Frequencies set I/O in BppO format. More...

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

Inheritance diagram for bpp::BppOFrequencySetFormat:

Collaboration diagram for bpp::BppOFrequencySetFormat:

Public Member Functions
	BppOFrequencySetFormat (unsigned char alphabetCode, bool verbose, int warn)

	BppOFrequencySetFormat (const BppOFrequencySetFormat &format)

BppOFrequencySetFormat &	operator= (const BppOFrequencySetFormat &format)

virtual	~BppOFrequencySetFormat ()

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< FrequencySetInterface >	readFrequencySet (std::shared_ptr< const Alphabet > alphabet, const std::string &freqDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true) override
	Read a frequencies set from a string. More...

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

void	writeFrequencySet (const FrequencySetInterface &freqset, 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	ALL = 1 \| 2 \| 4 \| 8 \| 16

Private Member Functions
void	initialize_ (FrequencySetInterface &freqSet, std::shared_ptr< const AlignmentDataInterface > data)

Private Attributes
unsigned char	alphabetCode_

bool	verbose_

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

std::shared_ptr< const GeneticCode >	geneticCode_

int	warningLevel_

Detailed Description

Frequencies set I/O in BppO format.

Allow to create a new frequencies set object according to model description syntax (see the Bio++ Program Suite manual for a detailed description of this syntax).

Definition at line 22 of file BppOFrequencySetFormat.h.

Constructor & Destructor Documentation

◆ BppOFrequencySetFormat() [1/2]

bpp::BppOFrequencySetFormat::BppOFrequencySetFormat	(	unsigned char	alphabetCode,
		bool	verbose,
		int	warn
	)

inline

Definition at line 43 of file BppOFrequencySetFormat.h.

◆ BppOFrequencySetFormat() [2/2]

bpp::BppOFrequencySetFormat::BppOFrequencySetFormat ( const BppOFrequencySetFormat & format )

inline

Definition at line 51 of file BppOFrequencySetFormat.h.

◆ ~BppOFrequencySetFormat()

virtual bpp::BppOFrequencySetFormat::~BppOFrequencySetFormat ( )

inlinevirtual

Definition at line 69 of file BppOFrequencySetFormat.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 32 of file IoFrequencySet.h.

◆ getFormatDescription()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 74 of file BppOFrequencySetFormat.h.

◆ getFormatName()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 72 of file BppOFrequencySetFormat.h.

◆ getUnparsedArguments()

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

inlineoverridevirtual

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

Implements bpp::IFrequencySet.

Definition at line 93 of file BppOFrequencySetFormat.h.

References unparsedArguments_.

Referenced by bpp::PhylogeneticsApplicationTools::getFrequencySet(), bpp::PhylogeneticsApplicationTools::getRootFrequencySets(), readFrequencySet(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOTransitionModelFormat::readTransitionModel(), and bpp::BppOSubstitutionModelFormat::readWord_().

◆ initialize_()

void BppOFrequencySetFormat::initialize_	(	FrequencySetInterface &	freqSet,
		std::shared_ptr< const AlignmentDataInterface >	data
	)

private

Definition at line 821 of file BppOFrequencySetFormat.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getDoubleParameter(), bpp::SequenceContainerTools::getFrequencies(), bpp::ParameterAliasable::getIndependentParameters(), bpp::StringTokenizer::hasMoreToken(), bpp::ParameterAliasable::matchParametersValues(), bpp::StringTokenizer::nextToken(), bpp::FrequencySetInterface::setFrequencies(), bpp::FrequencySetInterface::setFrequenciesFromAlphabetStatesFrequencies(), bpp::AutoParameter::setMessageHandler(), bpp::ParameterList::setParameter(), bpp::ParameterList::size(), bpp::TextTools::toDouble(), bpp::TextTools::toString(), and bpp::ApplicationTools::warning.

◆ operator=()

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

inline

Definition at line 59 of file BppOFrequencySetFormat.h.

References alphabetCode_, geneticCode_, unparsedArguments_, verbose_, and warningLevel_.

◆ readFrequencySet()

std::unique_ptr< FrequencySetInterface > BppOFrequencySetFormat::readFrequencySet	(	std::shared_ptr< const Alphabet >	alphabet,
		const std::string &	freqDescription,
		const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &	mData,
		size_t	nData,
		bool	parseArguments = `true`
	)

overridevirtual

Read a frequencies set from a string.

Parameters

alphabet	The alphabet to use in the model.
freqDescription	A string describing the frequencies set.
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 FrequencySet object according to options specified.

Exceptions

Exception if an error occurred.

Implements bpp::IFrequencySet.

Definition at line 44 of file BppOFrequencySetFormat.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::CodonFrequencySetInterface::F0, bpp::CodonFrequencySetInterface::F1X4, bpp::CodonFrequencySetInterface::F3X4, bpp::CodonFrequencySetInterface::F61, bpp::CodonFrequencySetInterface::getFrequencySetForCodons(), getUnparsedArguments(), bpp::BppOSubstitutionModelFormat::getUnparsedArguments(), bpp::AlphabetTools::isCodonAlphabet(), bpp::TextTools::isDecimalInteger(), bpp::TextTools::isEmpty(), bpp::AlphabetTools::isNucleicAlphabet(), bpp::AlphabetTools::isProteicAlphabet(), bpp::AlphabetTools::isWordAlphabet(), bpp::KeyvalTools::parseProcedure(), readFrequencySet(), bpp::BppOTransitionModelFormat::readTransitionModel(), bpp::BppOSubstitutionModelFormat::setGeneticCode(), bpp::ParameterList::size(), bpp::TextTools::toInt(), and bpp::TextTools::toString().

Referenced by bpp::PhylogeneticsApplicationTools::getFrequencySet(), bpp::PhylogeneticsApplicationTools::getRootFrequencySets(), readFrequencySet(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), bpp::BppOTransitionModelFormat::readTransitionModel(), and bpp::BppOSubstitutionModelFormat::readWord_().

◆ setGeneticCode()

void bpp::BppOFrequencySetFormat::setGeneticCode ( std::shared_ptr< 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 81 of file BppOFrequencySetFormat.h.

References geneticCode_.

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

◆ setVerbose()

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

inline

Definition at line 104 of file BppOFrequencySetFormat.h.

References verbose_.

◆ writeFrequencySet()

void BppOFrequencySetFormat::writeFrequencySet	(	const FrequencySetInterface &	pfreqset,
		OutputStream &	out,
		std::map< std::string, std::string > &	globalAliases,
		std::vector< std::string > &	writtenNames
	)		const

overridevirtual

Write a substitution model to a stream.

Parameters

pfreqset	A frequency set 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];

Implements bpp::OFrequencySet.

Definition at line 607 of file BppOFrequencySetFormat.cpp.

References bpp::BppOSubstitutionModelFormat::ALL, bpp::ParameterList::deleteParameter(), bpp::FrequencySetInterface::getFrequencies(), bpp::FullCodonFrequencySet::getMethod(), bpp::FrequencySetInterface::getName(), bpp::ParameterList::getParameterNames(), bpp::ParameterAliasable::getParameters(), bpp::OutputStream::getPrecision(), bpp::OutputStream::setPrecision(), bpp::ParameterList::size(), bpp::BppOSubstitutionModelFormat::write(), and bpp::BppOParametrizableFormat::write().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::printParameters(), bpp::PhylogeneticsApplicationTools::printParameters(), and bpp::BppOSubstitutionModelFormat::write().

Member Data Documentation

◆ ALL

unsigned char BppOFrequencySetFormat::ALL = 1 | 2 | 4 | 8 | 16

static

Definition at line 33 of file BppOFrequencySetFormat.h.

Referenced by bpp::IOFrequencySetFactory::createReader(), bpp::IOFrequencySetFactory::createWriter(), bpp::PhylogeneticsApplicationTools::getFrequencySet(), bpp::PhylogeneticsApplicationTools::getRootFrequencySets(), bpp::LegacyPhylogeneticsApplicationTools::printParameters(), bpp::PhylogeneticsApplicationTools::printParameters(), bpp::BppOSubstitutionModelFormat::readSubstitutionModel(), and bpp::BppOTransitionModelFormat::readTransitionModel().

◆ alphabetCode_

unsigned char bpp::BppOFrequencySetFormat::alphabetCode_

private

Definition at line 36 of file BppOFrequencySetFormat.h.

Referenced by operator=().

◆ CODON

unsigned char BppOFrequencySetFormat::CODON = 8

static

Definition at line 31 of file BppOFrequencySetFormat.h.

◆ DNA

unsigned char BppOFrequencySetFormat::DNA = 1

static

Definition at line 27 of file BppOFrequencySetFormat.h.

◆ geneticCode_

std::shared_ptr<const GeneticCode> bpp::BppOFrequencySetFormat::geneticCode_

private

Definition at line 39 of file BppOFrequencySetFormat.h.

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

◆ NUCLEOTIDE

unsigned char BppOFrequencySetFormat::NUCLEOTIDE = 1 | 2

static

Definition at line 29 of file BppOFrequencySetFormat.h.

◆ PROTEIN

unsigned char BppOFrequencySetFormat::PROTEIN = 4

static

Definition at line 30 of file BppOFrequencySetFormat.h.

◆ RNA

unsigned char BppOFrequencySetFormat::RNA = 2

static

Definition at line 28 of file BppOFrequencySetFormat.h.

◆ unparsedArguments_

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

private

Definition at line 38 of file BppOFrequencySetFormat.h.

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

◆ verbose_

bool bpp::BppOFrequencySetFormat::verbose_

private

Definition at line 37 of file BppOFrequencySetFormat.h.

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

◆ warningLevel_

int bpp::BppOFrequencySetFormat::warningLevel_

private

Definition at line 40 of file BppOFrequencySetFormat.h.

Referenced by operator=().

◆ WORD

unsigned char BppOFrequencySetFormat::WORD = 16

static

Definition at line 32 of file BppOFrequencySetFormat.h.

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

Bpp/Phyl/Io/BppOFrequencySetFormat.h
Bpp/Phyl/Io/BppOFrequencySetFormat.cpp

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BppOFrequencySetFormat() [1/2]

◆ BppOFrequencySetFormat() [2/2]

◆ ~BppOFrequencySetFormat()

Member Function Documentation

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ getUnparsedArguments()

◆ initialize_()

◆ operator=()

◆ readFrequencySet()

◆ setGeneticCode()

◆ setVerbose()

◆ writeFrequencySet()

Member Data Documentation

◆ ALL

◆ alphabetCode_

◆ CODON

◆ DNA

◆ geneticCode_

◆ NUCLEOTIDE

◆ PROTEIN

◆ RNA

◆ unparsedArguments_

◆ verbose_

◆ warningLevel_

◆ WORD