bpp::Stockholm Class Reference

The Stockholm alignment file format. More...

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

Inheritance diagram for bpp::Stockholm:

Collaboration diagram for bpp::Stockholm:

Public Member Functions
	Stockholm (bool checkSequenceNames=true)
	Build a new Stockholm object. More...
virtual	~Stockholm ()
bool	checkNames () const
void	checkNames (bool yn)
	Tell whether the sequence names should be checked when reading from files. More...
const std::string	getDataType () const
The OAlignment interface.
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...
The IOSequence interface.
const std::string	getFormatName () const
const std::string	getFormatDescription () const

Private Attributes
bool	checkNames_

Detailed Description

The Stockholm alignment file format.

Write to Stockholm files. Only sequence data is read/written, annotation and secondary structures are ignored.

Definition at line 57 of file Stockholm.h.

Constructor & Destructor Documentation

Stockholm()

bpp::Stockholm::Stockholm ( bool  checkSequenceNames = true )

inline

Build a new Stockholm object.

Parameters

checkSequenceNames

Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).

Definition at line 71 of file Stockholm.h.

~Stockholm()

virtual bpp::Stockholm::~Stockholm ( )

inlinevirtual

Definition at line 74 of file Stockholm.h.

Member Function Documentation

checkNames() [1/2]

bool bpp::Stockholm::checkNames ( ) const

inline

Warning

This is not used for now, will be when reading is implemented.

Returns

true if the names are to be checked when reading sequences from files.

Definition at line 106 of file Stockholm.h.

References checkNames_.

checkNames() [2/2]

void bpp::Stockholm::checkNames ( bool  yn )

inline

Tell whether the sequence names should be checked when reading from files.

Warning

This is not used for now, will be when reading is implemented.

Parameters

yn	whether the sequence names should be checked when reading from files.

Definition at line 114 of file Stockholm.h.

References checkNames_.

getDataType()

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

inlineinherited

Definition at line 65 of file IoSequence.h.

getFormatDescription()

const std::string bpp::Stockholm::getFormatDescription ( ) const

inline

Definition at line 96 of file Stockholm.h.

getFormatName()

const std::string bpp::Stockholm::getFormatName ( ) const

inline

Definition at line 95 of file Stockholm.h.

writeAlignment() [1/2]

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

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::AbstractOAlignment.

Definition at line 54 of file Stockholm.cpp.

writeAlignment() [2/2]

void bpp::Stockholm::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.

Reimplemented from bpp::AbstractOAlignment.

Definition at line 84 of file Stockholm.h.

References bpp::AbstractOAlignment::writeAlignment().

Member Data Documentation

checkNames_

bool bpp::Stockholm::checkNames_

private

Definition at line 62 of file Stockholm.h.

Referenced by checkNames().

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

• Bpp/Seq/Io/Stockholm.h
• Bpp/Seq/Io/Stockholm.cpp