Estimate a distance matrix from sequence data, according to a given model. More...

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

Inheritance diagram for bpp::DistanceEstimation:

Collaboration diagram for bpp::DistanceEstimation:

Public Member Functions
	DistanceEstimation (SubstitutionModel model, DiscreteDistribution rateDist, size_t verbose=1)
	Create a new DistanceEstimation object according to a given substitution model and a rate distribution. More...

	DistanceEstimation (SubstitutionModel model, DiscreteDistribution rateDist, const SiteContainer *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)
	Assigment operator. More...

virtual	~DistanceEstimation ()

DistanceEstimation *	clone () const

void	computeMatrix () throw (NullPointerException)
	Perform the distance computation. More...

DistanceMatrix *	getMatrix () const
	Get the distance matrix. More...

bool	hasSubstitutionModel () const

const SubstitutionModel &	getSubstitutionModel () const throw (Exception)

void	resetSubstitutionModel (SubstitutionModel *model=0)

bool	hasRateDistribution () const

const DiscreteDistribution &	getRateDistribution () const throw (Exception)

void	resetRateDistribution (DiscreteDistribution *rateDist=0)

void	setData (const SiteContainer *sites)

const SiteContainer *	getData () const

void	resetData ()

void	setOptimizer (const Optimizer *optimizer)

const Optimizer *	getOptimizer () const

Optimizer *	getOptimizer ()

void	resetOptimizer ()

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
auto_ptr< SubstitutionModel >	model_

auto_ptr< DiscreteDistribution >	rateDist_

const SiteContainer *	sites_

DistanceMatrix *	dist_

Optimizer *	optimizer_

MetaOptimizer *	defaultOptimizer_

size_t	verbose_

ParameterList	parameters_

Detailed Description

Estimate a distance matrix from sequence data, according to a given model.

By default, the parameters of the model are fixed to there given values. It is possible to estimate one or several parameters by setting them with the setAdditionalParameters() method. Parameters will be estimated separately for each pair of sequence.

For now it is not possible to retrieve estimated values. You'll have to specify a 'profiler' to the optimizer and then look at the file if you want to do so.

Definition at line 298 of file DistanceEstimation.h.

Constructor & Destructor Documentation

bpp::DistanceEstimation::DistanceEstimation	(	SubstitutionModel *	model,
		DiscreteDistribution *	rateDist,
		size_t	verbose = `1`
	)

inline

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

This instance will own the model and distribution, and will take car of their recopy and destruction.

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 327 of file DistanceEstimation.h.

bpp::DistanceEstimation::DistanceEstimation	(	SubstitutionModel *	model,
		DiscreteDistribution *	rateDist,
		const SiteContainer *	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.

This instance will own the model and distribution, and will take car of their recopy and destruction.

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 360 of file DistanceEstimation.h.

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 386 of file DistanceEstimation.h.

References dist_, and dist_.

virtual bpp::DistanceEstimation::~DistanceEstimation ( )

inlinevirtual

Definition at line 426 of file DistanceEstimation.h.

Member Function Documentation

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

inlinevirtual

Implements bpp::Clonable.

Definition at line 438 of file DistanceEstimation.h.

void DistanceEstimation::computeMatrix ( ) throw (NullPointerException)

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 652 of file DistanceEstimation.cpp.

References bpp::ParameterList::addParameters(), bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::displayGauge(), dist_, dist_, dist_, dist_, bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::TwoTreeLikelihood::getMinimumBranchLength(), bpp::TwoTreeLikelihood::getMinimumBranchLength(), bpp::TwoTreeLikelihood::initialize(), bpp::ApplicationTools::message, bpp::ApplicationTools::message, model_, optimizer_, optimizer_, optimizer_, optimizer_, optimizer_, rateDist_, sites_, sites_, sites_, sites_, sites_, sites_, sites_, verbose_, verbose_, verbose_, verbose_, and verbose_.

const SiteContainer* bpp::DistanceEstimation::getData ( ) const

inline

Definition at line 499 of file DistanceEstimation.h.

DistanceMatrix* bpp::DistanceEstimation::getMatrix ( ) const

inline

Get the distance matrix.

Returns: A pointer toward the computed distance matrix.

Definition at line 474 of file DistanceEstimation.h.

Referenced by bpp::TreeTools::MRP().

const Optimizer* bpp::DistanceEstimation::getOptimizer ( ) const

inline

Definition at line 507 of file DistanceEstimation.h.

Optimizer* bpp::DistanceEstimation::getOptimizer ( )

inline

Definition at line 508 of file DistanceEstimation.h.

const DiscreteDistribution& bpp::DistanceEstimation::getRateDistribution ( ) const throw (Exception)

inline

Definition at line 489 of file DistanceEstimation.h.

const SubstitutionModel& bpp::DistanceEstimation::getSubstitutionModel ( ) const throw (Exception)

inline

Definition at line 478 of file DistanceEstimation.h.

References bpp::TwoTreeLikelihood::model_.

size_t bpp::DistanceEstimation::getVerbose ( ) const

inline

Returns: Verbose level.

Definition at line 538 of file DistanceEstimation.h.

bool bpp::DistanceEstimation::hasRateDistribution ( ) const

inline

Definition at line 487 of file DistanceEstimation.h.

bool bpp::DistanceEstimation::hasSubstitutionModel ( ) const

inline

Definition at line 476 of file DistanceEstimation.h.

void bpp::DistanceEstimation::init_ ( )

inlineprivate

Definition at line 441 of file DistanceEstimation.h.

References bpp::MetaOptimizerInfos::addOptimizer(), bpp::MetaOptimizerInfos::addOptimizer(), bpp::ParameterList::addParameters(), bpp::MetaOptimizer::clone(), bpp::ParameterList::getParameterNames(), bpp::AbstractOptimizer::getStopCondition(), bpp::MetaOptimizerInfos::IT_TYPE_FULL, bpp::MetaOptimizerInfos::IT_TYPE_STEP, bpp::AbstractOptimizer::setMessageHandler(), and bpp::AbstractOptimizer::setProfiler().

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

inline

Assigment 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 410 of file DistanceEstimation.h.

References dist_, dist_, model_, optimizer_, parameters_, rateDist_, sites_, and verbose_.

void bpp::DistanceEstimation::resetAdditionalParameters ( )

inline

Reset all additional parameters.

Definition at line 526 of file DistanceEstimation.h.

References bpp::ParameterList::reset().

void bpp::DistanceEstimation::resetData ( )

inline

Definition at line 500 of file DistanceEstimation.h.

void bpp::DistanceEstimation::resetOptimizer ( )

inline

Definition at line 509 of file DistanceEstimation.h.

References bpp::MetaOptimizer::clone().

void bpp::DistanceEstimation::resetRateDistribution ( DiscreteDistribution * rateDist = 0 )

inline

Definition at line 496 of file DistanceEstimation.h.

void bpp::DistanceEstimation::resetSubstitutionModel ( SubstitutionModel * model = 0 )

inline

Definition at line 485 of file DistanceEstimation.h.

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 518 of file DistanceEstimation.h.

void bpp::DistanceEstimation::setData ( const SiteContainer * sites )

inline

Definition at line 498 of file DistanceEstimation.h.

void bpp::DistanceEstimation::setOptimizer ( const Optimizer * optimizer )

inline

Definition at line 502 of file DistanceEstimation.h.

References bpp::Clonable::clone().

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

inline

Parameters

verbose Verbose level.

Definition at line 534 of file DistanceEstimation.h.

Member Data Documentation

MetaOptimizer* bpp::DistanceEstimation::defaultOptimizer_

private

Definition at line 307 of file DistanceEstimation.h.

DistanceMatrix* bpp::DistanceEstimation::dist_

private

Definition at line 305 of file DistanceEstimation.h.

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

auto_ptr<SubstitutionModel> bpp::DistanceEstimation::model_

private

Definition at line 302 of file DistanceEstimation.h.

Referenced by computeMatrix(), and operator=().

Optimizer* bpp::DistanceEstimation::optimizer_

private

Definition at line 306 of file DistanceEstimation.h.

Referenced by computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), and operator=().

ParameterList bpp::DistanceEstimation::parameters_

private

Definition at line 309 of file DistanceEstimation.h.

Referenced by computeMatrix(), and operator=().

auto_ptr<DiscreteDistribution> bpp::DistanceEstimation::rateDist_

private

Definition at line 303 of file DistanceEstimation.h.

Referenced by computeMatrix(), and operator=().

const SiteContainer* bpp::DistanceEstimation::sites_

private

Definition at line 304 of file DistanceEstimation.h.

Referenced by computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), and operator=().

size_t bpp::DistanceEstimation::verbose_

private

Definition at line 308 of file DistanceEstimation.h.

Referenced by computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), computeMatrix(), and operator=().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation