bpp::PopgenlibIO Class Reference

The native I/O format for popgenlib. More...

#include <Bpp/PopGen/DataSet/Io/PopgenlibIO.h>

Inheritance diagram for bpp::PopgenlibIO:

Collaboration diagram for bpp::PopgenlibIO:

Public Member Functions
	PopgenlibIO ()
	PopgenlibIO (const std::string &missing_data_symbol, const std::string &data_separator)
	~PopgenlibIO ()
std::string	getMissingDataSymbol () const
	Get the code for missing data. More...
std::string	getDataSeparator () const
	Get the code for data separator. More...
char	getMissingDataChar () const
	Get the character for missing data. More...
char	getDataSeparatorChar () const
	Get the data separator char. More...
void	setMissingDataSymbol (const std::string &missing_data_symbol)
	Set the code for missing data. More...
void	setDataSeparator (const std::string &data_separator)
	Set the code for data separator. More...
The IDataSet interface.
void	read (std::istream &is, DataSet &data_set)
	Read a DataSet on istream. More...
void	read (const std::string &path, DataSet &data_set)
	Read a DataSet from a text file. More...
DataSet *	read (std::istream &is)
	Read istream and return a DataSet. More...
DataSet *	read (const std::string &path)
	Read a text file and return a DataSet. More...
The ODataSet interface.
void	write (std::ostream &os, const DataSet &data_set) const
	Write a DataSet on ostream. More...
void	write (const std::string &path, const DataSet &data_set, bool overwrite) const
	Write a DataSet in a text file. More...
The IOFormat interface
const std::string	getFormatName () const
const std::string	getFormatDescription () const

Static Public Attributes
static const std::string	WHITESPACE = string("WHITESPACE")
static const std::string	TAB = string("TAB")
static const std::string	COMA = string("COMA")
static const std::string	SEMICOLON = string("SEMICOLON")
static const std::string	DIPLOID = string("DIPLOID")
static const std::string	HAPLOID = string("HAPLOID")
static const std::string	HAPLODIPLOID = string("HAPLODIPLOID")
static const std::string	UNKNOWN = string("UNKNOWN")

Private Member Functions
std::vector< std::string >	getValues_ (std::string &param_line, const std::string &delim)
void	parseGeneral_ (const std::vector< std::string > &in, DataSet &data_set)
void	parseLocality_ (const std::vector< std::string > &in, DataSet &data_set)
void	parseSequence_ (const std::vector< std::string > &in, VectorSequenceContainer &vsc)
void	parseLoci_ (const std::vector< std::string > &in, std::vector< LocusInfo > &locus_info)
void	parseIndividual_ (const std::vector< std::string > &in, DataSet &data_set, const VectorSequenceContainer &vsc)
The IOFormat interface.
const std::string	getDataType () const

Private Attributes
char	data_separator_
char	missing_data_symbol_

Detailed Description

The native I/O format for popgenlib.

Author

Sylvain Gaillard

Definition at line 63 of file PopgenlibIO.h.

Constructor & Destructor Documentation

PopgenlibIO() [1/2]

PopgenlibIO::PopgenlibIO

(

)

Definition at line 55 of file PopgenlibIO.cpp.

PopgenlibIO() [2/2]

PopgenlibIO::PopgenlibIO	(	const std::string &	missing_data_symbol,
		const std::string &	data_separator
	)

Definition at line 58 of file PopgenlibIO.cpp.

References setDataSeparator(), and setMissingDataSymbol().

~PopgenlibIO()

PopgenlibIO::~PopgenlibIO

(

)

Definition at line 74 of file PopgenlibIO.cpp.

Member Function Documentation

getDataSeparator()

std::string PopgenlibIO::getDataSeparator

(

)

const

Get the code for data separator.

Definition at line 112 of file PopgenlibIO.cpp.

References COMA, data_separator_, SEMICOLON, TAB, bpp::TextTools::toString(), and WHITESPACE.

Referenced by write().

getDataSeparatorChar()

char PopgenlibIO::getDataSeparatorChar

(

)

const

Get the data separator char.

Definition at line 129 of file PopgenlibIO.cpp.

References data_separator_.

Referenced by getValues_(), and write().

getDataType()

const std::string bpp::IODataSet::getDataType ( ) const

inlineprivatevirtualinherited

Implements bpp::IOFormat.

Definition at line 67 of file IODataSet.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 178 of file PopgenlibIO.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 174 of file PopgenlibIO.h.

getMissingDataChar()

char PopgenlibIO::getMissingDataChar

(

)

const

Get the character for missing data.

Definition at line 124 of file PopgenlibIO.cpp.

References missing_data_symbol_.

Referenced by write().

getMissingDataSymbol()

std::string PopgenlibIO::getMissingDataSymbol

(

)

const

Get the code for missing data.

Definition at line 107 of file PopgenlibIO.cpp.

References missing_data_symbol_, and bpp::TextTools::toString().

Referenced by parseIndividual_(), setDataSeparator(), and write().

getValues_()

std::vector< std::string > PopgenlibIO::getValues_ ( std::string &  param_line, const std::string &  delim  )

private

Definition at line 694 of file PopgenlibIO.cpp.

References getDataSeparatorChar(), and bpp::TextTools::removeSurroundingWhiteSpaces().

Referenced by parseGeneral_(), parseIndividual_(), parseLocality_(), and parseLoci_().

parseGeneral_()

void PopgenlibIO::parseGeneral_ ( const std::vector< std::string > &  in, DataSet &  data_set  )

private

Definition at line 295 of file PopgenlibIO.cpp.

References bpp::FileTools::getNextLine(), getValues_(), bpp::DataSet::setAlphabet(), setDataSeparator(), and setMissingDataSymbol().

Referenced by read().

parseIndividual_()

void PopgenlibIO::parseIndividual_ ( const std::vector< std::string > &  in, DataSet &  data_set, const VectorSequenceContainer &  vsc  )

private

Definition at line 395 of file PopgenlibIO.cpp.

References bpp::DataSet::addAlleleInfoByLocusPosition(), bpp::DataSet::addEmptyGroup(), bpp::DataSet::addIndividualToGroup(), bpp::Individual::addSequence(), bpp::DataSet::getGroupPosition(), bpp::Individual::getId(), bpp::DataSet::getLocalityByName(), bpp::DataSet::getLocusInfoAtPosition(), getMissingDataSymbol(), bpp::DataSet::getNumberOfLoci(), bpp::VectorSequenceContainer::getSequence(), getValues_(), bpp::Individual::initGenotype(), bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::Individual::setCoord(), bpp::Individual::setDate(), bpp::Individual::setId(), bpp::Individual::setLocality(), bpp::Individual::setMonolocusGenotypeByAlleleId(), bpp::TextTools::toDouble(), and bpp::TextTools::toInt().

Referenced by read().

parseLocality_()

void PopgenlibIO::parseLocality_ ( const std::vector< std::string > &  in, DataSet &  data_set  )

private

Definition at line 315 of file PopgenlibIO.cpp.

References bpp::DataSet::addLocality(), bpp::Locality< T >::getName(), bpp::FileTools::getNextLine(), getValues_(), bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::Locality< T >::setName(), bpp::Point2D< class >::setX(), bpp::Point2D< class >::setY(), and bpp::TextTools::toDouble().

Referenced by read().

parseLoci_()

void PopgenlibIO::parseLoci_ ( const std::vector< std::string > &  in, std::vector< LocusInfo > &  locus_info  )

private

Definition at line 354 of file PopgenlibIO.cpp.

References DIPLOID, bpp::LocusInfo::DIPLOID, bpp::FileTools::getNextLine(), getValues_(), HAPLODIPLOID, bpp::LocusInfo::HAPLODIPLOID, HAPLOID, bpp::LocusInfo::HAPLOID, bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::TextTools::toUpper(), UNKNOWN, and bpp::LocusInfo::UNKNOWN.

Referenced by read().

parseSequence_()

void PopgenlibIO::parseSequence_ ( const std::vector< std::string > &  in, VectorSequenceContainer &  vsc  )

private

Definition at line 343 of file PopgenlibIO.cpp.

References bpp::Fasta::readSequences().

Referenced by read().

read() [1/4]

DataSet * PopgenlibIO::read ( const std::string &  path )

virtual

Read a text file and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 540 of file PopgenlibIO.cpp.

References bpp::AbstractIDataSet::read().

read() [2/4]

void PopgenlibIO::read ( const std::string &  path, DataSet &  data_set  )

virtual

Read a DataSet from a text file.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 530 of file PopgenlibIO.cpp.

References bpp::AbstractIDataSet::read().

read() [3/4]

DataSet * PopgenlibIO::read ( std::istream &  is )

virtual

Read istream and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 535 of file PopgenlibIO.cpp.

References bpp::AbstractIDataSet::read().

read() [4/4]

void PopgenlibIO::read ( std::istream &  is, DataSet &  data_set  )

virtual

Read a DataSet on istream.

Implements bpp::AbstractIDataSet.

Definition at line 134 of file PopgenlibIO.cpp.

References bpp::DataSet::getAlphabet(), bpp::FileTools::getNextLine(), bpp::DataSet::hasSequenceData(), parseGeneral_(), parseIndividual_(), parseLocality_(), parseLoci_(), parseSequence_(), bpp::DataSet::setAnalyzedLoci(), and bpp::AnalyzedLoci::setLocusInfo().

setDataSeparator()

void PopgenlibIO::setDataSeparator

(

const std::string &

data_separator

)

Set the code for data separator.

The character used to separate data can be every single non numerical character and can't be the same used for coding missing data. Most common characters used are:

• the white space: "WHITESPACE"
• the tabulation: "TAB"
• the coma: "COMA"
• the semicolon: "SEMICOLON"

The default value is "WHITESPACE".

Exceptions

Exception	if data_separator is a not allowed character.
Exception	if data_separator containes more than one character other than the two codes defined upper.

Definition at line 87 of file PopgenlibIO.cpp.

References COMA, data_separator_, getMissingDataSymbol(), SEMICOLON, TAB, and WHITESPACE.

Referenced by parseGeneral_(), and PopgenlibIO().

setMissingDataSymbol()

void PopgenlibIO::setMissingDataSymbol

(

const std::string &

missing_data_symbol

)

Set the code for missing data.

The character used to code missing data can be every single non numerical character and can't be the same used as data separator or a white space or a tabulation. The default value is '$'.

Exceptions

Excpetion	if missing_data_symbol is a not allowed character.
Exception	if missing_data_symbol contains more than one character.

Definition at line 76 of file PopgenlibIO.cpp.

References data_separator_, bpp::TextTools::isWhiteSpaceCharacter(), and missing_data_symbol_.

Referenced by parseGeneral_(), and PopgenlibIO().

write() [1/2]

void PopgenlibIO::write ( const std::string &  path, const DataSet &  data_set, bool  overwrite  ) const

virtual

Write a DataSet in a text file.

Reimplemented from bpp::AbstractODataSet.

Definition at line 689 of file PopgenlibIO.cpp.

References bpp::AbstractODataSet::write().

write() [2/2]

void PopgenlibIO::write ( std::ostream &  os, const DataSet &  data_set  ) const

virtual

Write a DataSet on ostream.

Implements bpp::AbstractODataSet.

Definition at line 545 of file PopgenlibIO.cpp.

References DIPLOID, bpp::LocusInfo::DIPLOID, bpp::MonolocusGenotype::getAlleleIndex(), bpp::LocusInfo::getAlleleInfoByKey(), bpp::DataSet::getAlphabetType(), getDataSeparator(), getDataSeparatorChar(), bpp::Individual::getDate(), bpp::Date::getDateStr(), bpp::Individual::getGenotype(), bpp::DataSet::getGroupAtPosition(), bpp::Individual::getId(), bpp::AlleleInfo::getId(), bpp::DataSet::getIndividualAtPositionFromGroup(), bpp::Individual::getLocality(), bpp::DataSet::getLocalityAtPosition(), bpp::DataSet::getLocusInfoAtPosition(), getMissingDataChar(), getMissingDataSymbol(), bpp::MultilocusGenotype::getMonolocusGenotype(), bpp::Locality< T >::getName(), bpp::LocusInfo::getName(), bpp::LocusInfo::getNumberOfAlleles(), bpp::DataSet::getNumberOfGroups(), bpp::DataSet::getNumberOfIndividualsInGroup(), bpp::DataSet::getNumberOfLocalities(), bpp::DataSet::getNumberOfLoci(), bpp::Individual::getNumberOfSequences(), bpp::LocusInfo::getPloidy(), bpp::Individual::getSequenceAtPosition(), bpp::Individual::getSequences(), bpp::Individual::getX(), bpp::Individual::getY(), HAPLODIPLOID, bpp::LocusInfo::HAPLODIPLOID, HAPLOID, bpp::LocusInfo::HAPLOID, bpp::DataSet::hasAlleleicData(), bpp::Individual::hasCoord(), bpp::Individual::hasDate(), bpp::Individual::hasGenotype(), bpp::DataSet::hasLocality(), bpp::Individual::hasLocality(), bpp::DataSet::hasSequenceData(), bpp::Individual::hasSequences(), bpp::MultilocusGenotype::isMonolocusGenotypeMissing(), bpp::MultilocusGenotype::size(), bpp::TextTools::toString(), UNKNOWN, bpp::LocusInfo::UNKNOWN, and bpp::Fasta::writeSequences().

Member Data Documentation

COMA

const string PopgenlibIO::COMA = string("COMA")

static

Definition at line 71 of file PopgenlibIO.h.

Referenced by getDataSeparator(), and setDataSeparator().

data_separator_

char bpp::PopgenlibIO::data_separator_

private

Definition at line 80 of file PopgenlibIO.h.

Referenced by getDataSeparator(), getDataSeparatorChar(), setDataSeparator(), and setMissingDataSymbol().

DIPLOID

const string PopgenlibIO::DIPLOID = string("DIPLOID")

static

Definition at line 74 of file PopgenlibIO.h.

Referenced by parseLoci_(), and write().

HAPLODIPLOID

const string PopgenlibIO::HAPLODIPLOID = string("HAPLODIPLOID")

static

Definition at line 76 of file PopgenlibIO.h.

Referenced by parseLoci_(), and write().

HAPLOID

const string PopgenlibIO::HAPLOID = string("HAPLOID")

static

Definition at line 75 of file PopgenlibIO.h.

Referenced by parseLoci_(), and write().

missing_data_symbol_

char bpp::PopgenlibIO::missing_data_symbol_

private

Definition at line 81 of file PopgenlibIO.h.

Referenced by getMissingDataChar(), getMissingDataSymbol(), and setMissingDataSymbol().

SEMICOLON

const string PopgenlibIO::SEMICOLON = string("SEMICOLON")

static

Definition at line 72 of file PopgenlibIO.h.

Referenced by getDataSeparator(), and setDataSeparator().

TAB

const string PopgenlibIO::TAB = string("TAB")

static

Definition at line 70 of file PopgenlibIO.h.

Referenced by getDataSeparator(), and setDataSeparator().

UNKNOWN

const string PopgenlibIO::UNKNOWN = string("UNKNOWN")

static

Definition at line 77 of file PopgenlibIO.h.

Referenced by parseLoci_(), and write().

WHITESPACE

const string PopgenlibIO::WHITESPACE = string("WHITESPACE")

static

Definition at line 69 of file PopgenlibIO.h.

Referenced by getDataSeparator(), and setDataSeparator().

---

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

• Bpp/PopGen/DataSet/Io/PopgenlibIO.h
• Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp