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 SiteContainerInterface &sc) const override
	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...
The IOSequence interface.
const std::string	getFormatName () const override
const std::string	getFormatDescription () const override

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 22 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 34 of file Stockholm.h.

~Stockholm()

virtual bpp::Stockholm::~Stockholm ( )

inlinevirtual

Definition at line 37 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 68 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 76 of file Stockholm.h.

References checkNames_.

getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Reimplemented in bpp::Pasta.

Definition at line 29 of file IoSequence.h.

getFormatDescription()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 58 of file Stockholm.h.

getFormatName()

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

inlineoverridevirtual

Implements bpp::IOFormat.

Definition at line 57 of file Stockholm.h.

writeAlignment() [1/2]

void bpp::Stockholm::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.

Reimplemented from bpp::AbstractOAlignment.

Definition at line 46 of file Stockholm.h.

References bpp::AbstractOAlignment::writeAlignment().

writeAlignment() [2/2]

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

overridevirtual

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 17 of file Stockholm.cpp.

References bpp::Commentable::getComments(), bpp::TemplateSequenceDataInterface< HashType >::getNumberOfSequences(), bpp::TemplateSequenceDataInterface< HashType >::getSequenceNames(), bpp::TextTools::removeWhiteSpaces(), bpp::TextTools::resizeRight(), and bpp::TemplateSequenceContainerInterface< SequenceType, HashType >::sequence().

Member Data Documentation

checkNames_

bool bpp::Stockholm::checkNames_

private

Definition at line 26 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