The fasta sequence file format. More...

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

Inheritance diagram for bpp::Fasta:

Collaboration diagram for bpp::Fasta:

Classes
class	FileIndex
	The SequenceFileIndex class for Fasta format. More...

Public Member Functions
	Fasta (unsigned int charsByLine=100, bool checkSequenceNames=true, bool extended=false, bool strictSequenceNames=false)
	Build a new Fasta object. More...

virtual	~Fasta ()

bool	checkNames () const

void	checkNames (bool yn)
	Tell whether the sequence names should be checked when reading from files. More...

bool	strictNames () const

void	strictNames (bool yn)
	Tell wethed the sequence name should be restrected to the first non blank characters. More...

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 AbstractIAlignment interface.
void	appendAlignmentFromStream (std::istream &input, SiteContainer &sc) const throw (Exception)
	Append sequences to a container from a stream. More...

The OSequence interface.
void	writeSequences (std::ostream &output, const SequenceContainer &sc) const throw (Exception)
	Write a container to a stream. More...

void	writeSequences (const std::string &path, const SequenceContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to a file. More...

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

const std::string	getFormatDescription () const

The ISequenceStream interface.
bool	nextSequence (std::istream &input, Sequence &seq) const throw (Exception)
	Read sequence from stream. More...

The OSequenceStream interface.
void	writeSequence (std::ostream &output, const Sequence &seq) const throw (Exception)
	Read sequence from stream. More...

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...

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

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

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

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

OAlignment methods:
As a SiteContainer is a specialization of SequenceContainer, it is assumed that a OSequence object can write aligned sequence just like a OAlignment object. Therefore it implements the OAlignment interface by down-casting the SiteContainer to a SequenceContainer.
void	writeAlignment (std::ostream &output, const SiteContainer &sc) const throw (Exception)
	Write a container to a stream. More...

void	writeAlignment (const std::string &path, const SiteContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to 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...

virtual void	appendAlignmentFromFile (const std::string &path, SiteContainer &sc) const throw (Exception)
	Append sequences to a container from a file. More...

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

virtual AlignedSequenceContainer *	readAlignmentFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Read sequences from a file. More...

Private Attributes
unsigned int	charsByLine_
	The maximum number of chars to be written on a line. More...

bool	checkNames_

bool	extended_

bool	strictNames_

Detailed Description

The fasta sequence file format.

Read and write from/to Fasta files.

Definition at line 63 of file Fasta.h.

Constructor & Destructor Documentation

◆ Fasta()

bpp::Fasta::Fasta	(	unsigned int	charsByLine = `100`,
		bool	checkSequenceNames = `true`,
		bool	extended = `false`,
		bool	strictSequenceNames = `false`
	)

inline

Build a new Fasta object.

Parameters

charsByLine	Number of character per line when writing files.
checkSequenceNames	Tells if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
extended	Tells if we should read general comments and sequence comments in HUPO-PSI format.
strictSequenceNames	Tells if the sequence names should be restricted to the characters between '>' and the first blank one.

Definition at line 90 of file Fasta.h.

◆ ~Fasta()

virtual bpp::Fasta::~Fasta ( )

inlinevirtual

Definition at line 93 of file Fasta.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	const std::string &	path,
		SiteContainer &	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 143 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment::readAlignment(), and bpp::AbstractIAlignment::readAlignmentFromFile().

◆ appendAlignmentFromStream()

void bpp::Fasta::appendAlignmentFromStream	(	std::istream &	input,
		SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtual

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::AbstractIAlignment.

Definition at line 110 of file Fasta.h.

References appendSequencesFromStream().

◆ 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 Fasta::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 147 of file Fasta.cpp.

Referenced by appendAlignmentFromStream().

◆ checkNames() [1/2]

bool bpp::Fasta::checkNames ( ) const

inline

Returns: true if the names are to be checked when reading sequences from files.

Definition at line 159 of file Fasta.h.

References checkNames_.

◆ checkNames() [2/2]

void bpp::Fasta::checkNames ( bool yn )

inline

Tell whether the sequence names should be checked when reading from files.

Parameters

yn	whether the sequence names should be checked when reading from files.

Definition at line 166 of file Fasta.h.

References checkNames_.

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ getFormatDescription()

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

inline

Definition at line 134 of file Fasta.h.

◆ getFormatName()

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

inline

Definition at line 133 of file Fasta.h.

◆ nextSequence()

bool Fasta::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 56 of file Fasta.cpp.

Referenced by bpp::Fasta::FileIndex::getSequence().

◆ readAlignment() [1/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		SiteContainer &	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 81 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::DCSE::readSequences(), bpp::Clustal::readSequences(), bpp::NexusIOSequence::readSequences(), and bpp::Phylip::readSequences().

◆ readAlignment() [2/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		SiteContainer &	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 93 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readAlignment() [3/4]

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	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 SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 104 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromFile().

◆ readAlignment() [4/4]

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	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 SiteContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::IAlignment.

Definition at line 115 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const
throw	(	Exception
	)

inlineprotectedvirtualinherited

Read sequences from a file.

Parameters

path	The path to the file 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 173 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

Referenced by bpp::AbstractIAlignment::readAlignment().

◆ readAlignmentFromStream()

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromStream	(	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 158 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment::readAlignment().

◆ 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().

◆ strictNames() [1/2]

bool bpp::Fasta::strictNames ( ) const

inline

Returns: true if the sequence name is restricted to be between '>' and the first space character.

Definition at line 171 of file Fasta.h.

References strictNames_.

◆ strictNames() [2/2]

void bpp::Fasta::strictNames ( bool yn )

inline

Tell wethed the sequence name should be restrected to the first non blank characters.

Parameters

yn	whether the sequence names should be restrected.

Definition at line 178 of file Fasta.h.

References strictNames_.

◆ writeAlignment() [1/2]

void bpp::AbstractOSequence::writeAlignment	(	std::ostream &	output,
		const SiteContainer &	sc
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Write a container to a stream.

Parameters

output	The output stream where to write.
sc	The container to write.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::OAlignment.

Definition at line 92 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeAlignment() [2/2]

void bpp::AbstractOSequence::writeAlignment	(	const std::string &	path,
		const SiteContainer &	sc,
		bool	overwrite = `true`
	)		const
throw	(	Exception
	)

inlinevirtualinherited

Write a container to a file.

Parameters

path	The path to the file to write.
sc	The container to write.
overwrite	If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::OAlignment.

Definition at line 96 of file AbstractOSequence.h.

References bpp::AbstractOSequence::writeSequences().

◆ writeSequence()

void Fasta::writeSequence	(	std::ostream &	output,
		const Sequence &	seq
	)		const
throw	(	Exception
	)

virtual

Read sequence from stream.

Read one sequence from a stream.

Parameters

output	The stream where write.
seq	The sequence to write.

Exceptions

Exception IOExecption.

Implements bpp::OSequenceStream.

Definition at line 116 of file Fasta.cpp.

◆ writeSequences() [1/2]

void Fasta::writeSequences	(	std::ostream &	output,
		const SequenceContainer &	sc
	)		const
throw	(	Exception
	)

virtual

Write a container to a stream.

Parameters

output	The output stream where to write.
sc	The container to write.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::AbstractOSequence.

Definition at line 204 of file Fasta.cpp.

◆ writeSequences() [2/2]

void bpp::Fasta::writeSequences	(	const std::string &	path,
		const SequenceContainer &	sc,
		bool	overwrite = `true`
	)		const
throw	(	Exception
	)

inlinevirtual

Write a container to a file.

Parameters

path	The path to the file to write.
sc	The container to write.
overwrite	If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost.

Exceptions

Exception If the file is not in the specified format.

Reimplemented from bpp::AbstractOSequence.

Definition at line 122 of file Fasta.h.

References bpp::AbstractOSequence::writeSequences().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Fasta::charsByLine_

private

The maximum number of chars to be written on a line.

Definition at line 75 of file Fasta.h.

◆ checkNames_

bool bpp::Fasta::checkNames_

private

Definition at line 76 of file Fasta.h.

Referenced by checkNames().

◆ extended_

bool bpp::Fasta::extended_

private

Definition at line 77 of file Fasta.h.

◆ strictNames_

bool bpp::Fasta::strictNames_

private

Definition at line 78 of file Fasta.h.

Referenced by strictNames().

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

Bpp/Seq/Io/Fasta.h
Bpp/Seq/Io/Fasta.cpp

Classes

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Fasta()

◆ ~Fasta()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ appendSequencesFromFile()

◆ appendSequencesFromStream()

◆ checkNames() [1/2]

◆ checkNames() [2/2]

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ nextSequence()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readSequences() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ readSequencesFromFile()

◆ readSequencesFromStream()

◆ strictNames() [1/2]

◆ strictNames() [2/2]

◆ writeAlignment() [1/2]

◆ writeAlignment() [2/2]

◆ writeSequence()

◆ writeSequences() [1/2]

◆ writeSequences() [2/2]

Member Data Documentation

◆ charsByLine_

◆ checkNames_

◆ extended_

◆ strictNames_