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< int > &pos) const throw (Exception)
	Read a SequenceWithQuality from stream and store chromatographic positions. More...
The ISequenceStream interface.
bool	nextSequence (std::istream &input, Sequence &seq) const throw (Exception)
	Read sequence from stream. More...
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< int > &pos) const
	Global file parser. More...
bool	parseDNA_ (std::istream &input, std::string &sequence, std::vector< int > &qual, std::vector< int > &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 78 of file PhredPhd.h.

Constructor & Destructor Documentation

PhredPhd()

bpp::PhredPhd::PhredPhd ( )

inline

Build a new PhredPhd object.

Definition at line 84 of file PhredPhd.h.

~PhredPhd()

virtual bpp::PhredPhd::~PhredPhd ( )

inlinevirtual

Definition at line 86 of file PhredPhd.h.

Member Function Documentation

getDataType()

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

inline

Definition at line 123 of file PhredPhd.h.

getFormatDescription()

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

inline

Definition at line 125 of file PhredPhd.h.

getFormatName()

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

inline

Definition at line 124 of file PhredPhd.h.

nextSequence() [1/2]

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

virtual

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.

Implements bpp::ISequenceStream.

Definition at line 52 of file PhredPhd.cpp.

nextSequence() [2/2]

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

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 stram to read.
seq	The sequence to fill.
pos	The vector of positions to fill.

Exceptions

Exception

IOException and Sequence related exceptions.

Definition at line 59 of file PhredPhd.cpp.

References bpp::SequenceWithQuality::setQualities().

parseDNA_()

bool PhredPhd::parseDNA_ ( std::istream &  input, std::string &  sequence, std::vector< int > &  qual, std::vector< int > &  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 115 of file PhredPhd.cpp.

Referenced by parseFile_().

parseFile_()

bool PhredPhd::parseFile_ ( std::istream &  input, std::string &  name, std::string &  sequence, std::vector< int > &  qual, std::vector< int > &  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 84 of file PhredPhd.cpp.

References parseDNA_().

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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