The clustal sequence file format. More...

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

Inheritance diagram for bpp::Clustal:

Collaboration diagram for bpp::Clustal:

Public Member Functions
	Clustal (bool checkSequenceNames=true, unsigned int nbExtraSpacesBeforeSeq=5, unsigned int charsByLine=100)
	Build a new Clustal object. More...

virtual	~Clustal ()

bool	checkNames () const

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

const std::string	getDataType () const

The AbstractIAlignment interface.
void	appendAlignmentFromStream (std::istream &input, SequenceContainerInterface &sc) const override
	Append sequences to a container from a stream. More...

The ISequence interface.
As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
std::unique_ptr< SequenceContainerInterface >	readSequences (std::istream &input, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a stream. More...

std::unique_ptr< SequenceContainerInterface >	readSequences (const std::string &path, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a file. More...

The AbstractOAlignment interface.
void	writeAlignment (std::ostream &output, const SiteContainerInterface &sc) const override
	Write a container to a stream. More...

void	writeAlignment (const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override
	Write a container to a file. More...

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

const std::string	getFormatDescription () const override

The ISequence interface.
As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
void	readSequences (std::istream &input, SequenceContainerInterface &sc) const override
	Create a new container from a stream. More...

void	readSequences (const std::string &path, SequenceContainerInterface &sc) const override
	Create a new container from a file. More...

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

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

std::unique_ptr< SiteContainerInterface >	readAlignment (const std::string &path, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a file. More...

std::unique_ptr< SiteContainerInterface >	readAlignment (std::istream &input, std::shared_ptr< const Alphabet > alpha) const override
	Create a new container from a stream. More...

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

virtual std::unique_ptr< SiteContainerInterface >	readAlignmentFromStream (std::istream &input, std::shared_ptr< const Alphabet > alpha) const
	Read sequences from a stream. More...

virtual std::unique_ptr< SiteContainerInterface >	readAlignmentFromFile (const std::string &path, std::shared_ptr< const Alphabet > alpha) const
	Read sequences from a file. More...

Private Attributes
bool	checkNames_

unsigned int	nbSpacesBeforeSeq_

unsigned int	charsByLine_

Detailed Description

The clustal sequence file format.

An AlignedSequenceContainer object is used instead of a VectorSequenceContainer.

Definition at line 23 of file Clustal.h.

Constructor & Destructor Documentation

◆ Clustal()

bpp::Clustal::Clustal	(	bool	checkSequenceNames = `true`,
		unsigned int	nbExtraSpacesBeforeSeq = `5`,
		unsigned int	charsByLine = `100`
	)

inline

Build a new Clustal object.

Parameters

checkSequenceNames	Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
nbExtraSpacesBeforeSeq	Specify the number of extra space characters separating the sequence name form content. The default is 5 (hence 6 spaces in total) for backward compatibility, using 0 will not allow for any space in the sequence names.
charsByLine	Number of character per line when writing file.

Definition at line 40 of file Clustal.h.

◆ ~Clustal()

virtual bpp::Clustal::~Clustal ( )

inlinevirtual

Definition at line 46 of file Clustal.h.

Member Function Documentation

◆ appendAlignmentFromFile()

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	const std::string &	path,
		SequenceContainerInterface &	sc
	)		const

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 93 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment::readAlignment(), bpp::AbstractIAlignment::readAlignmentFromFile(), and bpp::AbstractIAlignment2::readSequences().

◆ appendAlignmentFromStream()

void Clustal::appendAlignmentFromStream	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

overridevirtual

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 18 of file Clustal.cpp.

References bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence(), count(), bpp::TemplateSequenceDataInterface< HashType >::getAlphabet(), bpp::FileTools::getNextLine(), bpp::TextTools::isEmpty(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::Commentable::setComments().

◆ checkNames() [1/2]

bool bpp::Clustal::checkNames ( ) const

inline

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

Definition at line 103 of file Clustal.h.

References checkNames_.

◆ checkNames() [2/2]

void bpp::Clustal::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 110 of file Clustal.h.

References checkNames_.

◆ getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

◆ getFormatDescription()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 96 of file Clustal.h.

◆ getFormatName()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 94 of file Clustal.h.

◆ readAlignment() [1/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		SequenceContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

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.

Implements bpp::IAlignment.

Definition at line 57 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readAlignment() [2/4]

std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtualinherited

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 62 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromFile().

◆ readAlignment() [3/4]

virtual void bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		SequenceContainerInterface &	sc
	)		const

inlineoverridevirtualinherited

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.

Implements bpp::IAlignment.

Definition at line 45 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

Referenced by bpp::AbstractIAlignment2::readSequences(), readSequences(), bpp::DCSE::readSequences(), and bpp::Phylip::readSequences().

◆ readAlignment() [4/4]

std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtualinherited

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 67 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignmentFromStream().

◆ readAlignmentFromFile()

virtual std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignmentFromFile	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

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 125 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

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

◆ readAlignmentFromStream()

virtual std::unique_ptr<SiteContainerInterface> bpp::AbstractIAlignment::readAlignmentFromStream	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

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 110 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

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

◆ readSequences() [1/4]

void bpp::AbstractIAlignment2::readSequences	(	const std::string &	path,
		SequenceContainerInterface &	container
	)		const

inlineoverridevirtualinherited

Create a new container from a file.

Parameters

path	The path to the file to read.
container	The container where to add data.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 162 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromFile().

◆ readSequences() [2/4]

std::unique_ptr<SequenceContainerInterface> bpp::Clustal::readSequences	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtual

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.

Reimplemented from bpp::AbstractIAlignment2.

Definition at line 70 of file Clustal.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequences() [3/4]

void bpp::AbstractIAlignment2::readSequences	(	std::istream &	input,
		SequenceContainerInterface &	container
	)		const

inlineoverridevirtualinherited

Create a new container from a stream.

Parameters

input	The input stream to read.
container	The container where to add data.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Definition at line 157 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::appendAlignmentFromStream().

◆ readSequences() [4/4]

std::unique_ptr<SequenceContainerInterface> bpp::Clustal::readSequences	(	std::istream &	input,
		std::shared_ptr< const Alphabet >	alpha
	)		const

inlineoverridevirtual

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.

Reimplemented from bpp::AbstractIAlignment2.

Definition at line 65 of file Clustal.h.

References bpp::AbstractIAlignment::readAlignment().

◆ writeAlignment() [1/2]

void bpp::Clustal::writeAlignment	(	const std::string &	path,
		const SiteContainerInterface &	sc,
		bool	overwrite = `true`
	)		const

inlineoverridevirtual

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::AbstractOAlignment.

Definition at line 83 of file Clustal.h.

References bpp::AbstractOAlignment::writeAlignment().

◆ writeAlignment() [2/2]

void Clustal::writeAlignment	(	std::ostream &	output,
		const SiteContainerInterface &	sc
	)		const

overridevirtual

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::AbstractOAlignment.

Definition at line 93 of file Clustal.cpp.

References bpp::AbstractCoreSequence::getName(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TextTools::resizeRight(), and bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::Clustal::charsByLine_

private

Definition at line 30 of file Clustal.h.

◆ checkNames_

bool bpp::Clustal::checkNames_

private

Definition at line 28 of file Clustal.h.

Referenced by checkNames().

◆ nbSpacesBeforeSeq_

unsigned int bpp::Clustal::nbSpacesBeforeSeq_

private

Definition at line 29 of file Clustal.h.

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

Bpp/Seq/Io/Clustal.h
Bpp/Seq/Io/Clustal.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Clustal()

◆ ~Clustal()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ checkNames() [1/2]

◆ checkNames() [2/2]

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ 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]

◆ writeAlignment() [1/2]

◆ writeAlignment() [2/2]

Member Data Documentation

◆ charsByLine_

◆ checkNames_

◆ nbSpacesBeforeSeq_