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

This interface describes the evolution process of a sequence. More...

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

+ Inheritance diagram for bpp::SequenceEvolution:
+ Collaboration diagram for bpp::SequenceEvolution:

Public Member Functions

virtual SequenceEvolution * clone () const override=0
 
virtual bool isCompatibleWith (const AlignmentDataInterface &data) const =0
 
virtual const std::vector< size_t > & getSubstitutionProcessNumbers () const =0
 
virtual const SubstitutionProcessInterface & substitutionProcess (size_t number) const =0
 
virtual std::shared_ptr< const SubstitutionProcessInterface > getSubstitutionProcess (size_t number) const =0
 
const StateMapInterface & stateMap () const
 
std::shared_ptr< const StateMapInterface > getStateMap () const
 
virtual ParameterList getBranchLengthParameters (bool independent) const =0
 Get the branch lengths parameters. More...
 
virtual ParameterList getSubstitutionModelParameters (bool independent) const =0
 Get the parameters associated to substitution model(s). More...
 
virtual ParameterList getSubstitutionProcessParameters (bool independent) const =0
 Get the parameters associated to substitution processes(s). More...
 
virtual ParameterList getRateDistributionParameters (bool independent) const =0
 Get the parameters associated to the rate distribution(s). More...
 
virtual ParameterList getRootFrequenciesParameters (bool independent) const =0
 Get the parameters associated to the root frequencies(s). More...
 
virtual ParameterList getNonDerivableParameters () const =0
 All non derivable parameters. More...
 
virtual size_t getNumberOfIndependentParameters () const=0
 
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
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual const ParameterList & getIndependentParameters () const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual bool hasParameter (const std::string &name) const=0
 
virtual const ParameterList & getParameters () const=0
 
virtual const Parameter & parameter (const std::string &name) const=0
 
virtual double getParameterValue (const std::string &name) const=0
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
virtual void setParameterValue (const std::string &name, double value)=0
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
virtual void removeConstraint (const std::string &name)=0
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
virtual size_t getNumberOfParameters () const=0
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 

Protected Member Functions

virtual ParameterList & getParameters_ ()=0
 

Detailed Description

This interface describes the evolution process of a sequence.

It main purpose is to provide the necessary calculus for each management of site specific substitution process, such as partition models and HMM.

This object has the INDEPENDENT parameters of the processes.

Definition at line 33 of file SequenceEvolution.h.

Member Function Documentation

◆ clone()

virtual SequenceEvolution* bpp::SequenceEvolution::clone ( ) const
overridepure virtual

Implements bpp::ParameterAliasable.

Implemented in bpp::OneProcessSequenceEvolution, bpp::MixtureSequenceEvolution, bpp::PartitionSequenceEvolution, bpp::HmmSequenceEvolution, and bpp::AutoCorrelationSequenceEvolution.

◆ getBranchLengthParameters()

virtual ParameterList bpp::SequenceEvolution::getBranchLengthParameters ( bool  independent) const
pure virtual

Get the branch lengths parameters.

Returns
A ParameterList with all branch lengths.

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

◆ getNonDerivableParameters()

virtual ParameterList bpp::SequenceEvolution::getNonDerivableParameters ( ) const
pure virtual

All non derivable parameters.

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

Returns
A ParameterList.

Implemented in bpp::OneProcessSequenceEvolution, bpp::MixtureSequenceEvolution, bpp::MultiProcessSequenceEvolution, and bpp::AutoCorrelationSequenceEvolution.

◆ getRateDistributionParameters()

virtual ParameterList bpp::SequenceEvolution::getRateDistributionParameters ( bool  independent) const
pure virtual

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

Returns
A ParameterList.

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

◆ getRootFrequenciesParameters()

virtual ParameterList bpp::SequenceEvolution::getRootFrequenciesParameters ( bool  independent) const
pure virtual

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

Returns
A ParameterList.

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

◆ getStateMap()

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

Definition at line 53 of file SequenceEvolution.h.

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

◆ getSubstitutionModelParameters()

virtual ParameterList bpp::SequenceEvolution::getSubstitutionModelParameters ( bool  independent) const
pure virtual

Get the parameters associated to substitution model(s).

Returns
A ParameterList.

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

◆ getSubstitutionProcess()

virtual std::shared_ptr<const SubstitutionProcessInterface> bpp::SequenceEvolution::getSubstitutionProcess ( size_t  number) const
pure virtual

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

Referenced by bpp::SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator().

◆ getSubstitutionProcessNumbers()

virtual const std::vector<size_t>& bpp::SequenceEvolution::getSubstitutionProcessNumbers ( ) const
pure virtual

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

Referenced by getStateMap(), bpp::EvolutionSequenceSimulator::resetSiteSimulators(), stateMap(), and bpp::SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator().

◆ getSubstitutionProcessParameters()

virtual ParameterList bpp::SequenceEvolution::getSubstitutionProcessParameters ( bool  independent) const
pure virtual

Get the parameters associated to substitution processes(s).

Returns
A ParameterList.

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

◆ isCompatibleWith()

virtual bool bpp::SequenceEvolution::isCompatibleWith ( const AlignmentDataInterface &  data) const
pure virtual

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

◆ stateMap()

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

Definition at line 48 of file SequenceEvolution.h.

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

◆ substitutionProcess()

virtual const SubstitutionProcessInterface& bpp::SequenceEvolution::substitutionProcess ( size_t  number) const
pure virtual

Implemented in bpp::OneProcessSequenceEvolution, and bpp::MultiProcessSequenceEvolution.

Referenced by getStateMap(), stateMap(), and bpp::SubstitutionProcessSequenceSimulator::SubstitutionProcessSequenceSimulator().

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