bpp::IProbabilisticAlignment Class Reference

The IProbabilisticSequence interface. More...

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

Inheritance diagram for bpp::IProbabilisticAlignment:

Collaboration diagram for bpp::IProbabilisticAlignment:

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

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

Definition at line 206 of file ISequence.h.

Constructor & Destructor Documentation

IProbabilisticAlignment()

bpp::IProbabilisticAlignment::IProbabilisticAlignment ( )

inline

Definition at line 210 of file ISequence.h.

~IProbabilisticAlignment()

virtual bpp::IProbabilisticAlignment::~IProbabilisticAlignment ( )

inlinevirtual

Definition at line 211 of file ISequence.h.

Member Function Documentation

getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 44 of file IoSequence.h.

readAlignment() [1/4]

virtual void bpp::IProbabilisticAlignment::readAlignment ( const std::string &  path, ProbabilisticSequenceContainerInterface &  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::AbstractIProbabilisticAlignment.

readAlignment() [2/4]

virtual std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::IProbabilisticAlignment::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 ProbabilisticSiteContainer object.

Implemented in bpp::AbstractIProbabilisticAlignment.

readAlignment() [3/4]

virtual void bpp::IProbabilisticAlignment::readAlignment ( std::istream &  input, ProbabilisticSequenceContainerInterface &  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::AbstractIProbabilisticAlignment.

readAlignment() [4/4]

virtual std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::IProbabilisticAlignment::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 ProbabilisticSiteContainer object.

Implemented in bpp::AbstractIProbabilisticAlignment.

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

• Bpp/Seq/Io/ISequence.h