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

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

Inheritance diagram for bpp::BppOBranchModelFormat:

Collaboration diagram for bpp::BppOBranchModelFormat:

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

	BppOBranchModelFormat (const BppOTransitionModelFormat &format)

BppOBranchModelFormat &	operator= (const BppOBranchModelFormat &format)

std::unique_ptr< BranchModelInterface >	readBranchModel (std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true)

std::unique_ptr< TransitionModelInterface >	readTransitionModel (std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true)

const std::string	getFormatName () const override

const std::string	getFormatDescription () const override

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

std::unique_ptr< SubstitutionModelInterface >	readSubstitutionModel (std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true) override
	Read a substitution model from a string. More...

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

void	write (const BranchModelInterface &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const override
	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	INTEGER = 64

static unsigned char	ALL = 1 \| 2 \| 4 \| 8 \| 16 \| 32 \| 64

Protected Member Functions
void	updateParameters_ (BranchModelInterface &model, std::map< std::string, std::string > &args)
	Finish parsing of parameters, taking care of aliases. More...

void	initialize_ (BranchModelInterface &model, std::shared_ptr< const AlignmentDataInterface > data)
	Set parameter initial values of a given model according to options. More...

Protected Attributes
unsigned char	alphabetCode_

bool	allowCovarions_

bool	allowMixed_

bool	allowGaps_

bool	verbose_

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

std::shared_ptr< const GeneticCode >	geneticCode_

int	warningLevel_

Private Member Functions
std::unique_ptr< MixedTransitionModelInterface >	readMixed_ (std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData)

std::unique_ptr< SubstitutionModelInterface >	readWord_ (std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData)

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

Detailed Description

Branch model I/O in BppO format.

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

Definition at line 21 of file BppOBranchModelFormat.h.

Constructor & Destructor Documentation

◆ BppOBranchModelFormat() [1/2]

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

inline

Create a new BppOBranchModelFormat 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 35 of file BppOBranchModelFormat.h.

◆ BppOBranchModelFormat() [2/2]

bpp::BppOBranchModelFormat::BppOBranchModelFormat ( const BppOTransitionModelFormat & format )

inline

Definition at line 39 of file BppOBranchModelFormat.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 35 of file IoSubstitutionModel.h.

◆ getFormatDescription()

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

inlineoverridevirtualinherited

Implements bpp::IOFormat.

Definition at line 100 of file BppOSubstitutionModelFormat.h.

◆ getFormatName()

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

inlineoverridevirtualinherited

Implements bpp::IOFormat.

Definition at line 98 of file BppOSubstitutionModelFormat.h.

◆ getUnparsedArguments()

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

inlineoverridevirtualinherited

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 119 of file BppOSubstitutionModelFormat.h.

References bpp::BppOSubstitutionModelFormat::unparsedArguments_.

Referenced by bpp::PhylogeneticsApplicationTools::getBranchModel(), bpp::PhylogeneticsApplicationTools::getBranchModels(), bpp::PhylogeneticsApplicationTools::getSubstitutionModel(), readBranchModel(), bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOTransitionModelFormat::readMixed_(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOTransitionModelFormat::readTransitionModel(), bpp::BppOSubstitutionModelFormat::readWord_(), and bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ initialize_()

void BppOSubstitutionModelFormat::initialize_	(	BranchModelInterface &	model,
		std::shared_ptr< const AlignmentDataInterface >	data
	)

protectedinherited

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 AlignmentDataInterface 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 occurred.

Definition at line 2000 of file BppOSubstitutionModelFormat.cpp.

References bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::ApplicationTools::getDoubleParameter(), bpp::ParameterAliasable::getIndependentParameters(), bpp::BranchModelInterface::getName(), bpp::ParameterAliasable::getNamespace(), bpp::ApplicationTools::getStringParameter(), bpp::StringTokenizer::hasMoreToken(), bpp::ParameterAliasable::matchParametersValues(), bpp::StringTokenizer::nextToken(), bpp::AutoParameter::setMessageHandler(), bpp::ParameterList::setParameter(), bpp::ParameterList::size(), bpp::TextTools::toDouble(), bpp::TextTools::toString(), and bpp::ApplicationTools::warning.

◆ operator=()

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

inline

Definition at line 43 of file BppOBranchModelFormat.h.

References bpp::BppOTransitionModelFormat::operator=().

◆ readBranchModel()

std::unique_ptr< BranchModelInterface > BppOBranchModelFormat::readBranchModel	(	std::shared_ptr< const Alphabet >	alphabet,
		const std::string &	modelDescription,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mData,
		size_t	nData,
		bool	parseArguments = `true`
	)

Definition at line 37 of file BppOBranchModelFormat.cpp.

References bpp::ApplicationTools::displayResult(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::KeyvalTools::parseProcedure(), bpp::BppOTransitionModelFormat::readTransitionModel(), bpp::BppOSubstitutionModelFormat::setGeneticCode(), and bpp::TextTools::toString().

Referenced by bpp::PhylogeneticsApplicationTools::getBranchModel(), and bpp::PhylogeneticsApplicationTools::getBranchModels().

◆ readMixed_()

unique_ptr< MixedTransitionModelInterface > BppOTransitionModelFormat::readMixed_	(	std::shared_ptr< const Alphabet >	alphabet,
		const std::string &	modelDescription,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mData,
		size_t	nData
	)

privateinherited

Definition at line 284 of file BppOTransitionModelFormat.cpp.

References bpp::ApplicationTools::displayResult(), bpp::BppODiscreteDistributionFormat::getUnparsedArguments(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::KeyvalTools::parseProcedure(), bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOTransitionModelFormat::readTransitionModel(), bpp::BppOSubstitutionModelFormat::setGeneticCode(), and bpp::TextTools::toString().

◆ readSubstitutionModel()

unique_ptr< SubstitutionModelInterface > BppOSubstitutionModelFormat::readSubstitutionModel	(	std::shared_ptr< const Alphabet >	alphabet,
		const std::string &	modelDescription,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mData,
		size_t	nData,
		bool	parseArguments = `true`
	)

overridevirtualinherited

Read a substitution model from a string.

Parameters

alphabet	The alphabet to use in the model.
modelDescription	A string describing the model in the format.
mData	A map towards pointers of SiteContainer with the data to use to initialize frequency parameters
nData	Number of the SiteContainer in the mData. Can be set to 0, if none assigned.
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 occurred.

SIMPLE MODELS

Implements bpp::ISubstitutionModel.

Definition at line 118 of file BppOSubstitutionModelFormat.cpp.

References bpp::BppOFrequencySetFormat::ALL, bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::ApplicationTools::getStringParameter(), bpp::PhylogeneticsApplicationTools::getSubstitutionRegister(), bpp::BppODiscreteDistributionFormat::getUnparsedArguments(), bpp::BppOFrequencySetFormat::getUnparsedArguments(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::AlphabetTools::isBinaryAlphabet(), bpp::AlphabetTools::isCodonAlphabet(), bpp::TextTools::isEmpty(), bpp::AlphabetTools::isIntegerAlphabet(), bpp::AlphabetTools::isNucleicAlphabet(), bpp::AlphabetTools::isProteicAlphabet(), bpp::AlphabetTools::isRNYAlphabet(), bpp::KeyvalTools::parseProcedure(), bpp::BppORateDistributionFormat::readDiscreteDistribution(), bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOTransitionModelFormat::readTransitionModel(), bpp::BppOFrequencySetFormat::setGeneticCode(), bpp::BppOSubstitutionModelFormat::setGeneticCode(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

Referenced by bpp::PhylogeneticsApplicationTools::getSubstitutionModel(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOTransitionModelFormat::readTransitionModel(), and bpp::BppOSubstitutionModelFormat::readWord_().

◆ readTransitionModel()

unique_ptr< TransitionModelInterface > BppOTransitionModelFormat::readTransitionModel	(	std::shared_ptr< const Alphabet >	alphabet,
		const std::string &	modelDescription,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mData,
		size_t	nData,
		bool	parseArguments = `true`
	)

inherited

Definition at line 57 of file BppOTransitionModelFormat.cpp.

References bpp::BppOFrequencySetFormat::ALL, bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::ApplicationTools::getStringParameter(), bpp::PhylogeneticsApplicationTools::getSubstitutionRegister(), bpp::BppOFrequencySetFormat::getUnparsedArguments(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::StringTokenizer::hasMoreToken(), bpp::AlphabetTools::isCodonAlphabet(), bpp::AlphabetTools::isProteicAlphabet(), bpp::StringTokenizer::nextToken(), bpp::KeyvalTools::parseProcedure(), bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOFrequencySetFormat::setGeneticCode(), and bpp::BppOSubstitutionModelFormat::setGeneticCode().

Referenced by readBranchModel(), bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOTransitionModelFormat::readMixed_(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), and bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ readWord_()

unique_ptr< SubstitutionModelInterface > BppOSubstitutionModelFormat::readWord_	(	std::shared_ptr< const Alphabet >	alphabet,
		const std::string &	modelDescription,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mData,
		size_t	nData
	)

privateinherited

Reading the submodels

Dist

Freq

Default name in none used before

Definition at line 985 of file BppOSubstitutionModelFormat.cpp.

References bpp::ApplicationTools::displayWarning(), bpp::SequenceApplicationTools::getAlphabetIndex2(), bpp::BppOFrequencySetFormat::getUnparsedArguments(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::StringTokenizer::hasMoreToken(), bpp::AlphabetTools::isCodonAlphabet(), bpp::AlphabetTools::isWordAlphabet(), bpp::StringTokenizer::nextToken(), bpp::KeyvalTools::parseProcedure(), bpp::AlphabetTools::PROTEIN_ALPHABET, bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOFrequencySetFormat::setGeneticCode(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

◆ setGeneticCode()

void bpp::BppOSubstitutionModelFormat::setGeneticCode ( std::shared_ptr< const GeneticCode > gCode )

inlineinherited

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 107 of file BppOSubstitutionModelFormat.h.

References bpp::BppOSubstitutionModelFormat::geneticCode_.

Referenced by bpp::PhylogeneticsApplicationTools::getBranchModel(), bpp::PhylogeneticsApplicationTools::getBranchModels(), bpp::PhylogeneticsApplicationTools::getSubstitutionModel(), readBranchModel(), bpp::BppOFrequencySetFormat::readFrequencySet(), bpp::BppOTransitionModelFormat::readMixed_(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOTransitionModelFormat::readTransitionModel(), and bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ setVerbose()

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

inlineinherited

Definition at line 140 of file BppOSubstitutionModelFormat.h.

References bpp::BppOSubstitutionModelFormat::verbose_.

Referenced by bpp::PhylogeneticsApplicationTools::getBranchModels(), and bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelSet().

◆ updateParameters_()

void BppOSubstitutionModelFormat::updateParameters_	(	BranchModelInterface &	model,
		std::map< std::string, std::string > &	args
	)

protectedinherited

Finish parsing of parameters, taking care of aliases.

Definition at line 911 of file BppOSubstitutionModelFormat.cpp.

References bpp::BranchModelInterface::addRateParameter(), bpp::ParameterAliasable::aliasParameters(), bpp::ApplicationTools::displayResult(), bpp::ParameterAliasable::getIndependentParameters(), bpp::ParameterAliasable::getNamespace(), bpp::ParameterList::getParameterNames(), bpp::ParameterAliasable::getParameterNameWithoutNamespace(), bpp::ParameterAliasable::getParameters(), bpp::TextTools::isDecimalInteger(), and bpp::ParameterList::size().

◆ write()

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

overridevirtualinherited

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 occurred.

Implements bpp::OSubstitutionModel.

Definition at line 1515 of file BppOSubstitutionModelFormat.cpp.

References bpp::POMO::fitness(), bpp::BranchModelInterface::frequencySet(), bpp::Coala::getExch(), bpp::ParameterAliasable::getIndependentParameters(), bpp::BranchModelInterface::getName(), bpp::AbstractParameterAliasable::getNamespace(), bpp::CoalaCore::getNbrOfAxes(), bpp::AbstractWordSubstitutionModel::getNumberOfModels(), bpp::ParameterList::getParameterNames(), bpp::UserProteinSubstitutionModel::getPath(), bpp::OneChangeRegisterTransitionModel::getRegisterName(), bpp::RegisterRatesSubstitutionModel::getRegisterName(), bpp::OneChangeRegisterTransitionModel::getRegisterNumbers(), bpp::InMixedSubstitutionModel::getSubModelNumber(), bpp::POMO::hasFitness(), bpp::TextTools::hasSubstring(), bpp::InMixedSubstitutionModel::mixedModel(), bpp::AbstractFromSubstitutionModelTransitionModel::model(), bpp::AbstractWrappedTransitionModel::model(), bpp::POMO::mutationModel(), bpp::MarkovModulatedSubstitutionModel::nestedModel(), bpp::gBGC::nestedModel(), bpp::YpR::nestedModel(), bpp::RE08::nestedModel(), bpp::AbstractWordSubstitutionModel::nModel(), bpp::VectorTools::paste(), bpp::G2001::rateDistribution(), bpp::StdStr::str(), bpp::TextTools::toString(), bpp::BppOParametrizableFormat::write(), bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

Referenced by bpp::PhylogeneticsApplicationTools::printParameters(), bpp::LegacyPhylogeneticsApplicationTools::printParameters(), and bpp::BppOFrequencySetFormat::writeFrequencySet().

◆ writeMixed_()

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