bpp::PhredPhd Class Reference

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

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

Inheritance diagram for bpp::PhredPhd:

Collaboration diagram for bpp::PhredPhd:

Public Member Functions
	PhredPhd ()
	Build a new PhredPhd object. More...
virtual	~PhredPhd ()
bool	nextSequence (std::istream &input, Sequence &seq, std::vector< size_t > &pos) const
	Read a SequenceWithQuality from stream and store chromatographic positions. More...
virtual bool	nextSequence (std::istream &input, SequenceType &seq) const =0
	Read sequence from stream. More...
The ISequenceStream interface.
bool	nextSequence (std::istream &input, Sequence &seq) const
The IOFormat interface.
const std::string	getDataType () const
const std::string	getFormatName () const
const std::string	getFormatDescription () const

Private Member Functions
bool	parseFile_ (std::istream &input, std::string &name, std::string &sequence, std::vector< int > &qual, std::vector< size_t > &pos) const
	Global file parser. More...
bool	parseDNA_ (std::istream &input, std::string &sequence, std::vector< int > &qual, std::vector< size_t > &pos) const
	Parse the DNA part of the file. More...

Detailed Description

The phd sequence file format from phred software.

This class read DNA SequenceWithQuality from phd files produced by the phred program from the University of Washington.

Usage

// Creating a SequenceWithQuality object
DNA alpha;
SequenceWithQuality seq(&alpha);
std::vector<int> pos;
 
// Create a PhredPhd parser
PhredPhd pp;
 
// Opening the file
std::ifstream in("my_sequence.phd");
 
// Read the sequence
pp.nextSequence(in, seq, pos);
 
// Close the file
in.close();

Author

Sylvain Gaillard

Definition at line 44 of file PhredPhd.h.

Constructor & Destructor Documentation

PhredPhd()

bpp::PhredPhd::PhredPhd ( )

inline

Build a new PhredPhd object.

Definition at line 50 of file PhredPhd.h.

~PhredPhd()

virtual bpp::PhredPhd::~PhredPhd ( )

inlinevirtual

Definition at line 52 of file PhredPhd.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 89 of file PhredPhd.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 91 of file PhredPhd.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 90 of file PhredPhd.h.

nextSequence() [1/3]

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

Definition at line 18 of file PhredPhd.cpp.

nextSequence() [2/3]

bool PhredPhd::nextSequence	(	std::istream &	input,
		Sequence &	seq,
		std::vector< size_t > &	pos
	)		const

Read a SequenceWithQuality from stream and store chromatographic positions.

A more complete parser that read a SequenceWithQuality and store the position of each base call on the chromatogram in a vector of int.

Parameters

input	The stream to read.
seq	The sequence to fill.
pos	The vector of positions to fill.

Exceptions

Exception

IOException and Sequence related exceptions.

Definition at line 26 of file PhredPhd.cpp.

References parseFile_(), bpp::Sequence::setContent(), bpp::AbstractCoreSequence::setName(), and bpp::SequenceWithQuality::setQualities().

nextSequence() [3/3]

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.

parseDNA_()

bool PhredPhd::parseDNA_ ( std::istream &  input, std::string &  sequence, std::vector< int > &  qual, std::vector< size_t > &  pos  ) const

private

Parse the DNA part of the file.

Read the DNA part until ‘END_DNA’ or EOF.

Parameters

input	The stream to read
sequence	The string to store the sequence
qual	The vector to store qualities
pos	The vector to store positions

Definition at line 94 of file PhredPhd.cpp.

References bpp::StringTokenizer::getToken(), bpp::StringTokenizer::hasMoreToken(), bpp::StringTokenizer::numberOfRemainingTokens(), bpp::TextTools::toInt(), and bpp::TextTools::toUpper().

Referenced by parseFile_().

parseFile_()

bool PhredPhd::parseFile_ ( std::istream &  input, std::string &  name, std::string &  sequence, std::vector< int > &  qual, std::vector< size_t > &  pos  ) const

private

Global file parser.

Parameters

input	The stream to read
name	The string to store the sequence name
sequence	The string to store the sequence
qual	The vector to store qualities
pos	The vector to store positions

Definition at line 56 of file PhredPhd.cpp.

References bpp::StringTokenizer::getToken(), bpp::StringTokenizer::hasMoreToken(), and parseDNA_().

Referenced by nextSequence().

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

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