bpp::DistanceEstimation Class Reference

#include <Bpp/Phyl/Distance/DistanceEstimation.h>

Inheritance diagram for bpp::DistanceEstimation:

Collaboration diagram for bpp::DistanceEstimation:

Public Member Functions
	DistanceEstimation (std::shared_ptr< SubstitutionProcessInterface > process, size_t verbose=1)
	Create a new DistanceEstimation object according to a given substitution process. More...
	DistanceEstimation (std::shared_ptr< BranchModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rateDist, size_t verbose=1)
	Create a new DistanceEstimation object according to a given substitution model and a rate distribution. More...
	DistanceEstimation (std::shared_ptr< SubstitutionProcessInterface > process, std::shared_ptr< const AlignmentDataInterface > sites, size_t verbose=1, bool computeMat=true)
	Create a new DistanceEstimation object and compute distances according to a given substitution process. More...
	DistanceEstimation (std::shared_ptr< BranchModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rateDist, std::shared_ptr< const AlignmentDataInterface > sites, size_t verbose=1, bool computeMat=true)
	Create a new DistanceEstimation object and compute distances according to a given substitution model and a rate distribution. More...
	DistanceEstimation (const DistanceEstimation &distanceEstimation)
	Copy constructor. More...
DistanceEstimation &	operator= (const DistanceEstimation &distanceEstimation)
	Assignment operator. More...
virtual	~DistanceEstimation ()
DistanceEstimation *	clone () const override
void	computeMatrix ()
	Perform the distance computation. More...
std::unique_ptr< DistanceMatrix >	getMatrix () const
	Get the distance matrix. More...
bool	hasProcess () const
const SubstitutionProcessInterface &	process () const
std::shared_ptr< const SubstitutionProcessInterface >	getProcess () const
void	setProcess (std::shared_ptr< SubstitutionProcessInterface > process=nullptr)
void	setData (std::shared_ptr< const AlignmentDataInterface > sites=nullptr)
std::shared_ptr< const AlignmentDataInterface >	getData () const
const AlignmentDataInterface &	data () const
void	setOptimizer (std::shared_ptr< OptimizerInterface > optimizer)
std::shared_ptr< const OptimizerInterface >	getOptimizer () const
std::shared_ptr< OptimizerInterface >	getOptimizer ()
const OptimizerInterface &	optimizer () const
OptimizerInterface &	optimizer ()
void	resetOptimizer ()
bool	matchParametersValues (const ParameterList &parameters)
void	setAdditionalParameters (const ParameterList &parameters)
	Specify a list of parameters to be estimated. More...
void	resetAdditionalParameters ()
	Reset all additional parameters. More...
void	setVerbose (size_t verbose)
size_t	getVerbose () const

Private Member Functions
void	init_ ()

Private Attributes
std::shared_ptr< SubstitutionProcessInterface >	process_
size_t	numProc_
std::shared_ptr< const AlignmentDataInterface >	sites_
std::shared_ptr< DistanceMatrix >	dist_
std::shared_ptr< OptimizerInterface >	optimizer_
std::shared_ptr< MetaOptimizer >	defaultOptimizer_
size_t	verbose_
ParameterList	parameters_

Detailed Description

Definition at line 28 of file DistanceEstimation.h.

Constructor & Destructor Documentation

DistanceEstimation() [1/5]

bpp::DistanceEstimation::DistanceEstimation ( std::shared_ptr< SubstitutionProcessInterface >  process, size_t  verbose = 1  )

inline

Create a new DistanceEstimation object according to a given substitution process.

Parameters

process	The substitution process to use.
verbose	The verbose level: 0=Off, 1=one * by row computation 2=one * by row computation and one . by column computation 3=2 + optimization verbose enabled 4=3 + likelihood object verbose enabled

Definition at line 53 of file DistanceEstimation.h.

References init_().

Referenced by clone().

DistanceEstimation() [2/5]

bpp::DistanceEstimation::DistanceEstimation ( std::shared_ptr< BranchModelInterface >  model, std::shared_ptr< DiscreteDistributionInterface >  rateDist, size_t  verbose = 1  )

inline

Create a new DistanceEstimation object according to a given substitution model and a rate distribution.

Parameters

model	The substitution model to use.
rateDist	The discrete rate distribution to use.
verbose	The verbose level: 0=Off, 1=one * by row computation 2=one * by row computation and one . by column computation 3=2 + optimization verbose enabled 4=3 + likelihood object verbose enabled

Definition at line 80 of file DistanceEstimation.h.

References init_(), and process_.

DistanceEstimation() [3/5]

bpp::DistanceEstimation::DistanceEstimation ( std::shared_ptr< SubstitutionProcessInterface >  process, std::shared_ptr< const AlignmentDataInterface >  sites, size_t  verbose = 1, bool  computeMat = true  )

inline

Create a new DistanceEstimation object and compute distances according to a given substitution process.

Parameters

process	The substitution process to use.
sites	The sequence data.
verbose	The verbose level: 0=Off, 1=one * by row computation 2=one * by row computation and one . by column computation 3=2 + optimization verbose enabled 4=3 + likelihood object verbose enabled
computeMat	if true the computeMatrix() method is called.

Definition at line 111 of file DistanceEstimation.h.

References computeMatrix(), and init_().

DistanceEstimation() [4/5]

bpp::DistanceEstimation::DistanceEstimation ( std::shared_ptr< BranchModelInterface >  model, std::shared_ptr< DiscreteDistributionInterface >  rateDist, std::shared_ptr< const AlignmentDataInterface >  sites, size_t  verbose = 1, bool  computeMat = true  )

inline

Create a new DistanceEstimation object and compute distances according to a given substitution model and a rate distribution.

Parameters

model	The substitution model to use.
rateDist	The discrete rate distribution to use.
sites	The sequence data.
verbose	The verbose level: 0=Off, 1=one * by row computation 2=one * by row computation and one . by column computation 3=2 + optimization verbose enabled 4=3 + likelihood object verbose enabled
computeMat	if true the computeMatrix() method is called.

Definition at line 144 of file DistanceEstimation.h.

References computeMatrix(), init_(), and process_.

DistanceEstimation() [5/5]

bpp::DistanceEstimation::DistanceEstimation ( const DistanceEstimation &  distanceEstimation )

inline

Copy constructor.

Only the distance matrix is hard-copied, if there is one.

Parameters

distanceEstimation

The object to copy.

Definition at line 171 of file DistanceEstimation.h.

References dist_.

~DistanceEstimation()

virtual bpp::DistanceEstimation::~DistanceEstimation ( )

inlinevirtual

Definition at line 211 of file DistanceEstimation.h.

Member Function Documentation

clone()

DistanceEstimation* bpp::DistanceEstimation::clone ( ) const

inlineoverridevirtual

Implements bpp::Clonable.

Definition at line 213 of file DistanceEstimation.h.

References DistanceEstimation().

computeMatrix()

void DistanceEstimation::computeMatrix

(

)

Perform the distance computation.

Result can be called by the getMatrix() method.

Exceptions

NullPointerException

if at least one of the model, rate distribution or data are not initialized.

Definition at line 72 of file DistanceEstimation.cpp.

References bpp::ParameterList::addParameters(), bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::message, bpp::Newick::parenthesisToPhyloTree(), and bpp::TextTools::toString().

Referenced by bpp::OptimizationTools::buildDistanceTree(), DistanceEstimation(), and bpp::OptimizationTools::estimateDistanceMatrix().

data()

const AlignmentDataInterface& bpp::DistanceEstimation::data ( ) const

inline

Definition at line 260 of file DistanceEstimation.h.

References sites_.

getData()

std::shared_ptr<const AlignmentDataInterface> bpp::DistanceEstimation::getData ( ) const

inline

Definition at line 258 of file DistanceEstimation.h.

References sites_.

Referenced by bpp::OptimizationTools::buildDistanceTree().

getMatrix()

std::unique_ptr<DistanceMatrix> bpp::DistanceEstimation::getMatrix ( ) const

inline

Get the distance matrix.

Returns

A pointer toward the computed distance matrix.

Definition at line 234 of file DistanceEstimation.h.

References dist_.

Referenced by bpp::OptimizationTools::buildDistanceTree(), and bpp::OptimizationTools::estimateDistanceMatrix().

getOptimizer() [1/2]

std::shared_ptr<OptimizerInterface> bpp::DistanceEstimation::getOptimizer ( )

inline

Definition at line 269 of file DistanceEstimation.h.

References optimizer_.

getOptimizer() [2/2]

std::shared_ptr<const OptimizerInterface> bpp::DistanceEstimation::getOptimizer ( ) const

inline

Definition at line 267 of file DistanceEstimation.h.

References optimizer_.

getProcess()

std::shared_ptr<const SubstitutionProcessInterface> bpp::DistanceEstimation::getProcess ( ) const

inline

Definition at line 249 of file DistanceEstimation.h.

References process_.

getVerbose()

size_t bpp::DistanceEstimation::getVerbose ( ) const

inline

Returns

Verbose level.

Definition at line 311 of file DistanceEstimation.h.

References verbose_.

Referenced by bpp::OptimizationTools::buildDistanceTree().

hasProcess()

bool bpp::DistanceEstimation::hasProcess ( ) const

inline

Definition at line 239 of file DistanceEstimation.h.

References process_.

Referenced by matchParametersValues(), and process().

init_()

void DistanceEstimation::init_ ( )

private

Definition at line 36 of file DistanceEstimation.cpp.

References bpp::ParameterList::addParameters(), bpp::ParameterList::getParameterNames(), bpp::MetaOptimizerInfos::IT_TYPE_FULL, bpp::MetaOptimizerInfos::IT_TYPE_STEP, and bpp::TextTools::toString().

Referenced by DistanceEstimation().

matchParametersValues()

bool bpp::DistanceEstimation::matchParametersValues ( const ParameterList &  parameters )

inline

Definition at line 277 of file DistanceEstimation.h.

References hasProcess(), and process_.

Referenced by bpp::OptimizationTools::buildDistanceTree().

operator=()

DistanceEstimation& bpp::DistanceEstimation::operator= ( const DistanceEstimation &  distanceEstimation )

inline

Assignment operator.

Only the distance matrix is hard-copied, if there is one.

Parameters

distanceEstimation

The object to copy.

Returns

A reference toward this object.

Definition at line 195 of file DistanceEstimation.h.

References dist_, numProc_, optimizer_, parameters_, process_, sites_, and verbose_.

optimizer() [1/2]

OptimizerInterface& bpp::DistanceEstimation::optimizer ( )

inline

Definition at line 273 of file DistanceEstimation.h.

References optimizer_.

optimizer() [2/2]

const OptimizerInterface& bpp::DistanceEstimation::optimizer ( ) const

inline

Definition at line 271 of file DistanceEstimation.h.

References optimizer_.

Referenced by setOptimizer().

process()

const SubstitutionProcessInterface& bpp::DistanceEstimation::process ( ) const

inline

Definition at line 241 of file DistanceEstimation.h.

References hasProcess(), and process_.

Referenced by bpp::OptimizationTools::buildDistanceTree(), bpp::OptimizationTools::estimateDistanceMatrix(), and setProcess().

resetAdditionalParameters()

void bpp::DistanceEstimation::resetAdditionalParameters ( )

inline

Reset all additional parameters.

Definition at line 299 of file DistanceEstimation.h.

References parameters_, and bpp::ParameterList::reset().

Referenced by bpp::OptimizationTools::buildDistanceTree(), and bpp::OptimizationTools::estimateDistanceMatrix().

resetOptimizer()

void bpp::DistanceEstimation::resetOptimizer ( )

inline

Definition at line 275 of file DistanceEstimation.h.

References defaultOptimizer_, and optimizer_.

setAdditionalParameters()

void bpp::DistanceEstimation::setAdditionalParameters ( const ParameterList &  parameters )

inline

Specify a list of parameters to be estimated.

Parameters will be estimated separately for each distance.

Parameters

parameters

A list of parameters to estimate.

Definition at line 291 of file DistanceEstimation.h.

References parameters_.

Referenced by bpp::OptimizationTools::buildDistanceTree(), and bpp::OptimizationTools::estimateDistanceMatrix().

setData()

void bpp::DistanceEstimation::setData ( std::shared_ptr< const AlignmentDataInterface >  sites = nullptr )

inline

Definition at line 256 of file DistanceEstimation.h.

References sites_.

setOptimizer()

void bpp::DistanceEstimation::setOptimizer ( std::shared_ptr< OptimizerInterface >  optimizer )

inline

Definition at line 262 of file DistanceEstimation.h.

References optimizer(), and optimizer_.

setProcess()

void bpp::DistanceEstimation::setProcess ( std::shared_ptr< SubstitutionProcessInterface >  process = nullptr )

inline

Definition at line 254 of file DistanceEstimation.h.

References process(), and process_.

setVerbose()

void bpp::DistanceEstimation::setVerbose ( size_t  verbose )

inline

Parameters

verbose

Verbose level.

Definition at line 307 of file DistanceEstimation.h.

References verbose_.

Referenced by bpp::OptimizationTools::buildDistanceTree(), and bpp::OptimizationTools::estimateDistanceMatrix().

Member Data Documentation

defaultOptimizer_

std::shared_ptr<MetaOptimizer> bpp::DistanceEstimation::defaultOptimizer_

private

Definition at line 37 of file DistanceEstimation.h.

Referenced by resetOptimizer().

dist_

std::shared_ptr<DistanceMatrix> bpp::DistanceEstimation::dist_

private

Definition at line 35 of file DistanceEstimation.h.

Referenced by DistanceEstimation(), getMatrix(), and operator=().

numProc_

size_t bpp::DistanceEstimation::numProc_

private

Definition at line 33 of file DistanceEstimation.h.

Referenced by operator=().

optimizer_

std::shared_ptr<OptimizerInterface> bpp::DistanceEstimation::optimizer_

private

Definition at line 36 of file DistanceEstimation.h.

Referenced by getOptimizer(), operator=(), optimizer(), resetOptimizer(), and setOptimizer().

parameters_

ParameterList bpp::DistanceEstimation::parameters_

private

Definition at line 39 of file DistanceEstimation.h.

Referenced by operator=(), resetAdditionalParameters(), and setAdditionalParameters().

process_

std::shared_ptr<SubstitutionProcessInterface> bpp::DistanceEstimation::process_

private

Definition at line 32 of file DistanceEstimation.h.

Referenced by DistanceEstimation(), getProcess(), hasProcess(), matchParametersValues(), operator=(), process(), and setProcess().

sites_

std::shared_ptr<const AlignmentDataInterface> bpp::DistanceEstimation::sites_

private

Definition at line 34 of file DistanceEstimation.h.

Referenced by data(), getData(), operator=(), and setData().

verbose_

size_t bpp::DistanceEstimation::verbose_

private

Definition at line 38 of file DistanceEstimation.h.

Referenced by getVerbose(), operator=(), and setVerbose().

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

• Bpp/Phyl/Distance/DistanceEstimation.h
• Bpp/Phyl/Distance/DistanceEstimation.cpp