Substitution model I/O in BppO format. More...

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

Inheritance diagram for bpp::BppOSubstitutionModelFormat:

Collaboration diagram for bpp::BppOSubstitutionModelFormat:

Public Member Functions
	BppOSubstitutionModelFormat (unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn)
	Create a new BppOSubstitutionModelFormat object. More...

	BppOSubstitutionModelFormat (const BppOSubstitutionModelFormat &format)

BppOSubstitutionModelFormat &	operator= (const BppOSubstitutionModelFormat &format)

virtual	~BppOSubstitutionModelFormat ()

const std::string	getFormatName () const

const std::string	getFormatDescription () const

void	setGeneticCode (const GeneticCode *gCode)
	Set the genetic code to use in case a codon frequencies set should be built. More...

SubstitutionModel *	read (const Alphabet alphabet, const std::string &modelDescription, const SiteContainer data=0, bool parseArguments=true)
	Read a substitution model from a string. More...

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

void	write (const SubstitutionModel &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const
	Write a substitution model to a stream. More...

void	setVerbose (bool verbose)

virtual const std::string	getDataType () const

Static Public Attributes
static unsigned char	DNA = 1

static unsigned char	RNA = 2

static unsigned char	NUCLEOTIDE = 1 \| 2

static unsigned char	PROTEIN = 4

static unsigned char	CODON = 8

static unsigned char	WORD = 16

static unsigned char	BINARY = 32

static unsigned char	ALL = 1 \| 2 \| 4 \| 8 \| 16 \| 32

Private Member Functions
MixedSubstitutionModel *	readMixed_ (const Alphabet alphabet, const std::string &modelDescription, const SiteContainer data)

SubstitutionModel *	readWord_ (const Alphabet alphabet, const std::string &modelDescription, const SiteContainer data)

void	initialize_ (SubstitutionModel &model, const SiteContainer *data) throw (Exception)
	Set parameter initial values of a given model according to options. More...

void	writeMixed_ (const MixedSubstitutionModel &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const

Private Attributes
unsigned char	alphabetCode_

bool	allowCovarions_

bool	allowMixed_

bool	allowGaps_

bool	verbose_

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

const GeneticCode *	geneticCode_

int	warningLevel_

Detailed Description

Substitution model I/O in BppO format.

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

Definition at line 59 of file BppOSubstitutionModelFormat.h.

Constructor & Destructor Documentation

◆ BppOSubstitutionModelFormat() [1/2]

bpp::BppOSubstitutionModelFormat::BppOSubstitutionModelFormat	(	unsigned char	alphabetCode,
		bool	allowCovarions,
		bool	allowMixed,
		bool	allowGaps,
		bool	verbose,
		int	warn
	)

inline

Create a new BppOSubstitutionModelFormat object.

Parameters

alphabetCode	Bit saying which alphabets are allowed in the model specification.
allowCovarions	Tell is a covarion model can be returned.
allowMixed	Tell is a mixture model can be returned.
allowGaps	Tell is a gap model can be returned.
verbose	Tell if the construction is verbose.
warn	Set the warning level (0: always display warnings, >0 display warnings on demand).

Definition at line 94 of file BppOSubstitutionModelFormat.h.

◆ BppOSubstitutionModelFormat() [2/2]

bpp::BppOSubstitutionModelFormat::BppOSubstitutionModelFormat ( const BppOSubstitutionModelFormat & format )

inline

Definition at line 105 of file BppOSubstitutionModelFormat.h.

◆ ~BppOSubstitutionModelFormat()

virtual bpp::BppOSubstitutionModelFormat::~BppOSubstitutionModelFormat ( )

inlinevirtual

Definition at line 129 of file BppOSubstitutionModelFormat.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Definition at line 69 of file IoSubstitutionModel.h.

◆ getFormatDescription()

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

inline

Definition at line 134 of file BppOSubstitutionModelFormat.h.

◆ getFormatName()

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

inline

Definition at line 132 of file BppOSubstitutionModelFormat.h.

◆ getUnparsedArguments()

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

inlinevirtual

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

Implements bpp::ISubstitutionModel.

Definition at line 147 of file BppOSubstitutionModelFormat.h.

References unparsedArguments_.

Referenced by read(), readMixed_(), readWord_(), and bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ initialize_()

void BppOSubstitutionModelFormat::initialize_	(	SubstitutionModel &	model,
		const SiteContainer *	data
	)
throw	(	Exception
	)

private

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

Parameters actually depends on the model passed as argument. See getSubstitutionModel for more information.

This function is mainly for internal usage, you're probably looking for the getSubstitutionModel or getSubstitutionModelSet function.

Parameters

model	The model to set.
data	A pointer toward the SiteContainer for which the substitution model is designed. The alphabet associated to the data must be of the same type as the one specified for the model. May be equal to NULL, but in this case use_observed_freq option will be unavailable.

Exceptions

Exception if an error occured.

Definition at line 1298 of file BppOSubstitutionModelFormat.cpp.

◆ operator=()

BppOSubstitutionModelFormat& bpp::BppOSubstitutionModelFormat::operator= ( const BppOSubstitutionModelFormat & format )

inline

Definition at line 116 of file BppOSubstitutionModelFormat.h.

References allowCovarions_, allowGaps_, allowMixed_, alphabetCode_, geneticCode_, unparsedArguments_, verbose_, and warningLevel_.

◆ read()

SubstitutionModel * BppOSubstitutionModelFormat::read	(	const Alphabet *	alphabet,
		const std::string &	modelDescription,
		const SiteContainer *	data = `0`,
		bool	parseArguments = `true`
	)

virtual

Read a substitution model from a string.

Parameters

alphabet	The alpabet to use in the model.
modelDescription	A string describing the model in the format.
data	A pointer toward a SiteContainer, which can be used to initial some parmaeters like frequencies.
parseArguments	Attempt to parse function arguments. If not, only store them and use default values instead.

Returns: A new SubstitutionModel object according to options specified.

Exceptions

Exception if an error occured.

Implements bpp::ISubstitutionModel.

Definition at line 131 of file BppOSubstitutionModelFormat.cpp.

References bpp::BppOFrequenciesSetFormat::ALL, bpp::BppOFrequenciesSetFormat::getUnparsedArguments(), getUnparsedArguments(), bpp::BppOFrequenciesSetFormat::read(), read(), bpp::SubstitutionModel::setFreqFromData(), and bpp::BppOFrequenciesSetFormat::setGeneticCode().

Referenced by bpp::PhylogeneticsApplicationTools::getSubstitutionModel(), read(), readMixed_(), readWord_(), and bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ readMixed_()

MixedSubstitutionModel * BppOSubstitutionModelFormat::readMixed_	(	const Alphabet *	alphabet,
		const std::string &	modelDescription,
		const SiteContainer *	data
	)

private

Definition at line 953 of file BppOSubstitutionModelFormat.cpp.

References bpp::SubstitutionModel::getName(), bpp::MixedSubstitutionModel::getNumberOfModels(), getUnparsedArguments(), and read().

◆ readWord_()

SubstitutionModel * BppOSubstitutionModelFormat::readWord_	(	const Alphabet *	alphabet,
		const std::string &	modelDescription,
		const SiteContainer *	data
	)

private

Definition at line 689 of file BppOSubstitutionModelFormat.cpp.

References bpp::BppOFrequenciesSetFormat::getUnparsedArguments(), getUnparsedArguments(), bpp::BppOFrequenciesSetFormat::read(), read(), and bpp::BppOFrequenciesSetFormat::setGeneticCode().

◆ setGeneticCode()

void bpp::BppOSubstitutionModelFormat::setGeneticCode ( const GeneticCode * gCode )

inline

Set the genetic code to use in case a codon frequencies set should be built.

Parameters

gCode The genetic code to use.

Definition at line 141 of file BppOSubstitutionModelFormat.h.

References geneticCode_.

Referenced by bpp::PhylogeneticsApplicationTools::getSubstitutionModel(), and bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ setVerbose()

void bpp::BppOSubstitutionModelFormat::setVerbose ( bool verbose )

inline

Definition at line 165 of file BppOSubstitutionModelFormat.h.

References verbose_.

Referenced by bpp::PhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ write()

void BppOSubstitutionModelFormat::write	(	const SubstitutionModel &	model,
		OutputStream &	out,
		std::map< std::string, std::string > &	globalAliases,
		std::vector< std::string > &	writtenNames
	)		const

virtual

Write a substitution model to a stream.

Parameters

model	A substitution model object;
out	The output stream;
globalAliases	parameters linked to global alias. The output will be "name=alias_name";
writtenNames	is the vector of the written parameters so far [in, out];

Exceptions

Exception If an error occured.

Implements bpp::OSubstitutionModel.

Definition at line 1070 of file BppOSubstitutionModelFormat.cpp.

References bpp::Coala::getExch(), bpp::AbstractCodonFitnessSubstitutionModel::getFitness(), bpp::SubstitutionModel::getFrequenciesSet(), bpp::SubstitutionModel::getName(), bpp::CoalaCore::getNbrOfAxes(), bpp::gBGC::getNestedModel(), bpp::YpR::getNestedModel(), bpp::RE08::getNestedModel(), bpp::MarkovModulatedSubstitutionModel::getNestedModel(), bpp::AbstractWordSubstitutionModel::getNModel(), bpp::AbstractWordSubstitutionModel::getNumberOfModels(), bpp::UserProteinSubstitutionModel::getPath(), bpp::G2001::getRateDistribution(), and bpp::BppOFrequenciesSetFormat::write().

Referenced by bpp::PhylogeneticsApplicationTools::printParameters().

◆ writeMixed_()

void BppOSubstitutionModelFormat::writeMixed_	(	const MixedSubstitutionModel &	model,
		OutputStream &	out,
		std::map< std::string, std::string > &	globalAliases,
		std::vector< std::string > &	writtenNames
	)		const