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

#include <Bpp/Phyl/Io/BppORateDistributionFormat.h>

Inheritance diagram for bpp::BppORateDistributionFormat:

Collaboration diagram for bpp::BppORateDistributionFormat:

Public Member Functions
	BppORateDistributionFormat (bool allowConstant)
	Build a new BppORateDistributionFormat object. More...

virtual	~BppORateDistributionFormat ()

std::unique_ptr< DiscreteDistributionInterface >	readDiscreteDistribution (const std::string &distDescription, bool parseArguments)

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

const std::string	getFormatName () const

const std::string	getFormatDescription () const

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

virtual const std::string	getDataType () const

Protected Member Functions
void	initialize_ (DiscreteDistributionInterface &rDist)

Protected Attributes
bool	verbose_

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

Private Attributes
bool	allowConstant_

Detailed Description

Rate Distribution I/O in BppO format.

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

Rate distributions are normalized and have a mean of 1, so that branch lengths are measured in mean number of substitutions per site.

See also: BppODiscreteDistribtution for a more generic parser.

Definition at line 25 of file BppORateDistributionFormat.h.

Constructor & Destructor Documentation

◆ BppORateDistributionFormat()

bpp::BppORateDistributionFormat::BppORateDistributionFormat ( bool allowConstant )

inline

Build a new BppORateDistributionFormat object.

Parameters

allowConstant Is constant distribution allowed.

Definition at line 37 of file BppORateDistributionFormat.h.

◆ ~BppORateDistributionFormat()

virtual bpp::BppORateDistributionFormat::~BppORateDistributionFormat ( )

inlinevirtual

Definition at line 42 of file BppORateDistributionFormat.h.

Member Function Documentation

◆ readDiscreteDistribution()

unique_ptr< DiscreteDistributionInterface > BppORateDistributionFormat::readDiscreteDistribution	(	const std::string &	distDescription,
		bool	parseArguments
	)

virtual

Reimplemented from bpp::BppODiscreteDistributionFormat.

Definition at line 26 of file BppORateDistributionFormat.cpp.

References allowConstant_, bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::BppODiscreteDistributionFormat::getUnparsedArguments(), bpp::StringTokenizer::hasMoreToken(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::TextTools::isEmpty(), bpp::StringTokenizer::nextToken(), bpp::KeyvalTools::parseProcedure(), readDiscreteDistribution(), bpp::TextTools::toDouble(), bpp::TextTools::toInt(), bpp::TextTools::toString(), bpp::BppODiscreteDistributionFormat::unparsedArguments_, and bpp::BppODiscreteDistributionFormat::verbose_.

Referenced by bpp::PhylogeneticsApplicationTools::getRateDistribution(), bpp::PhylogeneticsApplicationTools::getRateDistributions(), readDiscreteDistribution(), and bpp::BppOSubstitutionModelFormat::readSubstitutionModel().

◆ writeDiscreteDistribution()

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