bpp::Genetix Class Reference

The Genetix input format for popgenlib. More...

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

Inheritance diagram for bpp::Genetix:

Collaboration diagram for bpp::Genetix:

Public Member Functions
	Genetix ()
	~Genetix ()
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 IOFormat interface
const std::string	getFormatName () const
const std::string	getFormatDescription () const

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

Detailed Description

The Genetix input format for popgenlib.

Author

Sylvain Gaillard

Definition at line 60 of file Genetix.h.

Constructor & Destructor Documentation

Genetix()

Genetix::Genetix

(

)

Definition at line 46 of file Genetix.cpp.

~Genetix()

Genetix::~Genetix

(

)

Definition at line 48 of file Genetix.cpp.

Member Function Documentation

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::Genetix::getFormatDescription ( ) const

inlinevirtual

Implements bpp::IOFormat.

Definition at line 89 of file Genetix.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 85 of file Genetix.h.

read() [1/4]

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

virtual

Read a text file and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 131 of file Genetix.cpp.

References bpp::AbstractIDataSet::read().

read() [2/4]

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

virtual

Read a DataSet from a text file.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 121 of file Genetix.cpp.

References bpp::AbstractIDataSet::read().

read() [3/4]

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

virtual

Read istream and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 126 of file Genetix.cpp.

References bpp::AbstractIDataSet::read().

read() [4/4]

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

virtual

Read a DataSet on istream.

Implements bpp::AbstractIDataSet.

Definition at line 50 of file Genetix.cpp.

References bpp::LocusInfo::addAlleleInfo(), bpp::DataSet::addEmptyGroup(), bpp::DataSet::addEmptyIndividualToGroup(), bpp::FileTools::getNextLine(), bpp::DataSet::initAnalyzedLoci(), bpp::DataSet::initIndividualGenotypeInGroup(), bpp::StringTokenizer::nextToken(), bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::DataSet::setGroupName(), bpp::DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup(), bpp::DataSet::setLocusInfo(), and bpp::TextTools::toString().

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

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