Definition at line 111 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::dPij_dt(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 128 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::enableEigenDecomposition(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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inlinevirtualinherited |
Tell if eigenValues and Vectors must be computed.
Implements bpp::SubstitutionModel.
Definition at line 130 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::enableEigenDecomposition(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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.
Definition at line 177 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::updateMatrices().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 106 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::freq(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 153 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getAlphabet(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 100 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getAlphabetStateAsChar(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 98 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 94 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getAlphabetStates(), and bpp::AbstractBiblioSubstitutionModel::getModel().
Referenced by YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().
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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 141 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getColumnRightEigenVectors(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 126 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getd2Pij_dt2(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 124 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getdPij_dt(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioSubstitutionModel::getdPij_dt().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 136 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getEigenValues(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 118 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getExchangeabilityMatrix(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 114 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getFrequencies(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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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inlineprivatevirtual |
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
Reimplemented from bpp::AbstractBiblioSubstitutionModel.
Definition at line 120 of file YNGKP_M1.h.
References pmixmodel_.
Referenced by YNGKP_M1().
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inlinevirtualinherited |
See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.
Implements bpp::SubstitutionModel.
Definition at line 116 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getGenerator(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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 138 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getIEigenValues(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().
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inlinevirtualinherited |
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.
Definition at line 157 of file AbstractBiblioSubstitutionModel.h.
References bpp::SubstitutionModel::getInitValue(), and bpp::AbstractBiblioSubstitutionModel::getModel().
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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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inlinevirtual |
Implements bpp::AbstractBiblioMixedSubstitutionModel.
Definition at line 111 of file YNGKP_M1.h.
References pmixmodel_.
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inlineprivatevirtual |
Implements bpp::AbstractBiblioMixedSubstitutionModel.
Definition at line 118 of file YNGKP_M1.h.
References pmixmodel_.
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inlinevirtual |
Implements bpp::AbstractBiblioSubstitutionModel.
Definition at line 109 of file YNGKP_M1.h.
References pmixmodel_.
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inlineprivatevirtual |
Implements bpp::AbstractBiblioSubstitutionModel.
Definition at line 116 of file YNGKP_M1.h.
References pmixmodel_.
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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 102 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getModelStates().
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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 104 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getModelStates().
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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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inlinevirtual |
Get the name of the model.
Implements bpp::SubstitutionModel.
Definition at line 113 of file YNGKP_M1.h.
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inlinevirtualinherited |
Returns a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 78 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNModel().
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inlinevirtualinherited |
Implements bpp::MixedSubstitutionModel.
Definition at line 83 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNModel().
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inlinevirtualinherited |
Returns the probability of a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 91 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNProbability().
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inlinevirtualinherited |
Returns the rate of a specific model from the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 155 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNRate().
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inlinevirtualinherited |
Returns the number of submodels.
Implements bpp::MixedSubstitutionModel.
Definition at line 120 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getNumberOfModels().
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inlinevirtualinherited |
Get the number of states.
For most models, this equals the size of the alphabet.
Implements bpp::SubstitutionModel.
Definition at line 155 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getNumberOfStates().
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pure virtualinherited |
Get the number of states.
For most models, this equals the size of the alphabet.
Implemented in bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.
Referenced by bpp::SubstitutionModelSet::addModel(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::TwoTreeLikelihood::getNumberOfStates(), bpp::AbstractBiblioSubstitutionModel::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 122 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getPij_t().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.
Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionReward::computeRewards_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), and bpp::AbstractBiblioSubstitutionModel::getPij_t().
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inlinevirtualinherited |
Returns the vector of the probabilities of the submodels of the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 102 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getProbabilities().
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inlinevirtualinherited |
Get the rate.
Implements bpp::SubstitutionModel.
Definition at line 143 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getRate().
Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), and bpp::LLG08_UL3::LLG08_UL3().
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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 140 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getRowLeftEigenVectors().
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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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inlinevirtualinherited |
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 190 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getScale().
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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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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 96 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::getStateMap().
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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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virtualinherited |
Implements bpp::MixedSubstitutionModel.
Definition at line 62 of file AbstractBiblioMixedSubstitutionModel.cpp.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getSubmodelNumbers().
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inlinevirtualinherited |
Returns the vector of all the rates of the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 147 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::getVRates().
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 132 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::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 134 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::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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inlinevirtualinherited |
normalizes the rates of the submodels.
Implements bpp::MixedSubstitutionModel.
Definition at line 138 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::normalizeVRates().
Definition at line 131 of file YNGKP_M1.cpp.
References bpp::AbstractBiblioSubstitutionModel::operator=(), pmixmodel_, synfrom_, and synto_.
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inlinevirtualinherited |
Implements bpp::SubstitutionModel.
Definition at line 110 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Pij_t().
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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.
Definition at line 108 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Qij().
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pure virtualinherited |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.
Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), and bpp::YpR::updateMatrices().
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virtualinherited |
Set equilibrium frequencies.
frequencies | The map of the frequencies to use. |
Reimplemented from bpp::SubstitutionModel.
Definition at line 95 of file AbstractBiblioSubstitutionModel.cpp.
References bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, and bpp::SubstitutionModel::setFreq().
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inlinevirtualinherited |
Set equilibrium frequencies.
frequencies | The map of the frequencies to use. |
Reimplemented in bpp::AbstractSubstitutionModel, bpp::F84, bpp::HKY85, bpp::T92, bpp::MixtureOfSubstitutionModels, bpp::AbstractWordSubstitutionModel, bpp::GTR, bpp::RN95, bpp::TN93, bpp::RN95s, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::BinarySubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::SSR, bpp::L95, bpp::CodonRateFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, and bpp::AbstractCodonFitnessSubstitutionModel.
Definition at line 473 of file SubstitutionModel.h.
Referenced by bpp::AbstractBiblioSubstitutionModel::setFreq().
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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.
Definition at line 110 of file AbstractBiblioSubstitutionModel.cpp.
References bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, and bpp::SubstitutionModel::setFreqFromData().
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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 probabilities of the submodels of the mixture.
Implements bpp::MixedSubstitutionModel.
Definition at line 111 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::setNProbability().
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inlinevirtualinherited |
Set the rate of the model (must be positive).
rate | must be positive. |
Implements bpp::SubstitutionModel.
Definition at line 145 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::setRate().
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pure virtualinherited |
Set the rate of the model (must be positive).
rate | must be positive. |
Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, and bpp::TS98.
Referenced by bpp::AbstractBiblioSubstitutionModel::setRate(), and bpp::MarkovModulatedSubstitutionModel::setRate().
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inlinevirtualinherited |
Multiplies the current generator by the given scale.
scale | the scale by which the generator is multiplied. |
Implements bpp::SubstitutionModel.
Definition at line 192 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::setScale().
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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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inlinevirtualinherited |
sets the rates of the submodels.
Implements bpp::MixedSubstitutionModel.
Definition at line 129 of file AbstractBiblioMixedSubstitutionModel.h.
References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), and bpp::MixedSubstitutionModel::setVRates().
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inlinevirtualinherited |
By definition Sij(i,j) = Sij(j,i).
Implements bpp::SubstitutionModel.
Definition at line 120 of file AbstractBiblioSubstitutionModel.h.
References bpp::AbstractBiblioSubstitutionModel::getModel(), and bpp::SubstitutionModel::Sij().
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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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protectedvirtual |
Reimplemented from bpp::AbstractBiblioSubstitutionModel.
Definition at line 144 of file YNGKP_M1.cpp.
References pmixmodel_, synfrom_, synto_, and bpp::AbstractBiblioSubstitutionModel::updateMatrices().
Referenced by YNGKP_M1().
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protectedinherited |
Definition at line 70 of file AbstractBiblioSubstitutionModel.h.
Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::GY94::GY94(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::YNGKP_M3::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), bpp::YN98::YN98(), YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().
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protectedinherited |
Tools to make the link between the Parameters of the object and those of pmixmodel_.
Definition at line 68 of file AbstractBiblioSubstitutionModel.h.
Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::GY94::GY94(), bpp::LG10_EX_EHO::LG10_EX_EHO(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), bpp::LLG08_UL3::LLG08_UL3(), bpp::MG94::MG94(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioSubstitutionModel::setFreq(), bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), bpp::YNGKP_M3::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), bpp::YN98::YN98(), YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().
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private |
Definition at line 84 of file YNGKP_M1.h.
Referenced by getFrequenciesSet(), getMixedModel(), getModel(), operator=(), updateMatrices(), and YNGKP_M1().
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private |
indexes of 2 codons states between which the substitution is synonymous, to set a basis to the homogeneization of the rates.
Definition at line 92 of file YNGKP_M1.h.
Referenced by operator=(), updateMatrices(), and YNGKP_M1().
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private |
Definition at line 92 of file YNGKP_M1.h.
Referenced by operator=(), updateMatrices(), and YNGKP_M1().