bpp::AbstractOAlignment Class Reference

Partial implementation of the OAlignment interface. More...

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

Inheritance diagram for bpp::AbstractOAlignment:

Collaboration diagram for bpp::AbstractOAlignment:

Public Member Functions
	AbstractOAlignment ()
virtual	~AbstractOAlignment ()
const std::string	getDataType () const
virtual const std::string	getFormatName () const=0
virtual const std::string	getFormatDescription () const=0
OAlignment methods:
void	writeAlignment (std::ostream &output, const SiteContainerInterface &sc) const override=0
	Write a container to a stream. More...
void	writeAlignment (const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override
	Write a container to a file. More...

Detailed Description

Partial implementation of the OAlignment interface.

Definition at line 22 of file AbstractOAlignment.h.

Constructor & Destructor Documentation

AbstractOAlignment()

bpp::AbstractOAlignment::AbstractOAlignment ( )

inline

Definition at line 26 of file AbstractOAlignment.h.

~AbstractOAlignment()

virtual bpp::AbstractOAlignment::~AbstractOAlignment ( )

inlinevirtual

Definition at line 27 of file AbstractOAlignment.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.

writeAlignment() [1/2]

void bpp::AbstractOAlignment::writeAlignment ( const std::string &  path, const SiteContainerInterface &  sc, bool  overwrite = true  ) const

inlineoverridevirtual

Write a container to a file.

Parameters

path	The path to the file to write.
sc	The container to write.
overwrite	If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost.

Exceptions

Exception

If the file is not in the specified format.

Implements bpp::OAlignment.

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

Definition at line 37 of file AbstractOAlignment.h.

References writeAlignment().

writeAlignment() [2/2]

void bpp::AbstractOAlignment::writeAlignment ( std::ostream &  output, const SiteContainerInterface &  sc  ) const

overridepure virtual

Write a container to a stream.

Parameters

output	The output stream where to write.
sc	The container to write.

Exceptions

Exception

If the file is not in the specified format.

Implements bpp::OAlignment.

Implemented in bpp::Stockholm, bpp::Phylip, and bpp::Clustal.

Referenced by bpp::Phylip::writeAlignment(), writeAlignment(), bpp::Clustal::writeAlignment(), and bpp::Stockholm::writeAlignment().

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

• Bpp/Seq/Io/AbstractOAlignment.h