bpp::AbstractOSequence Class Reference

Partial implementation of the OSequence and OAlignment interfaces. More...

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

Inheritance diagram for bpp::AbstractOSequence:

Collaboration diagram for bpp::AbstractOSequence:

Public Member Functions
	AbstractOSequence ()
virtual	~AbstractOSequence ()
const std::string	getDataType () const
OSequence methods:
void	writeSequences (std::ostream &output, const SequenceContainer &sc) const =0 throw (Exception)
	Write a container to a stream. More...
void	writeSequences (const std::string &path, const SequenceContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to a file. More...
OAlignment methods:
As a SiteContainer is a specialization of SequenceContainer, it is assumed that a OSequence object can write aligned sequence just like a OAlignment object. Therefore it implements the OAlignment interface by down-casting the SiteContainer to a SequenceContainer.
void	writeAlignment (std::ostream &output, const SiteContainer &sc) const throw (Exception)
	Write a container to a stream. More...
void	writeAlignment (const std::string &path, const SiteContainer &sc, bool overwrite=true) const throw (Exception)
	Write a container to a file. More...

Detailed Description

Partial implementation of the OSequence and OAlignment interfaces.

Definition at line 57 of file AbstractOSequence.h.

Constructor & Destructor Documentation

AbstractOSequence()

bpp::AbstractOSequence::AbstractOSequence ( )

inline

Definition at line 63 of file AbstractOSequence.h.

~AbstractOSequence()

virtual bpp::AbstractOSequence::~AbstractOSequence ( )

inlinevirtual

Definition at line 64 of file AbstractOSequence.h.

Member Function Documentation

getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

writeAlignment() [1/2]

void bpp::AbstractOSequence::writeAlignment ( std::ostream &  output, const SiteContainer &  sc  ) const throw ( Exception )

inlinevirtual

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.

Definition at line 92 of file AbstractOSequence.h.

References writeSequences().

writeAlignment() [2/2]

void bpp::AbstractOSequence::writeAlignment ( const std::string &  path, const SiteContainer &  sc, bool  overwrite = true  ) const throw ( Exception )

inlinevirtual

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.

Definition at line 96 of file AbstractOSequence.h.

References writeSequences().

writeSequences() [1/2]

void bpp::AbstractOSequence::writeSequences ( std::ostream &  output, const SequenceContainer &  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::OSequence.

Implemented in bpp::Mase, and bpp::Fasta.

Referenced by writeAlignment(), writeSequences(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

writeSequences() [2/2]

void bpp::AbstractOSequence::writeSequences ( const std::string &  path, const SequenceContainer &  sc, bool  overwrite = true  ) const throw ( Exception )

inlinevirtual

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::OSequence.

Reimplemented in bpp::Mase, and bpp::Fasta.

Definition at line 74 of file AbstractOSequence.h.

References writeSequences().

---

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

• Bpp/Seq/Io/AbstractOSequence.h