The GeneMapperCsvExport input format for popgenlib. More...

#include <Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h>

Inheritance diagram for bpp::GeneMapperCsvExport:

Collaboration diagram for bpp::GeneMapperCsvExport:

Classes
class	Allele
	Store data for one allele. More...

class	Record
	Store one line of the GeneMapper file. More...

Public Member Functions
	GeneMapperCsvExport ()

	~GeneMapperCsvExport ()

The IDataSet interface.
Set if allels are considered as independent markers.
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 IOFormat interface
virtual const std::string	getFormatName () const

virtual const std::string	getFormatDescription () const

Static Public Attributes
static const std::string	SAMPLE_FILE_H = "Sample File"

static const std::string	SAMPLE_NAME_H = "Sample Name"

static const std::string	PANEL_H = "Panel"

static const std::string	MARKER_H = "Marker"

static const std::string	DYE_H = "Dye"

static const std::string	ALLELE_H = "Allele "

static const std::string	SIZE_H = "Size "

static const std::string	HEIGHT_H = "Height "

static const std::string	PEAK_AREA_H = "Peak Area "

static const std::string	DAC_H = "DAC"

static const std::string	AN_H = "AN"

Private Member Functions
The IOFormat interface.
const std::string	getDataType () const

Detailed Description

The GeneMapperCsvExport input format for popgenlib.

This input format takes a csv file exported from GeneMapper® (Applied Biosystems).

Author: Sylvain Gaillard

Definition at line 28 of file GeneMapperCsvExport.h.

Constructor & Destructor Documentation

◆ GeneMapperCsvExport()

bpp::GeneMapperCsvExport::GeneMapperCsvExport ( )

inline

Definition at line 49 of file GeneMapperCsvExport.h.

◆ ~GeneMapperCsvExport()

GeneMapperCsvExport::~GeneMapperCsvExport ( )

Definition at line 24 of file GeneMapperCsvExport.cpp.

Member Function Documentation

◆ getDataType()

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

inlineprivatevirtualinherited

Implements bpp::IOFormat.

Definition at line 33 of file IODataSet.h.

◆ getFormatDescription()

virtual const std::string bpp::GeneMapperCsvExport::getFormatDescription ( ) const

inlinevirtual

Implements bpp::IOFormat.

Definition at line 80 of file GeneMapperCsvExport.h.

◆ getFormatName()

virtual const std::string bpp::GeneMapperCsvExport::getFormatName ( ) const

inlinevirtual

Implements bpp::IOFormat.

Definition at line 76 of file GeneMapperCsvExport.h.

◆ read() [1/4]

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

virtual

Read a text file and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 159 of file GeneMapperCsvExport.cpp.

References bpp::AbstractIDataSet::read().

◆ read() [2/4]

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

virtual

Read a DataSet from a text file.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 149 of file GeneMapperCsvExport.cpp.

References bpp::AbstractIDataSet::read().

◆ read() [3/4]

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

virtual

Read istream and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 154 of file GeneMapperCsvExport.cpp.

References bpp::AbstractIDataSet::read().

◆ read() [4/4]

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

virtual

Read a DataSet on istream.

Implements bpp::AbstractIDataSet.

Definition at line 26 of file GeneMapperCsvExport.cpp.

References bpp::AnalyzedLoci::addAlleleInfoByLocusName(), bpp::DataSet::addEmptyGroup(), bpp::DataSet::addIndividualToGroup(), bpp::DataSet::analyzedLoci(), bpp::VectorTools::countValues(), bpp::DataTable::getColumn(), bpp::DataTable::getColumnNames(), bpp::DataSet::getGroupPosition(), bpp::DataSet::getIndividualByIdFromGroup(), bpp::DataSet::getIndividualPositionInGroup(), bpp::DataSet::getLocusInfoByName(), bpp::AnalyzedLoci::getLocusInfoPosition(), bpp::DataTable::getNumberOfRows(), bpp::DataSet::initAnalyzedLoci(), bpp::DataSet::initIndividualGenotypeInGroup(), bpp::TextTools::isEmpty(), bpp::DataTable::read(), bpp::DataSet::setAnalyzedLoci(), bpp::DataSet::setIndividualMonolocusGenotypeInGroup(), bpp::AnalyzedLoci::setLocusInfo(), bpp::TextTools::startsWith(), bpp::TextTools::toString(), bpp::VectorTools::unique(), bpp::LocusInfo::UNKNOWN, and bpp::VectorTools::which().

Member Data Documentation

◆ ALLELE_H

const std::string GeneMapperCsvExport::ALLELE_H = "Allele "

static

Definition at line 36 of file GeneMapperCsvExport.h.

◆ AN_H

const std::string GeneMapperCsvExport::AN_H = "AN"

static

Definition at line 41 of file GeneMapperCsvExport.h.

◆ DAC_H

const std::string GeneMapperCsvExport::DAC_H = "DAC"

static

Definition at line 40 of file GeneMapperCsvExport.h.

◆ DYE_H

const std::string GeneMapperCsvExport::DYE_H = "Dye"

static

Definition at line 35 of file GeneMapperCsvExport.h.

◆ HEIGHT_H

const std::string GeneMapperCsvExport::HEIGHT_H = "Height "

static

Definition at line 38 of file GeneMapperCsvExport.h.

◆ MARKER_H

const std::string GeneMapperCsvExport::MARKER_H = "Marker"

static

Definition at line 34 of file GeneMapperCsvExport.h.

◆ PANEL_H

const std::string GeneMapperCsvExport::PANEL_H = "Panel"

static

Definition at line 33 of file GeneMapperCsvExport.h.

◆ PEAK_AREA_H

const std::string GeneMapperCsvExport::PEAK_AREA_H = "Peak Area "

static

Definition at line 39 of file GeneMapperCsvExport.h.

◆ SAMPLE_FILE_H

const std::string GeneMapperCsvExport::SAMPLE_FILE_H = "Sample File"

static

Definition at line 31 of file GeneMapperCsvExport.h.

◆ SAMPLE_NAME_H

const std::string GeneMapperCsvExport::SAMPLE_NAME_H = "Sample Name"

static

Definition at line 32 of file GeneMapperCsvExport.h.

◆ SIZE_H

const std::string GeneMapperCsvExport::SIZE_H = "Size "

static

Definition at line 37 of file GeneMapperCsvExport.h.

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

Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h
Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp

Classes

Public Member Functions

Static Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ GeneMapperCsvExport()

◆ ~GeneMapperCsvExport()

Member Function Documentation

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ read() [1/4]

◆ read() [2/4]

◆ read() [3/4]

◆ read() [4/4]

Member Data Documentation

◆ ALLELE_H

◆ AN_H

◆ DAC_H

◆ DYE_H

◆ HEIGHT_H

◆ MARKER_H

◆ PANEL_H

◆ PEAK_AREA_H

◆ SAMPLE_FILE_H

◆ SAMPLE_NAME_H

◆ SIZE_H