bpp-seq  2.2.0
bpp::PhredPoly Class Reference

The poly sequence file format from phred software. More...

#include <Bpp/Seq/Io/PhredPoly.h>

+ Inheritance diagram for bpp::PhredPoly:
+ Collaboration diagram for bpp::PhredPoly:

Public Member Functions

 PhredPoly (double ratio=0.8)
 Build a new PhredPoly object. More...
 
virtual ~PhredPoly ()
 
The AbstractISequence interface.
bool nextSequence (std::istream &input, Sequence &seq) const throw (Exception)
 Read sequence from stream. More...
 
The IOSequence interface.
const std::string getDataType () const
 
const std::string getFormatName () const
 
const std::string getFormatDescription () const
 

Protected Attributes

double ratio_
 

Detailed Description

The poly sequence file format from phred software.

This class read DNA sequence from poly files produced by the phred program from the University of Washington. For now, only read raw sequences and do a basic filter on heterozygous site.

Definition at line 55 of file PhredPoly.h.

Constructor & Destructor Documentation

◆ PhredPoly()

PhredPoly::PhredPoly ( double  ratio = 0.8)

Build a new PhredPoly object.

Definition at line 50 of file PhredPoly.cpp.

◆ ~PhredPoly()

virtual bpp::PhredPoly::~PhredPoly ( )
inlinevirtual

Definition at line 66 of file PhredPoly.h.

Member Function Documentation

◆ getDataType()

const std::string bpp::PhredPoly::getDataType ( ) const
inline

Definition at line 82 of file PhredPoly.h.

◆ getFormatDescription()

const std::string bpp::PhredPoly::getFormatDescription ( ) const
inline

Definition at line 84 of file PhredPoly.h.

◆ getFormatName()

const std::string bpp::PhredPoly::getFormatName ( ) const
inline

Definition at line 83 of file PhredPoly.h.

◆ nextSequence()

bool PhredPoly::nextSequence ( std::istream &  input,
Sequence seq 
) const
throw (Exception
)
virtual

Read sequence from stream.

Read one sequence from a stream.

Parameters
inputThe stream to read.
seqThe sequence to fill.
Returns
true if a sequence was read or false if not.
Exceptions
ExceptionIOExecption and Sequence related Exceptions.

Implements bpp::ISequenceStream.

Definition at line 54 of file PhredPoly.cpp.

References bpp::Alphabet::getGeneric().

Member Data Documentation

◆ ratio_

double bpp::PhredPoly::ratio_
protected

Definition at line 57 of file PhredPoly.h.


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