The Nexus format reader for sequences. More...

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

Inheritance diagram for bpp::NexusIOSequence:

Collaboration diagram for bpp::NexusIOSequence:

Public Member Functions
	NexusIOSequence (unsigned int charsByLine=100, bool checkSequenceNames=true)
	Build a new Phylip file reader. More...

virtual	~NexusIOSequence ()

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

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

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. 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...

Protected Member Functions
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...

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

bool	checkNames_

Private Member Functions
const std::vector< std::string >	splitNameAndSequence_ (const std::string &s) const throw (Exception)

Detailed Description

The Nexus format reader for sequences.

An AlignedSequenceContainer is used instead of a VectorSequenceContainer.

This reader is not supposed to be a full parser of the Nexus files, but only extract the sequence data. Only a basic subset of the options are and will be supported.

This format is described in the following paper: Maddison D, Swofford D, and Maddison W (1997), Syst Biol 46(4):590-621

Author: Julien Dutheil

Definition at line 69 of file NexusIoSequence.h.

Constructor & Destructor Documentation

◆ NexusIOSequence()

bpp::NexusIOSequence::NexusIOSequence	(	unsigned int	charsByLine = `100`,
		bool	checkSequenceNames = `true`
	)

inline

Build a new Phylip file reader.

Parameters

charsByLine	The number of base to display in a row (ignored for now, no writing support).
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).

Definition at line 89 of file NexusIoSequence.h.

◆ ~NexusIOSequence()

virtual bpp::NexusIOSequence::~NexusIOSequence ( )

inlinevirtual

Definition at line 92 of file NexusIoSequence.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 NexusIOSequence::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 70 of file NexusIoSequence.cpp.

References bpp::SequenceContainer::addSequence(), bpp::AlphabetTools::DEFAULT_ALPHABET, bpp::SequenceContainer::getAlphabet(), bpp::NexusTools::getNextCommand(), bpp::OrderedSequenceContainer::getNumberOfSequences(), bpp::OrderedSequenceContainer::getSequence(), and bpp::SiteContainerTools::resolveDottedAlignment().

◆ checkNames() [1/2]

bool bpp::NexusIOSequence::checkNames ( ) const

inline

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

Definition at line 132 of file NexusIoSequence.h.

References checkNames_.

◆ checkNames() [2/2]

void bpp::NexusIOSequence::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 139 of file NexusIoSequence.h.

References checkNames_.

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ getFormatDescription()

const std::string NexusIOSequence::getFormatDescription ( ) const

Definition at line 203 of file NexusIoSequence.cpp.

◆ getFormatName()

const std::string NexusIOSequence::getFormatName ( ) const

Definition at line 199 of file NexusIoSequence.cpp.

◆ 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(), 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() [1/2]

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

inlinevirtual

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 112 of file NexusIoSequence.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequences() [2/2]

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

inlinevirtual

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 115 of file NexusIoSequence.h.

References bpp::AbstractIAlignment::readAlignment().

◆ splitNameAndSequence_()

const std::vector< std::string > NexusIOSequence::splitNameAndSequence_	(	const std::string &	s	)	const
throw	(	Exception
	)

private

Definition at line 57 of file NexusIoSequence.cpp.

Member Data Documentation

◆ charsByLine_

unsigned int bpp::NexusIOSequence::charsByLine_

protected

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

Definition at line 78 of file NexusIoSequence.h.

◆ checkNames_

bool bpp::NexusIOSequence::checkNames_

protected

Definition at line 80 of file NexusIoSequence.h.

Referenced by checkNames().

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

Bpp/Seq/Io/NexusIoSequence.h
Bpp/Seq/Io/NexusIoSequence.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ NexusIOSequence()

◆ ~NexusIOSequence()

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() [1/2]

◆ readSequences() [2/2]

◆ splitNameAndSequence_()

Member Data Documentation

◆ charsByLine_

◆ checkNames_