The GenBank sequence file format. More...

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

Inheritance diagram for bpp::GenBank:

Collaboration diagram for bpp::GenBank:

Public Member Functions
	GenBank ()
	Build a new GenBank object. More...

virtual	~GenBank ()

const std::string	getDataType () const

The AbstractISequence interface.
void	appendSequencesFromStream (std::istream &input, SequenceContainer &sc) const throw (Exception)
	Append sequences to a container from a stream. More...

The IOSequence interface.
const std::string	getFormatName () const

const std::string	getFormatDescription () const

ISequence methods:
virtual void	readSequences (std::istream &input, SequenceContainer &sc) const throw (Exception)
	Add sequences to a container from a stream. More...

virtual void	readSequences (const std::string &path, SequenceContainer &sc) const throw (Exception)
	Add sequences to a container from a file. More...

virtual VectorSequenceContainer *	readSequences (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream. More...

virtual VectorSequenceContainer *	readSequences (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file. More...

Protected Member Functions
virtual void	appendSequencesFromFile (const std::string &path, SequenceContainer &sc) const throw (Exception)
	Append sequences to a container from a file. More...

virtual VectorSequenceContainer *	readSequencesFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream. More...

virtual VectorSequenceContainer *	readSequencesFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Append sequences to a container from a file. More...

Detailed Description

The GenBank sequence file format.

For now, only read raw sequences. Features are not yet supported.

Definition at line 56 of file GenBank.h.

Constructor & Destructor Documentation

◆ GenBank()

bpp::GenBank::GenBank ( )

inline

Build a new GenBank object.

Definition at line 64 of file GenBank.h.

◆ ~GenBank()

virtual bpp::GenBank::~GenBank ( )

inlinevirtual

Definition at line 66 of file GenBank.h.

Member Function Documentation

◆ appendSequencesFromFile()

virtual void bpp::AbstractISequence::appendSequencesFromFile	(	const std::string &	path,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

inlineprotectedvirtualinherited

Append sequences to a container from a file.

Parameters

path	The path to the file to read.
sc	The sequence container to update.

Exceptions

Exception If the file is not in the specified format.

Definition at line 142 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromStream().

Referenced by bpp::AbstractISequence::readSequences(), and bpp::AbstractISequence::readSequencesFromFile().

◆ appendSequencesFromStream()

void GenBank::appendSequencesFromStream	(	std::istream &	input,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

virtual

Append sequences to a container from a stream.

This is the unique method to implement!

Parameters

input	The input stream to read.
sc	The sequence container to update.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::AbstractISequence.

Definition at line 50 of file GenBank.cpp.

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ getFormatDescription()

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

inline

Definition at line 84 of file GenBank.h.

◆ getFormatName()

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

inline

Definition at line 83 of file GenBank.h.

◆ readSequences() [1/4]

virtual void bpp::AbstractISequence::readSequences	(	std::istream &	input,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Add sequences to a container from a stream.

Parameters

input	The input stream to read.
sc	The sequence container to update.

Exceptions

Exception If the file is not in the specified format.

Definition at line 82 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromStream().

Referenced by bpp::Mase::readMeta().

◆ readSequences() [2/4]

virtual void bpp::AbstractISequence::readSequences	(	const std::string &	path,
		SequenceContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Add sequences to a container from a file.

Parameters

path	The path to the file to read.
sc	The sequence container to update.

Exceptions

Exception If the file is not in the specified format.

Definition at line 94 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromFile().

◆ readSequences() [3/4]

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Create a new container from a stream.

Parameters

input	The input stream to read.
alpha	The alphabet to be associated to the container.

Returns: A new SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 105 of file AbstractISequence.h.

References bpp::AbstractISequence::readSequencesFromStream().

◆ readSequences() [4/4]

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequences	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Create a new container from a file.

Parameters

path	The path to the file to read.
alpha	The alphabet to be associated to the container.

Returns: A new SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 116 of file AbstractISequence.h.

References bpp::AbstractISequence::readSequencesFromFile().

◆ readSequencesFromFile()

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequencesFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlineprotectedvirtualinherited

Append sequences to a container from a file.

Parameters

path	The path to the file to read.
alpha	The alphabet to use.

Exceptions

Exception If the file is not in the specified format.

Definition at line 171 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromFile().

Referenced by bpp::AbstractISequence::readSequences().

◆ readSequencesFromStream()

virtual VectorSequenceContainer* bpp::AbstractISequence::readSequencesFromStream	(	std::istream &	input,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlineprotectedvirtualinherited

Read sequences from a stream.

Parameters

input	The input stream to read.
alpha	The alphabet to use.

Returns: A sequence container.

Exceptions

Exception If the file is not in the specified format.

Definition at line 157 of file AbstractISequence.h.

References bpp::AbstractISequence::appendSequencesFromStream().

Referenced by bpp::AbstractISequence::readSequences().

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

Bpp/Seq/Io/GenBank.h
Bpp/Seq/Io/GenBank.cpp

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ GenBank()

◆ ~GenBank()

Member Function Documentation

◆ appendSequencesFromFile()

◆ appendSequencesFromStream()

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequencesFromFile()

◆ readSequencesFromStream()