Discrete Distribution I/O in BppO format. More...

#include <Bpp/Io/BppODiscreteDistributionFormat.h>

Inheritance diagram for bpp::BppODiscreteDistributionFormat:

Collaboration diagram for bpp::BppODiscreteDistributionFormat:

Public Member Functions
	BppODiscreteDistributionFormat (bool verbose=true)

virtual	~BppODiscreteDistributionFormat ()

const std::string	getFormatName () const
	Get the name of the file format. More...

const std::string	getFormatDescription () const
	Get a description of the file format. More...

std::unique_ptr< DiscreteDistributionInterface >	readDiscreteDistribution (const std::string &distDescription, bool parseArguments=true)
	Read a discrete distribution from a string. More...

const std::map< std::string, std::string > &	getUnparsedArguments () const

void	writeDiscreteDistribution (const DiscreteDistributionInterface &dist, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const
	Write a discrete distribution to a stream. More...

virtual const std::string	getDataType () const
	Get the type of data this format deals with. More...

Protected Member Functions
void	initialize_ (DiscreteDistributionInterface &rDist)
	Set parameter initial values of a given distribution according to options. More...

Protected Attributes
bool	verbose_

std::map< std::string, std::string >	unparsedArguments_

Detailed Description

Discrete Distribution I/O in BppO format.

Creates a new discrete distribution object according to distribution description syntax (see the Bio++ Progam Suite manual for a detailed description of this syntax).

Definition at line 21 of file BppODiscreteDistributionFormat.h.

Constructor & Destructor Documentation

◆ BppODiscreteDistributionFormat()

bpp::BppODiscreteDistributionFormat::BppODiscreteDistributionFormat ( bool verbose = true )

inline

Definition at line 30 of file BppODiscreteDistributionFormat.h.

◆ ~BppODiscreteDistributionFormat()

virtual bpp::BppODiscreteDistributionFormat::~BppODiscreteDistributionFormat ( )

inlinevirtual

Definition at line 31 of file BppODiscreteDistributionFormat.h.

Member Function Documentation

◆ getDataType()

virtual const std::string bpp::IoDiscreteDistribution::getDataType ( ) const

inlinevirtualinherited

Get the type of data this format deals with.

Returns: The type of data.

Implements bpp::IOFormat.

Definition at line 27 of file IoDiscreteDistribution.h.

◆ getFormatDescription()

const std::string bpp::BppODiscreteDistributionFormat::getFormatDescription ( ) const

inlinevirtual

Get a description of the file format.

Returns: A description of the format implemented.

Implements bpp::IOFormat.

Definition at line 36 of file BppODiscreteDistributionFormat.h.

References readDiscreteDistribution().

◆ getFormatName()

const std::string bpp::BppODiscreteDistributionFormat::getFormatName ( ) const

inlinevirtual

Get the name of the file format.

Returns: The name of the format implemented.

Implements bpp::IOFormat.

Definition at line 34 of file BppODiscreteDistributionFormat.h.

◆ getUnparsedArguments()

const std::map<std::string, std::string>& bpp::BppODiscreteDistributionFormat::getUnparsedArguments ( ) const

inlinevirtual

Returns: The arguments and their unparsed values from the last call of the read function, if there are any.

Implements bpp::IDiscreteDistribution.

Definition at line 40 of file BppODiscreteDistributionFormat.h.

References initialize_(), unparsedArguments_, and writeDiscreteDistribution().

Referenced by readDiscreteDistribution().

◆ initialize_()

void BppODiscreteDistributionFormat::initialize_ ( DiscreteDistributionInterface & rDist )

protected

Set parameter initial values of a given distribution according to options.

Parameters actually depends on the distribution passed as argument.

Parameters

rDist The distribution to set up.

Exceptions

Exception if an error occured.

Definition at line 392 of file BppODiscreteDistributionFormat.cpp.

References bpp::ApplicationTools::displayResult(), bpp::DiscreteDistributionInterface::getCategory(), bpp::ApplicationTools::getDoubleParameter(), bpp::ParameterAliasable::getIndependentParameters(), bpp::DiscreteDistributionInterface::getNumberOfCategories(), bpp::DiscreteDistributionInterface::getProbability(), bpp::Parametrizable::matchParametersValues(), bpp::AutoParameter::setMessageHandler(), bpp::ParameterList::setParameter(), bpp::ParameterList::size(), bpp::TextTools::toString(), and bpp::ApplicationTools::warning.

Referenced by getUnparsedArguments().

◆ readDiscreteDistribution()

unique_ptr< DiscreteDistributionInterface > BppODiscreteDistributionFormat::readDiscreteDistribution	(	const std::string &	distrDescription,
		bool	parseArguments = `true`
	)

virtual

Read a discrete distribution from a string.

Parameters

distrDescription	A string describing the distribution in the format.
parseArguments	Attempt to parse function arguments. If not, only store them and use default values instead.

Returns: A new DiscreteDistribution object according to options specified.

Exceptions

Exception if an error occured.

Implements bpp::IDiscreteDistribution.

Definition at line 32 of file BppODiscreteDistributionFormat.cpp.

References bpp::ApplicationTools::displayResult(), bpp::DiscreteDistributionInterface::getNumberOfCategories(), bpp::ParameterList::getParameterNames(), bpp::Parametrizable::getParameterNameWithoutNamespace(), bpp::Parametrizable::getParameters(), bpp::Parametrizable::getParameterValue(), getUnparsedArguments(), bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::isEmpty(), bpp::StringTokenizer::nextToken(), bpp::KeyvalTools::parseProcedure(), readDiscreteDistribution(), bpp::DiscreteDistributionInterface::setMedian(), bpp::TextTools::toDouble(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

Referenced by getFormatDescription(), and readDiscreteDistribution().

◆ writeDiscreteDistribution()

void BppODiscreteDistributionFormat::writeDiscreteDistribution	(	const DiscreteDistributionInterface &	dist,
		OutputStream &	out,
		std::map< std::string, std::string > &	globalAliases,
		std::vector< std::string > &	writtenNames
	)		const

virtual

Write a discrete distribution to a stream.

Parameters

dist	A discrete distribution object;
out	The output stream;
globalAliases	parameters linked to global alias.
writtenNames	is the vector of the written parameters so far [in, out];

Exceptions

Exception if an error occured.

Implements bpp::ODiscreteDistribution.

Definition at line 259 of file BppODiscreteDistributionFormat.cpp.

References bpp::ParameterAliasable::getIndependentParameters(), bpp::DiscreteDistributionInterface::getName(), bpp::DiscreteDistributionInterface::getNumberOfCategories(), bpp::AbstractDiscreteDistribution::getNumberOfCategories(), bpp::MixtureOfDiscreteDistributions::getNumberOfDistributions(), bpp::Parametrizable::getNumberOfParameters(), bpp::ParameterList::getParameterNames(), bpp::TextTools::toString(), bpp::InvariantMixedDiscreteDistribution::variableSubDistribution(), and bpp::BppOParametrizableFormat::write().

Referenced by getUnparsedArguments().