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 ()
virtual bool	nextSequence (std::istream &input, SequenceType &seq) const =0
	Read sequence from stream. More...
The AbstractISequence interface.
bool	nextSequence (std::istream &input, Sequence &seq) const
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 21 of file PhredPoly.h.

Constructor & Destructor Documentation

PhredPoly()

PhredPoly::PhredPoly

(

double

ratio = 0.8

)

Build a new PhredPoly object.

Definition at line 16 of file PhredPoly.cpp.

~PhredPoly()

virtual bpp::PhredPoly::~PhredPoly ( )

inlinevirtual

Definition at line 32 of file PhredPoly.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 48 of file PhredPoly.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 50 of file PhredPoly.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 49 of file PhredPoly.h.

nextSequence() [1/2]

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

Definition at line 20 of file PhredPoly.cpp.

References bpp::AbstractTemplateSymbolList< T >::getAlphabet(), bpp::StringTokenizer::getToken(), bpp::StringTokenizer::numberOfRemainingTokens(), ratio_, bpp::Sequence::setContent(), bpp::AbstractCoreSequence::setName(), bpp::NumTools::swap(), and bpp::TextTools::toDouble().

nextSequence() [2/2]

template<class SequenceType >

virtual bool bpp::TemplateISequenceStream< SequenceType >::nextSequence ( std::istream &  input, SequenceType &  seq  ) const

pure virtualinherited

Read sequence from stream.

Read one sequence from a stream.

Parameters

input	The stream to read.
seq	The sequence to fill.

Returns

true if a sequence was read or false if not.

Exceptions

Exception

IOExecption and Sequence related Exceptions.

Member Data Documentation

ratio_

double bpp::PhredPoly::ratio_

protected

Definition at line 24 of file PhredPoly.h.

Referenced by nextSequence().

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

• Bpp/Seq/Io/PhredPoly.h
• Bpp/Seq/Io/PhredPoly.cpp