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 Nexus 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, SequenceContainerInterface &sc) const override
	Append sequences to a container from a stream. 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...

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...

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...

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

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 34 of file NexusIoSequence.h.

Constructor & Destructor Documentation

◆ NexusIOSequence()

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

inline

Build a new Nexus 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 53 of file NexusIoSequence.h.

◆ ~NexusIOSequence()

virtual bpp::NexusIOSequence::~NexusIOSequence ( )

inlinevirtual

Definition at line 56 of file NexusIoSequence.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 NexusIOSequence::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 37 of file NexusIoSequence.cpp.

References bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::addSequence(), bpp::AlphabetTools::DEFAULT_ALPHABET, bpp::TextTools::endsWith(), bpp::NexusTools::getNextCommand(), bpp::FileTools::getNextLine(), bpp::TextTools::hasSubstring(), bpp::KeyvalTools::multipleKeyvals(), bpp::TextTools::removeSurroundingWhiteSpaces(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::TextTools::startsWith(), and bpp::TextTools::toUpper().

◆ 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 80 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 87 of file NexusIoSequence.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 NexusIOSequence::getFormatDescription ( ) const

overridevirtual

Implements bpp::IOFormat.

Definition at line 180 of file NexusIoSequence.cpp.

◆ getFormatName()

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

overridevirtual

Implements bpp::IOFormat.

Definition at line 176 of file NexusIoSequence.cpp.

◆ 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(), bpp::Clustal::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::AbstractIAlignment2::readSequences	(	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 SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Reimplemented in bpp::Phylip, bpp::DCSE, and bpp::Clustal.

Definition at line 174 of file AbstractIAlignment.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::AbstractIAlignment2::readSequences	(	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 SequenceContainer object.

Exceptions

Exception If the file is not in the specified format.

Implements bpp::ISequence.

Reimplemented in bpp::Phylip, bpp::DCSE, and bpp::Clustal.

Definition at line 167 of file AbstractIAlignment.h.

References bpp::AbstractIAlignment::readAlignment().

◆ splitNameAndSequence_()

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

private

Definition at line 23 of file NexusIoSequence.cpp.

References bpp::TextTools::removeFirstWhiteSpaces(), and bpp::TextTools::removeSurroundingWhiteSpaces().

Member Data Documentation

◆ charsByLine_

unsigned int bpp::NexusIOSequence::charsByLine_

protected

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

Definition at line 42 of file NexusIoSequence.h.

◆ checkNames_

bool bpp::NexusIOSequence::checkNames_

protected

Definition at line 44 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() [1/4]

◆ readSequences() [2/4]

◆ readSequences() [3/4]

◆ readSequences() [4/4]

◆ splitNameAndSequence_()

Member Data Documentation

◆ charsByLine_

◆ checkNames_