bpp::ISequence Class Reference

The ISequence interface. More...

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

Inheritance diagram for bpp::ISequence:

Collaboration diagram for bpp::ISequence:

Public Member Functions
	ISequence ()
virtual	~ISequence ()
virtual void	readSequences (std::istream &input, SequenceContainerInterface &container) const =0
	Create a new container from a stream. More...
virtual void	readSequences (const std::string &path, SequenceContainerInterface &container) const =0
	Create a new container from a file. More...
virtual std::unique_ptr< SequenceContainerInterface >	readSequences (std::istream &input, std::shared_ptr< const Alphabet > alpha) const =0
	Create a new container from a stream. More...
virtual std::unique_ptr< SequenceContainerInterface >	readSequences (const std::string &path, std::shared_ptr< const Alphabet > alpha) const =0
	Create a new container from a file. More...
const std::string	getDataType () const
virtual const std::string	getFormatName () const=0
virtual const std::string	getFormatDescription () const=0

Detailed Description

The ISequence interface.

This interface defines the basic methods for reading sequences from a file.

Definition at line 27 of file ISequence.h.

Constructor & Destructor Documentation

ISequence()

bpp::ISequence::ISequence ( )

inline

Definition at line 31 of file ISequence.h.

~ISequence()

virtual bpp::ISequence::~ISequence ( )

inlinevirtual

Definition at line 32 of file ISequence.h.

Member Function Documentation

getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

readSequences() [1/4]

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

pure virtual

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.

Implemented in bpp::AbstractISequence, and bpp::AbstractIAlignment2.

readSequences() [2/4]

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

pure 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.

Implemented in bpp::Phylip, bpp::DCSE, bpp::Clustal, bpp::AbstractISequence, and bpp::AbstractIAlignment2.

readSequences() [3/4]

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

pure virtual

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.

Implemented in bpp::AbstractISequence, and bpp::AbstractIAlignment2.

readSequences() [4/4]

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

pure 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.

Implemented in bpp::Phylip, bpp::DCSE, bpp::Clustal, bpp::AbstractISequence, and bpp::AbstractIAlignment2.

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

• Bpp/Seq/Io/ISequence.h