bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::AutoCorrelationSequenceEvolution Class Referenceabstract

Sequence evolution framework based on an auto-correlation of substitution processes. More...

#include <Bpp/Phyl/Likelihood/AutoCorrelationSequenceEvolution.h>

+ Inheritance diagram for bpp::AutoCorrelationSequenceEvolution:
+ Collaboration diagram for bpp::AutoCorrelationSequenceEvolution:

Public Member Functions

 AutoCorrelationSequenceEvolution (std::shared_ptr< SubstitutionProcessCollection > processColl, std::vector< size_t > &nProc)
 
 AutoCorrelationSequenceEvolution (const AutoCorrelationSequenceEvolution &mlc)
 
AutoCorrelationSequenceEvolution & operator= (const AutoCorrelationSequenceEvolution &mlc)
 
virtual ~AutoCorrelationSequenceEvolution ()
 
AutoCorrelationSequenceEvolution * clone () const
 
void setNamespace (const std::string &nameSpace)
 
void fireParameterChanged (const ParameterList &parameters)
 
const AutoCorrelationTransitionMatrix & hmmTransitionMatrix () const
 
AutoCorrelationTransitionMatrix & hmmTransitionMatrix ()
 
std::shared_ptr< AutoCorrelationTransitionMatrix > getHmmTransitionMatrix ()
 
std::shared_ptr< const AutoCorrelationTransitionMatrix > getHmmTransitionMatrix () const
 
HmmProcessAlphabet & hmmProcessAlphabet ()
 
const HmmProcessAlphabet & hmmProcessAlphabet () const
 
std::shared_ptr< HmmProcessAlphabet > getHmmProcessAlphabet ()
 
std::shared_ptr< const HmmProcessAlphabet > getHmmProcessAlphabet () const
 
ParameterList getNonDerivableParameters () const
 All non derivable parameters. More...
 
const SubstitutionProcessCollection & collection () const
 The collection. More...
 
SubstitutionProcessCollection & collection ()
 
std::shared_ptr< const SubstitutionProcessCollection > getCollection () const
 
std::shared_ptr< SubstitutionProcessCollection > getCollection ()
 
size_t getNumberOfSubstitutionProcess () const
 Return the number of process used for computation. More...
 
const SubstitutionProcessInterface & substitutionProcess (size_t number) const
 Return the SubstitutionProcess of a given index position (in nProc_ vector). More...
 
std::shared_ptr< const SubstitutionProcessInterface > getSubstitutionProcess (size_t number) const
 
const std::vector< size_t > & getSubstitutionProcessNumbers () const
 
ParameterList getSubstitutionProcessParameters (bool independent) const
 Get the parameters associated to substitution processes(s). More...
 
ParameterList getSubstitutionModelParameters (bool independent) const
 Get the parameters associated to substitution model(s). More...
 
ParameterList getRateDistributionParameters (bool independent) const
 Get the parameters associated to the rate distribution(s). More...
 
ParameterList getRootFrequenciesParameters (bool independent) const
 Get the parameters associated to the root frequencies(s). More...
 
ParameterList getBranchLengthParameters (bool independent) const
 Get the branch lengths parameters. More...
 
void setParameters (const ParameterList &parameters)
 
virtual bool isCompatibleWith (const AlignmentDataInterface &data) const
 test if data fits this model More...
 
const StateMapInterface & stateMap () const
 
std::shared_ptr< const StateMapInterface > getStateMap () const
 
virtual size_t getNumberOfIndependentParameters () const=0
 
size_t getNumberOfIndependentParameters () const
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
virtual const ParameterList & getIndependentParameters () const=0
 
const ParameterList & getIndependentParameters () const
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const=0
 
bool hasParameter (const std::string &name) const override
 
virtual const ParameterList & getParameters () const=0
 
const ParameterList & getParameters () const override
 
virtual const Parameter & parameter (const std::string &name) const=0
 
const Parameter & parameter (const std::string &name) const override
 
virtual double getParameterValue (const std::string &name) const=0
 
double getParameterValue (const std::string &name) const override
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
void setAllParametersValues (const ParameterList &parameters) override
 
virtual void setParameterValue (const std::string &name, double value)=0
 
void setParameterValue (const std::string &name, double value) override
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
void setParametersValues (const ParameterList &parameters) override
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
bool matchParametersValues (const ParameterList &parameters) override
 
virtual void removeConstraint (const std::string &name)=0
 
void removeConstraint (const std::string &name) override
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
virtual size_t getNumberOfParameters () const=0
 
size_t getNumberOfParameters () const override
 
virtual std::string getNamespace () const=0
 
std::string getNamespace () const override
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 

Protected Member Functions

virtual ParameterList & getParameters_ ()=0
 
ParameterList & getParameters_ () override
 
const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
Parameter & getParameter_ (const std::string &name)
 
Parameter & getParameter_ (size_t index)
 
const Parameter & getParameter_ (size_t index) const
 
Parameter & getParameterWithNamespace_ (const std::string &name)
 
const Parameter & getParameterWithNamespace_ (const std::string &name) const
 

Protected Attributes

std::shared_ptr< SubstitutionProcessCollection > processColl_
 
std::vector< size_t > nProc_
 the vector of the substitution process numbers, as they are used in this order. More...
 

Private Attributes

std::shared_ptr< HmmProcessAlphabet > hmmAlph_
 
std::shared_ptr< AutoCorrelationTransitionMatrix > autoCorrTransMat_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Sequence evolution framework based on an auto-correlation of substitution processes.

Definition at line 24 of file AutoCorrelationSequenceEvolution.h.

Constructor & Destructor Documentation

◆ AutoCorrelationSequenceEvolution() [1/2]

AutoCorrelationSequenceEvolution::AutoCorrelationSequenceEvolution ( std::shared_ptr< SubstitutionProcessCollection >  processColl,
std::vector< size_t > &  nProc 
)

Definition at line 12 of file AutoCorrelationSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), autoCorrTransMat_, hmmAlph_, and bpp::MultiProcessSequenceEvolution::processColl_.

Referenced by clone().

◆ AutoCorrelationSequenceEvolution() [2/2]

bpp::AutoCorrelationSequenceEvolution::AutoCorrelationSequenceEvolution ( const AutoCorrelationSequenceEvolution &  mlc)
inline

Definition at line 36 of file AutoCorrelationSequenceEvolution.h.

◆ ~AutoCorrelationSequenceEvolution()

virtual bpp::AutoCorrelationSequenceEvolution::~AutoCorrelationSequenceEvolution ( )
inlinevirtual

Definition at line 51 of file AutoCorrelationSequenceEvolution.h.

Member Function Documentation

◆ clone()

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

Implements bpp::AbstractParameterAliasable.

Definition at line 53 of file AutoCorrelationSequenceEvolution.h.

References AutoCorrelationSequenceEvolution().

◆ collection() [1/2]

SubstitutionProcessCollection& bpp::MultiProcessSequenceEvolution::collection ( )
inlineinherited

Definition at line 69 of file MultiProcessSequenceEvolution.h.

◆ collection() [2/2]

const SubstitutionProcessCollection& bpp::MultiProcessSequenceEvolution::collection ( ) const
inlineinherited

The collection.

Definition at line 65 of file MultiProcessSequenceEvolution.h.

◆ fireParameterChanged()

void AutoCorrelationSequenceEvolution::fireParameterChanged ( const ParameterList &  parameters)
virtual

Reimplemented from bpp::MultiProcessSequenceEvolution.

Definition at line 42 of file AutoCorrelationSequenceEvolution.cpp.

References autoCorrTransMat_, bpp::MultiProcessSequenceEvolution::fireParameterChanged(), and hmmAlph_.

◆ getBranchLengthParameters()

ParameterList MultiProcessSequenceEvolution::getBranchLengthParameters ( bool  independent) const
virtualinherited

Get the branch lengths parameters.

Returns
A ParameterList with all branch lengths.

Implements bpp::SequenceEvolution.

Definition at line 85 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getCollection() [1/2]

std::shared_ptr<SubstitutionProcessCollection> bpp::MultiProcessSequenceEvolution::getCollection ( )
inlineinherited

Definition at line 71 of file MultiProcessSequenceEvolution.h.

◆ getCollection() [2/2]

std::shared_ptr<const SubstitutionProcessCollection> bpp::MultiProcessSequenceEvolution::getCollection ( ) const
inlineinherited

Definition at line 67 of file MultiProcessSequenceEvolution.h.

◆ getHmmProcessAlphabet() [1/2]

std::shared_ptr<HmmProcessAlphabet> bpp::AutoCorrelationSequenceEvolution::getHmmProcessAlphabet ( )
inline

Definition at line 90 of file AutoCorrelationSequenceEvolution.h.

References hmmAlph_.

◆ getHmmProcessAlphabet() [2/2]

std::shared_ptr<const HmmProcessAlphabet> bpp::AutoCorrelationSequenceEvolution::getHmmProcessAlphabet ( ) const
inline

Definition at line 95 of file AutoCorrelationSequenceEvolution.h.

References hmmAlph_.

◆ getHmmTransitionMatrix() [1/2]

std::shared_ptr<AutoCorrelationTransitionMatrix> bpp::AutoCorrelationSequenceEvolution::getHmmTransitionMatrix ( )
inline

Definition at line 70 of file AutoCorrelationSequenceEvolution.h.

References autoCorrTransMat_.

◆ getHmmTransitionMatrix() [2/2]

std::shared_ptr<const AutoCorrelationTransitionMatrix> bpp::AutoCorrelationSequenceEvolution::getHmmTransitionMatrix ( ) const
inline

Definition at line 75 of file AutoCorrelationSequenceEvolution.h.

References autoCorrTransMat_.

◆ getNonDerivableParameters()

ParameterList AutoCorrelationSequenceEvolution::getNonDerivableParameters ( ) const
virtual

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution, and alias.

Returns
A ParameterList.

Reimplemented from bpp::MultiProcessSequenceEvolution.

Definition at line 50 of file AutoCorrelationSequenceEvolution.cpp.

References autoCorrTransMat_, bpp::MultiProcessSequenceEvolution::getNonDerivableParameters(), and bpp::ParameterList::includeParameters().

◆ getNumberOfSubstitutionProcess()

size_t bpp::MultiProcessSequenceEvolution::getNumberOfSubstitutionProcess ( ) const
inlineinherited

Return the number of process used for computation.

Definition at line 76 of file MultiProcessSequenceEvolution.h.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters().

◆ getRateDistributionParameters()

ParameterList MultiProcessSequenceEvolution::getRateDistributionParameters ( bool  independent) const
virtualinherited

Get the parameters associated to the rate distribution(s).

Returns
A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 61 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getRootFrequenciesParameters()

ParameterList MultiProcessSequenceEvolution::getRootFrequenciesParameters ( bool  independent) const
virtualinherited

Get the parameters associated to the root frequencies(s).

Returns
A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 73 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::SequenceEvolution::getStateMap ( ) const
inlineinherited

Definition at line 53 of file SequenceEvolution.h.

References bpp::SubstitutionProcessInterface::getStateMap(), bpp::SequenceEvolution::getSubstitutionProcessNumbers(), and bpp::SequenceEvolution::substitutionProcess().

◆ getSubstitutionModelParameters()

ParameterList MultiProcessSequenceEvolution::getSubstitutionModelParameters ( bool  independent) const
virtualinherited

Get the parameters associated to substitution model(s).

Returns
A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 49 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ getSubstitutionProcess()

std::shared_ptr<const SubstitutionProcessInterface> bpp::MultiProcessSequenceEvolution::getSubstitutionProcess ( size_t  number) const
inlinevirtualinherited

Implements bpp::SequenceEvolution.

Definition at line 87 of file MultiProcessSequenceEvolution.h.

◆ getSubstitutionProcessNumbers()

const std::vector<size_t>& bpp::MultiProcessSequenceEvolution::getSubstitutionProcessNumbers ( ) const
inlinevirtualinherited

Implements bpp::SequenceEvolution.

Definition at line 92 of file MultiProcessSequenceEvolution.h.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters().

◆ getSubstitutionProcessParameters()

ParameterList MultiProcessSequenceEvolution::getSubstitutionProcessParameters ( bool  independent) const
virtualinherited

Get the parameters associated to substitution processes(s).

Returns
A ParameterList.

Implements bpp::SequenceEvolution.

Definition at line 37 of file MultiProcessSequenceEvolution.cpp.

References bpp::ParameterList::includeParameters(), bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ hmmProcessAlphabet() [1/2]

HmmProcessAlphabet& bpp::AutoCorrelationSequenceEvolution::hmmProcessAlphabet ( )
inline

Definition at line 80 of file AutoCorrelationSequenceEvolution.h.

References hmmAlph_.

◆ hmmProcessAlphabet() [2/2]

const HmmProcessAlphabet& bpp::AutoCorrelationSequenceEvolution::hmmProcessAlphabet ( ) const
inline

Definition at line 85 of file AutoCorrelationSequenceEvolution.h.

References hmmAlph_.

◆ hmmTransitionMatrix() [1/2]

AutoCorrelationTransitionMatrix& bpp::AutoCorrelationSequenceEvolution::hmmTransitionMatrix ( )
inline

Definition at line 65 of file AutoCorrelationSequenceEvolution.h.

References autoCorrTransMat_.

◆ hmmTransitionMatrix() [2/2]

const AutoCorrelationTransitionMatrix& bpp::AutoCorrelationSequenceEvolution::hmmTransitionMatrix ( ) const
inline

Definition at line 60 of file AutoCorrelationSequenceEvolution.h.

References autoCorrTransMat_.

Referenced by bpp::PhylogeneticsApplicationTools::printParameters(), and bpp::EvolutionSequenceSimulator::resetSiteSimulators().

◆ isCompatibleWith()

bool MultiProcessSequenceEvolution::isCompatibleWith ( const AlignmentDataInterface &  data) const
virtualinherited

test if data fits this model

Implements bpp::SequenceEvolution.

Definition at line 122 of file MultiProcessSequenceEvolution.cpp.

References bpp::MultiProcessSequenceEvolution::nProc_, and bpp::MultiProcessSequenceEvolution::processColl_.

◆ operator=()

AutoCorrelationSequenceEvolution& bpp::AutoCorrelationSequenceEvolution::operator= ( const AutoCorrelationSequenceEvolution &  mlc)
inline

Definition at line 41 of file AutoCorrelationSequenceEvolution.h.

References autoCorrTransMat_, hmmAlph_, and bpp::MultiProcessSequenceEvolution::operator=().

◆ setNamespace()

void AutoCorrelationSequenceEvolution::setNamespace ( const std::string &  nameSpace)
virtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 29 of file AutoCorrelationSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), autoCorrTransMat_, bpp::AbstractParameterAliasable::deleteParameters_(), and hmmAlph_.

◆ setParameters()

void MultiProcessSequenceEvolution::setParameters ( const ParameterList &  parameters)
inherited

Definition at line 114 of file MultiProcessSequenceEvolution.cpp.

References bpp::AbstractParameterAliasable::setParametersValues().

◆ stateMap()

const StateMapInterface& bpp::SequenceEvolution::stateMap ( ) const
inlineinherited

Definition at line 48 of file SequenceEvolution.h.

References bpp::SequenceEvolution::getSubstitutionProcessNumbers(), bpp::SubstitutionProcessInterface::stateMap(), and bpp::SequenceEvolution::substitutionProcess().

◆ substitutionProcess()

const SubstitutionProcessInterface& bpp::MultiProcessSequenceEvolution::substitutionProcess ( size_t  number) const
inlinevirtualinherited

Return the SubstitutionProcess of a given index position (in nProc_ vector).

Implements bpp::SequenceEvolution.

Definition at line 82 of file MultiProcessSequenceEvolution.h.

Member Data Documentation

◆ autoCorrTransMat_

std::shared_ptr<AutoCorrelationTransitionMatrix> bpp::AutoCorrelationSequenceEvolution::autoCorrTransMat_
private

Definition at line 29 of file AutoCorrelationSequenceEvolution.h.

Referenced by AutoCorrelationSequenceEvolution(), fireParameterChanged(), getHmmTransitionMatrix(), getNonDerivableParameters(), hmmTransitionMatrix(), operator=(), and setNamespace().

◆ hmmAlph_

std::shared_ptr<HmmProcessAlphabet> bpp::AutoCorrelationSequenceEvolution::hmmAlph_
private

Definition at line 28 of file AutoCorrelationSequenceEvolution.h.

Referenced by AutoCorrelationSequenceEvolution(), fireParameterChanged(), getHmmProcessAlphabet(), hmmProcessAlphabet(), operator=(), and setNamespace().

◆ nProc_

std::vector<size_t> bpp::MultiProcessSequenceEvolution::nProc_
protectedinherited

the vector of the substitution process numbers, as they are used in this order.

Definition at line 37 of file MultiProcessSequenceEvolution.h.

Referenced by bpp::MultiProcessSequenceEvolution::getBranchLengthParameters(), bpp::MultiProcessSequenceEvolution::getNonDerivableParameters(), bpp::MultiProcessSequenceEvolution::getRateDistributionParameters(), bpp::MultiProcessSequenceEvolution::getRootFrequenciesParameters(), bpp::MultiProcessSequenceEvolution::getSubstitutionModelParameters(), bpp::MultiProcessSequenceEvolution::getSubstitutionProcessParameters(), bpp::MultiProcessSequenceEvolution::isCompatibleWith(), bpp::MultiProcessSequenceEvolution::MultiProcessSequenceEvolution(), bpp::MultiProcessSequenceEvolution::operator=(), and bpp::PartitionSequenceEvolution::PartitionSequenceEvolution().

◆ processColl_

std::shared_ptr<SubstitutionProcessCollection> bpp::MultiProcessSequenceEvolution::processColl_
protectedinherited

Definition at line 31 of file MultiProcessSequenceEvolution.h.

Referenced by AutoCorrelationSequenceEvolution(), bpp::MultiProcessSequenceEvolution::fireParameterChanged(), bpp::MultiProcessSequenceEvolution::getBranchLengthParameters(), bpp::MultiProcessSequenceEvolution::getNonDerivableParameters(), bpp::MultiProcessSequenceEvolution::getRateDistributionParameters(), bpp::MultiProcessSequenceEvolution::getRootFrequenciesParameters(), bpp::MultiProcessSequenceEvolution::getSubstitutionModelParameters(), bpp::MultiProcessSequenceEvolution::getSubstitutionProcessParameters(), bpp::HmmSequenceEvolution::HmmSequenceEvolution(), bpp::MultiProcessSequenceEvolution::isCompatibleWith(), bpp::MultiProcessSequenceEvolution::MultiProcessSequenceEvolution(), bpp::MultiProcessSequenceEvolution::operator=(), and bpp::PartitionSequenceEvolution::PartitionSequenceEvolution().

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