bpp::DarwinVarSingle Class Reference

The Darwin .don output format for popgenlib. More...

#include <Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h>

Inheritance diagram for bpp::DarwinVarSingle:

Collaboration diagram for bpp::DarwinVarSingle:

Public Member Functions
	DarwinVarSingle (size_t missingData=999)
	~DarwinVarSingle ()
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
virtual const std::string	getFormatName () const
virtual const std::string	getFormatDescription () const

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

Private Attributes
size_t	missingData_

Detailed Description

The Darwin .don output format for popgenlib.

Author

Sylvain Gaillard

Definition at line 58 of file DarwinVarSingle.h.

Constructor & Destructor Documentation

DarwinVarSingle()

DarwinVarSingle::DarwinVarSingle

(

size_t

missingData = 999

)

Definition at line 45 of file DarwinVarSingle.cpp.

~DarwinVarSingle()

DarwinVarSingle::~DarwinVarSingle

(

)

Definition at line 47 of file DarwinVarSingle.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()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 88 of file DarwinVarSingle.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 84 of file DarwinVarSingle.h.

write() [1/2]

void DarwinVarSingle::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 110 of file DarwinVarSingle.cpp.

References bpp::AbstractODataSet::write().

write() [2/2]

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

virtual

Write a DataSet on ostream.

Implements bpp::AbstractODataSet.

Definition at line 49 of file DarwinVarSingle.cpp.

References bpp::VectorTools::contains(), bpp::MonolocusGenotype::getAlleleIndex(), bpp::LocusInfo::getAlleleInfoByKey(), bpp::DataSet::getAnalyzedLoci(), bpp::Individual::getGenotype(), bpp::AlleleInfo::getId(), bpp::DataSet::getIndividualAtPositionFromGroup(), bpp::DataSet::getLocusInfoAtPosition(), bpp::MultilocusGenotype::getMonolocusGenotype(), bpp::LocusInfo::getName(), bpp::AnalyzedLoci::getNumberOfAlleles(), bpp::LocusInfo::getNumberOfAlleles(), bpp::DataSet::getNumberOfGroups(), bpp::DataSet::getNumberOfIndividualsInGroup(), bpp::DataSet::getNumberOfLoci(), bpp::MultilocusGenotype::isMonolocusGenotypeMissing(), missingData_, bpp::VectorTools::paste(), bpp::VectorTools::print(), and bpp::MultilocusGenotype::size().

Member Data Documentation

missingData_

size_t bpp::DarwinVarSingle::missingData_

private

Definition at line 62 of file DarwinVarSingle.h.

Referenced by write().

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

• Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h
• Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.cpp