bpp::IAlignment Class Reference

The IAlignment interface. More...

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

Inheritance diagram for bpp::IAlignment:

Collaboration diagram for bpp::IAlignment:

Public Member Functions
	IAlignment ()
virtual	~IAlignment ()
virtual void	readAlignment (std::istream &input, SequenceContainerInterface &container) const =0
	Add the content of a stream to a new container. More...
virtual void	readAlignment (const std::string &path, SequenceContainerInterface &container) const =0
	Create a new container from a file. More...
virtual std::unique_ptr< SiteContainerInterface >	readAlignment (std::istream &input, std::shared_ptr< const Alphabet > alpha) const =0
	Create a new container from a stream. More...
virtual std::unique_ptr< SiteContainerInterface >	readAlignment (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 IAlignment interface.

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

Definition at line 85 of file ISequence.h.

Constructor & Destructor Documentation

IAlignment()

bpp::IAlignment::IAlignment ( )

inline

Definition at line 89 of file ISequence.h.

~IAlignment()

virtual bpp::IAlignment::~IAlignment ( )

inlinevirtual

Definition at line 90 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.

readAlignment() [1/4]

virtual void bpp::IAlignment::readAlignment ( 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. Needs not be a SiteContainer, as aligned sequences can be stored in a simple SequenceContainer.

Exceptions

Exception

If the file is not in the specified format.

Implemented in bpp::AbstractIAlignment.

readAlignment() [2/4]

virtual std::unique_ptr<SiteContainerInterface> bpp::IAlignment::readAlignment ( 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 SiteContainer object.

Exceptions

Exception

If the file is not in the specified format.

Implemented in bpp::AbstractIAlignment.

readAlignment() [3/4]

virtual void bpp::IAlignment::readAlignment ( std::istream &  input, SequenceContainerInterface &  container  ) const

pure virtual

Add the content of a stream to a new container.

Parameters

input	The input stream to read.
container	The container where to add data. Needs not be a SiteContainer, as aligned sequences can be stored in a simple SequenceContainer.

Exceptions

Exception

If the file is not in the specified format.

Implemented in bpp::AbstractIAlignment.

readAlignment() [4/4]

virtual std::unique_ptr<SiteContainerInterface> bpp::IAlignment::readAlignment ( 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 SiteContainer object.

Exceptions

Exception

If the file is not in the specified format.

Implemented in bpp::AbstractIAlignment.

---

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

• Bpp/Seq/Io/ISequence.h