bpp-popgen  2.2.0
Classes | Public Member Functions | Static Public Attributes | List of all members
bpp::GeneMapperCsvExport Class Reference

The GeneMapperCsvExport input format for popgenlib. More...

#include <Bpp/PopGen/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 concidered as independent markers.

void read (std::istream &is, DataSet &data_set) throw (Exception)
 Read a DataSet on istream. More...
 
void read (const std::string &path, DataSet &data_set) throw (Exception)
 Read a DataSet from a text file. More...
 
DataSet * read (std::istream &is) throw (Exception)
 Read istream and return a DataSet. More...
 
DataSet * read (const std::string &path) throw (Exception)
 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"
 

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 63 of file GeneMapperCsvExport.h.

Constructor & Destructor Documentation

◆ GeneMapperCsvExport()

bpp::GeneMapperCsvExport::GeneMapperCsvExport ( )
inline

Definition at line 84 of file GeneMapperCsvExport.h.

◆ ~GeneMapperCsvExport()

GeneMapperCsvExport::~GeneMapperCsvExport ( )

Definition at line 59 of file GeneMapperCsvExport.cpp.

Member Function Documentation

◆ getFormatDescription()

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

Definition at line 115 of file GeneMapperCsvExport.h.

◆ getFormatName()

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

Definition at line 111 of file GeneMapperCsvExport.h.

◆ read() [1/4]

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

Read a DataSet on istream.

Implements bpp::AbstractIDataSet.

Definition at line 61 of file GeneMapperCsvExport.cpp.

References bpp::LocusInfo::UNKNOWN.

◆ read() [2/4]

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

Read a DataSet from a text file.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 185 of file GeneMapperCsvExport.cpp.

References bpp::AbstractIDataSet::read().

◆ read() [3/4]

DataSet * GeneMapperCsvExport::read ( std::istream &  is)
throw (Exception
)
virtual

Read istream and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 190 of file GeneMapperCsvExport.cpp.

References bpp::AbstractIDataSet::read().

◆ read() [4/4]

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

Read a text file and return a DataSet.

Reimplemented from bpp::AbstractIDataSet.

Definition at line 195 of file GeneMapperCsvExport.cpp.

References bpp::AbstractIDataSet::read().

Member Data Documentation

◆ ALLELE_H

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

Definition at line 71 of file GeneMapperCsvExport.h.

◆ AN_H

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

Definition at line 76 of file GeneMapperCsvExport.h.

◆ DAC_H

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

Definition at line 75 of file GeneMapperCsvExport.h.

◆ DYE_H

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

Definition at line 70 of file GeneMapperCsvExport.h.

◆ HEIGHT_H

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

Definition at line 73 of file GeneMapperCsvExport.h.

◆ MARKER_H

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

Definition at line 69 of file GeneMapperCsvExport.h.

◆ PANEL_H

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

Definition at line 68 of file GeneMapperCsvExport.h.

◆ PEAK_AREA_H

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

Definition at line 74 of file GeneMapperCsvExport.h.

◆ SAMPLE_FILE_H

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

Definition at line 66 of file GeneMapperCsvExport.h.

◆ SAMPLE_NAME_H

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

Definition at line 67 of file GeneMapperCsvExport.h.

◆ SIZE_H

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

Definition at line 72 of file GeneMapperCsvExport.h.

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