bpp::GivenDataSubstitutionProcessSequenceSimulator Class Reference

Sequences simulation under a unique substitution process, but with site specific posterior probabilities. More...

#include <Bpp/Phyl/Simulation/GivenDataSubstitutionProcessSequenceSimulator.h>

Inheritance diagram for bpp::GivenDataSubstitutionProcessSequenceSimulator:

Collaboration diagram for bpp::GivenDataSubstitutionProcessSequenceSimulator:

Public Member Functions
	GivenDataSubstitutionProcessSequenceSimulator (std::shared_ptr< LikelihoodCalculationSingleProcess > calcul, std::vector< uint > vPrior=std::vector< uint >())
virtual	~GivenDataSubstitutionProcessSequenceSimulator ()
	GivenDataSubstitutionProcessSequenceSimulator (const GivenDataSubstitutionProcessSequenceSimulator &nhss)
GivenDataSubstitutionProcessSequenceSimulator *	clone () const override
void	outputInternalSequences (bool yn) override
	Sets whether we will output the internal sequences or not. More...
The SequenceSimulator interface
Here the numberOfSites is unused (awkward inheritance...)
std::unique_ptr< SiteContainerInterface >	simulate () const
std::unique_ptr< SiteContainerInterface >	simulate (size_t numberOfSites) const override
const SiteSimulatorInterface &	siteSimulator (size_t pos) const override
SiteSimulator and SequenceSimulator interface
std::shared_ptr< const Alphabet >	getAlphabet () const override
const Alphabet &	alphabet () const override
std::vector< std::string >	getSequenceNames () const override
size_t	getNumberOfSites () const
	the number of mapped sites. More...

Private Attributes
std::shared_ptr< LikelihoodCalculationSingleProcess >	calcul_
std::vector< std::shared_ptr< GivenDataSubstitutionProcessSiteSimulator > >	vSiteSim_
std::vector< uint >	vPriorBranch_

Detailed Description

Sequences simulation under a unique substitution process, but with site specific posterior probabilities.

Definition at line 18 of file GivenDataSubstitutionProcessSequenceSimulator.h.

Constructor & Destructor Documentation

GivenDataSubstitutionProcessSequenceSimulator() [1/2]

bpp::GivenDataSubstitutionProcessSequenceSimulator::GivenDataSubstitutionProcessSequenceSimulator ( std::shared_ptr< LikelihoodCalculationSingleProcess >  calcul, std::vector< uint >  vPrior = std::vector<uint>()  )

inline

Definition at line 42 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References calcul_, vPriorBranch_, and vSiteSim_.

Referenced by clone().

~GivenDataSubstitutionProcessSequenceSimulator()

virtual bpp::GivenDataSubstitutionProcessSequenceSimulator::~GivenDataSubstitutionProcessSequenceSimulator ( )

inlinevirtual

Definition at line 51 of file GivenDataSubstitutionProcessSequenceSimulator.h.

GivenDataSubstitutionProcessSequenceSimulator() [2/2]

bpp::GivenDataSubstitutionProcessSequenceSimulator::GivenDataSubstitutionProcessSequenceSimulator ( const GivenDataSubstitutionProcessSequenceSimulator &  nhss )

inline

Definition at line 54 of file GivenDataSubstitutionProcessSequenceSimulator.h.

Member Function Documentation

alphabet()

const Alphabet & bpp::GivenDataSubstitutionProcessSequenceSimulator::alphabet ( ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 92 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References vSiteSim_.

clone()

GivenDataSubstitutionProcessSequenceSimulator * bpp::GivenDataSubstitutionProcessSequenceSimulator::clone ( ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 58 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References GivenDataSubstitutionProcessSequenceSimulator().

getAlphabet()

std::shared_ptr< const Alphabet > bpp::GivenDataSubstitutionProcessSequenceSimulator::getAlphabet ( ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 87 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References vSiteSim_.

Referenced by simulate().

getNumberOfSites()

size_t bpp::GivenDataSubstitutionProcessSequenceSimulator::getNumberOfSites ( ) const

inline

the number of mapped sites.

Definition at line 105 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References calcul_.

getSequenceNames()

std::vector< std::string > bpp::GivenDataSubstitutionProcessSequenceSimulator::getSequenceNames ( ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 97 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References vSiteSim_.

outputInternalSequences()

void bpp::GivenDataSubstitutionProcessSequenceSimulator::outputInternalSequences ( bool  yn )

inlineoverridevirtual

Sets whether we will output the internal sequences or not.

Parameters

yn	Tell if we should output internal sequences.

Implements bpp::SequenceSimulatorInterface.

Definition at line 118 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References vSiteSim_.

simulate() [1/2]

std::unique_ptr< SiteContainerInterface > bpp::GivenDataSubstitutionProcessSequenceSimulator::simulate ( ) const

inline

Definition at line 69 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References calcul_, and simulate().

Referenced by simulate().

simulate() [2/2]

unique_ptr< SiteContainerInterface > GivenDataSubstitutionProcessSequenceSimulator::simulate ( size_t  numberOfSites ) const

overridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 15 of file GivenDataSubstitutionProcessSequenceSimulator.cpp.

References calcul_, getAlphabet(), and vSiteSim_.

siteSimulator()

const SiteSimulatorInterface & bpp::GivenDataSubstitutionProcessSequenceSimulator::siteSimulator ( size_t  pos ) const

inlineoverridevirtual

Implements bpp::SequenceSimulatorInterface.

Definition at line 76 of file GivenDataSubstitutionProcessSequenceSimulator.h.

References calcul_, and vSiteSim_.

Member Data Documentation

calcul_

std::shared_ptr<LikelihoodCalculationSingleProcess> bpp::GivenDataSubstitutionProcessSequenceSimulator::calcul_

private

Definition at line 22 of file GivenDataSubstitutionProcessSequenceSimulator.h.

Referenced by getNumberOfSites(), GivenDataSubstitutionProcessSequenceSimulator(), simulate(), and siteSimulator().

vPriorBranch_

std::vector<uint> bpp::GivenDataSubstitutionProcessSequenceSimulator::vPriorBranch_

private

Definition at line 39 of file GivenDataSubstitutionProcessSequenceSimulator.h.

Referenced by GivenDataSubstitutionProcessSequenceSimulator().

vSiteSim_

std::vector<std::shared_ptr<GivenDataSubstitutionProcessSiteSimulator> > bpp::GivenDataSubstitutionProcessSequenceSimulator::vSiteSim_

private

Definition at line 31 of file GivenDataSubstitutionProcessSequenceSimulator.h.

Referenced by alphabet(), getAlphabet(), getSequenceNames(), GivenDataSubstitutionProcessSequenceSimulator(), outputInternalSequences(), simulate(), and siteSimulator().

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

• Bpp/Phyl/Simulation/GivenDataSubstitutionProcessSequenceSimulator.h
• Bpp/Phyl/Simulation/GivenDataSubstitutionProcessSequenceSimulator.cpp