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) throw (Exception)
	Build a new Clustal object.
virtual	~Clustal ()
bool	checkNames () const
void	checkNames (bool yn)
	Tell whether the sequence names should be checked when reading from files.
const std::string	getDataType () const
The AbstractIAlignment interface.
void	appendAlignmentFromStream (std::istream &input, SiteContainer &sc) const throw (Exception)
	Append sequences to a container from a stream.
The ISequence interface.
As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
virtual SequenceContainer *	readSequences (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream.
virtual SequenceContainer *	readSequences (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file.
The AbstractOAlignment interface.
void	writeAlignment (std::ostream &output, const SiteContainer &sc) const throw (Exception)
	Write a container to a stream.
void	writeAlignment (const std::string &path, const SiteContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to a file.
The IOSequence interface.
const std::string	getFormatName () const
const std::string	getFormatDescription () const
IAlignment methods:
virtual void	readAlignment (std::istream &input, SiteContainer &sc) const throw (Exception)
	Add sequences to a container from a stream.
virtual void	readAlignment (const std::string &path, SiteContainer &sc) const throw (Exception)
	Add sequences to a container from a file.
virtual AlignedSequenceContainer *	readAlignment (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Create a new container from a file.
virtual AlignedSequenceContainer *	readAlignment (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Create a new container from a stream.
Protected Member Functions
virtual void	appendAlignmentFromFile (const std::string &path, SiteContainer &sc) const throw (Exception)
	Append sequences to a container from a file.
virtual AlignedSequenceContainer *	readAlignmentFromStream (std::istream &input, const Alphabet *alpha) const throw (Exception)
	Read sequences from a stream.
virtual AlignedSequenceContainer *	readAlignmentFromFile (const std::string &path, const Alphabet *alpha) const throw (Exception)
	Read sequences from a file.
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 57 of file Clustal.h.

Constructor & Destructor Documentation

bpp::Clustal::Clustal	(	bool	checkSequenceNames = `true`,
		unsigned int	nbExtraSpacesBeforeSeq = `5`,
		unsigned int	charsByLine = `100`
	)		throw (Exception) `[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 75 of file Clustal.h.

virtual bpp::Clustal::~Clustal ( ) [inline, virtual]

Definition at line 81 of file Clustal.h.

Member Function Documentation

virtual void bpp::AbstractIAlignment::appendAlignmentFromFile	(	const std::string &	path,
		SiteContainer &	sc
	)		const throw (Exception) `[inline, protected, virtual, inherited]`

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().

void Clustal::appendAlignmentFromStream	(	std::istream &	input,
		SiteContainer &	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::AbstractIAlignment.

Definition at line 52 of file Clustal.cpp.

References bpp::FileTools::getNextLine(), bpp::TextTools::isEmpty(), and bpp::TextTools::removeSurroundingWhiteSpaces().

bool bpp::Clustal::checkNames ( ) const [inline]

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

Definition at line 134 of file Clustal.h.

References checkNames_.

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 141 of file Clustal.h.

References checkNames_.

const std::string bpp::IOSequence::getDataType ( ) const [inline, virtual, inherited]

Implements bpp::IOFormat.

Definition at line 65 of file IoSequence.h.

const std::string bpp::Clustal::getFormatDescription ( ) const [inline, virtual]

Implements bpp::IOFormat.

Definition at line 127 of file Clustal.h.

const std::string bpp::Clustal::getFormatName ( ) const [inline, virtual]

Implements bpp::IOFormat.

Definition at line 125 of file Clustal.h.

virtual void bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		SiteContainer &	sc
	)		const throw (Exception) `[inline, virtual, inherited]`

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(), readSequences(), bpp::NexusIOSequence::readSequences(), and bpp::Phylip::readSequences().

virtual void bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		SiteContainer &	sc
	)		const throw (Exception) `[inline, virtual, inherited]`

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().

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	const std::string &	path,
		const Alphabet *	alpha
	)		const throw (Exception) `[inline, virtual, inherited]`

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().

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignment	(	std::istream &	input,
		const Alphabet *	alpha
	)		const throw (Exception) `[inline, virtual, inherited]`

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().

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromFile	(	const std::string &	path,
		const Alphabet *	alpha
	)		const throw (Exception) `[inline, protected, virtual, inherited]`

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().

virtual AlignedSequenceContainer* bpp::AbstractIAlignment::readAlignmentFromStream	(	std::istream &	input,
		const Alphabet *	alpha
	)		const throw (Exception) `[inline, protected, virtual, inherited]`

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().

virtual SequenceContainer* bpp::Clustal::readSequences	(	std::istream &	input,
		const Alphabet *	alpha
	)		const throw (Exception) `[inline, virtual]`

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 100 of file Clustal.h.

References bpp::AbstractIAlignment::readAlignment().

virtual SequenceContainer* bpp::Clustal::readSequences	(	const std::string &	path,
		const Alphabet *	alpha
	)		const throw (Exception) `[inline, virtual]`

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 103 of file Clustal.h.

References bpp::AbstractIAlignment::readAlignment().

void Clustal::writeAlignment	(	std::ostream &	output,
		const SiteContainer &	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::AbstractOAlignment.

Definition at line 114 of file Clustal.cpp.

References bpp::Sequence::getName(), and bpp::TextTools::resizeRight().

Referenced by writeAlignment().

void bpp::Clustal::writeAlignment	(	const std::string &	path,
		const SiteContainer &	sc,
		bool	overwrite = `true`
	)		const throw (Exception) `[inline, virtual]`

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 114 of file Clustal.h.

References writeAlignment().