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

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

Inheritance diagram for bpp::BppOFrequenciesSetFormat:

Collaboration diagram for bpp::BppOFrequenciesSetFormat:

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

	BppOFrequenciesSetFormat (const BppOFrequenciesSetFormat &format)

BppOFrequenciesSetFormat &	operator= (const BppOFrequenciesSetFormat &format)

virtual	~BppOFrequenciesSetFormat ()

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...

FrequenciesSet *	read (const Alphabet alphabet, const std::string &freqDescription, const SiteContainer data, bool parseArguments=true)
	Read a frequencies set from a string. More...

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

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

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_ (FrequenciesSet &freqSet, const SiteContainer *data)

Private Attributes
unsigned char	alphabetCode_

bool	verbose_

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

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++ Progam Suite manual for a detailed description of this syntax).

Definition at line 56 of file BppOFrequenciesSetFormat.h.

Constructor & Destructor Documentation

◆ BppOFrequenciesSetFormat() [1/2]

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

inline

Definition at line 77 of file BppOFrequenciesSetFormat.h.

◆ BppOFrequenciesSetFormat() [2/2]

bpp::BppOFrequenciesSetFormat::BppOFrequenciesSetFormat ( const BppOFrequenciesSetFormat & format )

inline

Definition at line 85 of file BppOFrequenciesSetFormat.h.

◆ ~BppOFrequenciesSetFormat()

virtual bpp::BppOFrequenciesSetFormat::~BppOFrequenciesSetFormat ( )

inlinevirtual

Definition at line 103 of file BppOFrequenciesSetFormat.h.

Member Function Documentation

◆ getDataType()

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

inlinevirtualinherited

Definition at line 69 of file IoFrequenciesSet.h.

◆ getFormatDescription()

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

inline

Definition at line 108 of file BppOFrequenciesSetFormat.h.

◆ getFormatName()

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

inline

Definition at line 106 of file BppOFrequenciesSetFormat.h.

◆ getUnparsedArguments()

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

inlinevirtual

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

Implements bpp::IFrequenciesSet.

Definition at line 125 of file BppOFrequenciesSetFormat.h.

References unparsedArguments_.

Referenced by read(), bpp::BppOSubstitutionModelFormat::read(), and bpp::BppOSubstitutionModelFormat::readWord_().

◆ initialize_()

void BppOFrequenciesSetFormat::initialize_	(	FrequenciesSet &	freqSet,
		const SiteContainer *	data
	)

private

Definition at line 617 of file BppOFrequenciesSetFormat.cpp.

References bpp::FrequenciesSet::setFrequencies(), and bpp::FrequenciesSet::setFrequenciesFromAlphabetStatesFrequencies().

◆ operator=()

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

inline

Definition at line 93 of file BppOFrequenciesSetFormat.h.

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

◆ read()

FrequenciesSet * BppOFrequenciesSetFormat::read	(	const Alphabet *	alphabet,
		const std::string &	freqDescription,
		const SiteContainer *	data,
		bool	parseArguments = `true`
	)

virtual

Read a frequencies set from a string.

Parameters

alphabet	The alpabet to use in the model.
freqDescription	A string describing the frequencies set.
data	A SiteContainer with the data to use to initialize fequency parameters. Can be set to 0.
parseArguments	Attempt to parse function arguments. If not, only store them and use default values instead.

Returns: A new FrequenciesSet object according to options specified.

Exceptions

Exception if an error occured.

Implements bpp::IFrequenciesSet.

Definition at line 76 of file BppOFrequenciesSetFormat.cpp.

References bpp::CodonFrequenciesSet::F0, bpp::CodonFrequenciesSet::F1X4, bpp::CodonFrequenciesSet::F3X4, bpp::CodonFrequenciesSet::F61, bpp::CodonFrequenciesSet::getFrequenciesSetForCodons(), bpp::FrequenciesSet::getName(), getUnparsedArguments(), and read().

Referenced by bpp::PhylogeneticsApplicationTools::getFrequenciesSet(), read(), bpp::BppOSubstitutionModelFormat::read(), and bpp::BppOSubstitutionModelFormat::readWord_().

◆ setGeneticCode()

void bpp::BppOFrequenciesSetFormat::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 115 of file BppOFrequenciesSetFormat.h.

References geneticCode_.

Referenced by bpp::PhylogeneticsApplicationTools::getFrequenciesSet(), bpp::BppOSubstitutionModelFormat::read(), and bpp::BppOSubstitutionModelFormat::readWord_().

◆ write()

void BppOFrequenciesSetFormat::write	(	const FrequenciesSet *	pfreqset,
		OutputStream &	out,
		std::vector< std::string > &	writtenNames
	)		const

virtual

Write a substitution model to a stream.

Parameters

pfreqset	A pointer towards a frequencies set object;
out	The output stream;
writtenNames	is the vector of the written parameters so far [in, out];

Implements bpp::OFrequenciesSet.

Definition at line 496 of file BppOFrequenciesSetFormat.cpp.

References bpp::FrequenciesSet::getFrequencies(), bpp::WordFromIndependentFrequenciesSet::getFrequenciesSetForLetter(), bpp::WordFromUniqueFrequenciesSet::getFrequenciesSetForLetter(), bpp::WordFromIndependentFrequenciesSet::getLength(), bpp::WordFromUniqueFrequenciesSet::getLength(), bpp::FullCodonFrequenciesSet::getMethod(), bpp::FullPerAACodonFrequenciesSet::getMethod(), bpp::FrequenciesSet::getName(), and bpp::FullPerAACodonFrequenciesSet::getProteinFrequenciesSet().

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

Member Data Documentation

◆ ALL

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

static

Definition at line 67 of file BppOFrequenciesSetFormat.h.

Referenced by bpp::IOFrequenciesSetFactory::createReader(), bpp::IOFrequenciesSetFactory::createWriter(), bpp::PhylogeneticsApplicationTools::getFrequenciesSet(), bpp::PhylogeneticsApplicationTools::printParameters(), and bpp::BppOSubstitutionModelFormat::read().

◆ alphabetCode_

unsigned char bpp::BppOFrequenciesSetFormat::alphabetCode_

private

Definition at line 70 of file BppOFrequenciesSetFormat.h.

Referenced by operator=().

◆ CODON

unsigned char BppOFrequenciesSetFormat::CODON = 8

static

Definition at line 65 of file BppOFrequenciesSetFormat.h.

◆ DNA

unsigned char BppOFrequenciesSetFormat::DNA = 1

static

Definition at line 61 of file BppOFrequenciesSetFormat.h.

◆ geneticCode_

const GeneticCode* bpp::BppOFrequenciesSetFormat::geneticCode_

private

Definition at line 73 of file BppOFrequenciesSetFormat.h.

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

◆ NUCLEOTIDE

unsigned char BppOFrequenciesSetFormat::NUCLEOTIDE = 1 | 2

static

Definition at line 63 of file BppOFrequenciesSetFormat.h.

◆ PROTEIN

unsigned char BppOFrequenciesSetFormat::PROTEIN = 4

static

Definition at line 64 of file BppOFrequenciesSetFormat.h.

◆ RNA

unsigned char BppOFrequenciesSetFormat::RNA = 2

static

Definition at line 62 of file BppOFrequenciesSetFormat.h.

◆ unparsedArguments_

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

private

Definition at line 72 of file BppOFrequenciesSetFormat.h.

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

◆ verbose_

bool bpp::BppOFrequenciesSetFormat::verbose_

private

Definition at line 71 of file BppOFrequenciesSetFormat.h.

Referenced by operator=().

◆ warningLevel_

int bpp::BppOFrequenciesSetFormat::warningLevel_

private

Definition at line 74 of file BppOFrequenciesSetFormat.h.

Referenced by operator=().

◆ WORD

unsigned char BppOFrequenciesSetFormat::WORD = 16

static

Definition at line 66 of file BppOFrequenciesSetFormat.h.

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

Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BppOFrequenciesSetFormat() [1/2]

◆ BppOFrequenciesSetFormat() [2/2]

◆ ~BppOFrequenciesSetFormat()

Member Function Documentation

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ getUnparsedArguments()

◆ initialize_()

◆ operator=()

◆ read()

◆ setGeneticCode()

◆ write()

Member Data Documentation

◆ ALL

◆ alphabetCode_

◆ CODON

◆ DNA

◆ geneticCode_

◆ NUCLEOTIDE

◆ PROTEIN

◆ RNA

◆ unparsedArguments_

◆ verbose_

◆ warningLevel_

◆ WORD