bpp::Fastq Class Reference

The fastq sequence file format. More...

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

Inheritance diagram for bpp::Fastq:

Collaboration diagram for bpp::Fastq:

Public Member Functions
	Fastq (bool repName=false)
	Build a new Fastq object. More...
virtual	~Fastq ()
bool	repeatName () const
void	repeatName (bool yn)
The IOSequence interface.
const std::string	getFormatName () const
const std::string	getFormatDescription () const
const std::string	getDataType () const
The ISequenceStream interface.
bool	nextSequence (std::istream &input, Sequence &seq) const
The OSequenceStream interface.
void	writeSequence (std::ostream &output, const Sequence &seq) const

Private Attributes
bool	repeatName_

Detailed Description

The fastq sequence file format.

Author

Sylvain Gaillard

Definition at line 56 of file Fastq.h.

Constructor & Destructor Documentation

Fastq()

bpp::Fastq::Fastq ( bool  repName = false )

inline

Build a new Fastq object.

Parameters

repName

Tell if the names in the file is repeated (tested on input) or must be repeated (for output).

Definition at line 70 of file Fastq.h.

~Fastq()

virtual bpp::Fastq::~Fastq ( )

inlinevirtual

Definition at line 73 of file Fastq.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 85 of file Fastq.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 82 of file Fastq.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 81 of file Fastq.h.

nextSequence()

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

virtual

Author

Sylvain Gaillard

Usage

// Creating a SequenceWithQuality object
DNA alpha;
SequenceWithQuality seq(&alpha);
 
// Create a FastQ parser
Fastq fq;
 
// Opening the file
std::ifstream in("reads.fastq");
 
// Read the sequences
while (fq.nextSequence(in, seq)) {
  // ... do something with the sequence ...
}
 
// Close the file
in.close();

Implements bpp::ISequenceStream.

Definition at line 47 of file Fastq.cpp.

References bpp::Sequence::getName(), bpp::TextTools::isEmpty(), repeatName(), bpp::Sequence::setContent(), bpp::Sequence::setName(), and bpp::SequenceWithQuality::setQuality().

repeatName() [1/2]

bool bpp::Fastq::repeatName ( ) const

inline

Definition at line 87 of file Fastq.h.

References repeatName_.

Referenced by nextSequence(), and writeSequence().

repeatName() [2/2]

void bpp::Fastq::repeatName ( bool  yn )

inline

Definition at line 88 of file Fastq.h.

References repeatName_.

writeSequence()

void Fastq::writeSequence ( std::ostream &  output, const Sequence &  seq  ) const

virtual

Author

Sylvain Gaillard

Implements bpp::OSequenceStream.

Definition at line 88 of file Fastq.cpp.

References bpp::Sequence::getName(), bpp::SequenceWithQuality::getQuality(), repeatName(), bpp::SequenceWithQuality::size(), bpp::Sequence::size(), and bpp::Sequence::toString().

Member Data Documentation

repeatName_

bool bpp::Fastq::repeatName_

private

Definition at line 61 of file Fastq.h.

Referenced by repeatName().

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

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