Support for the Dedicated Comparative Sequence Editor format. More...

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

Inheritance diagram for bpp::DCSE:

Collaboration diagram for bpp::DCSE:

Public Member Functions
	DCSE ()

virtual	~DCSE ()

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...

Detailed Description

Support for the Dedicated Comparative Sequence Editor format.

Only the sequence information is retrieved. All structural information is dropped for now.

A description of this format may be found here: http://www.psb.ugent.be/rRNA/help/formats/aliformat.html

Definition at line 60 of file Dcse.h.

Constructor & Destructor Documentation

◆ DCSE()

bpp::DCSE::DCSE ( )

inline

Definition at line 66 of file Dcse.h.

◆ ~DCSE()

virtual bpp::DCSE::~DCSE ( )

inlinevirtual

Definition at line 67 of file Dcse.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 DCSE::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 Dcse.cpp.

◆ getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

◆ getFormatDescription()

const string DCSE::getFormatDescription ( ) const

Definition at line 96 of file Dcse.cpp.

◆ getFormatName()

const string DCSE::getFormatName ( ) const

Definition at line 94 of file Dcse.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 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() [1/2]

virtual SequenceContainer* bpp::DCSE::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 87 of file Dcse.h.

References bpp::AbstractIAlignment::readAlignment().

◆ readSequences() [2/2]

virtual SequenceContainer* bpp::DCSE::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 90 of file Dcse.h.

References bpp::AbstractIAlignment::readAlignment().

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

Bpp/Seq/Io/Dcse.h
Bpp/Seq/Io/Dcse.cpp

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ DCSE()

◆ ~DCSE()

Member Function Documentation

◆ appendAlignmentFromFile()

◆ appendAlignmentFromStream()

◆ getDataType()

◆ getFormatDescription()

◆ getFormatName()

◆ readAlignment() [1/4]

◆ readAlignment() [2/4]

◆ readAlignment() [3/4]

◆ readAlignment() [4/4]

◆ readAlignmentFromFile()

◆ readAlignmentFromStream()

◆ readSequences() [1/2]

◆ readSequences() [2/2]