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:

List of all members.

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 SiteContainer &sc) const =0 throw (Exception)
	Write a container to a stream.
void	writeAlignment (const std::string &path, const SiteContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to a file.

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Detailed Description

Partial implementation of the OAlignment interface.

Definition at line 57 of file AbstractOAlignment.h.

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Constructor & Destructor Documentation

bpp::AbstractOAlignment::AbstractOAlignment

(

)

[inline]

Definition at line 62 of file AbstractOAlignment.h.

virtual bpp::AbstractOAlignment::~AbstractOAlignment

(

)

[inline, virtual]

Definition at line 63 of file AbstractOAlignment.h.

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Member Function Documentation

const std::string bpp::IOSequence::getDataType

(

)

const [inline, virtual, inherited]

Implements bpp::IOFormat.

Definition at line 65 of file IoSequence.h.

void bpp::AbstractOAlignment::writeAlignment	(	std::ostream &	output,
		const SiteContainer &	sc
	)		const throw (Exception) [pure 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::Phylip, bpp::Clustal, and bpp::Stockholm.

Referenced by writeAlignment().

void bpp::AbstractOAlignment::writeAlignment	(	const std::string &	path,
		const SiteContainer &	sc,
		bool	overwrite = true
	)		const throw (Exception) [inline, virtual]

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

Definition at line 73 of file AbstractOAlignment.h.

References writeAlignment().

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

• Bpp/Seq/Io/AbstractOAlignment.h