bpp::BppOAlignmentWriterFormat Class Reference

Sequence I/O in BppO format. More...

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

Inheritance diagram for bpp::BppOAlignmentWriterFormat:

Collaboration diagram for bpp::BppOAlignmentWriterFormat:

Public Member Functions
	BppOAlignmentWriterFormat (int warningLevel)
virtual	~BppOAlignmentWriterFormat ()
const std::string	getFormatName () const
const std::string	getFormatDescription () const
const std::string	getDataType () const
std::unique_ptr< OAlignment >	read (const std::string &description)
	Read a OAlignment object from a string. More...
virtual const std::map< std::string, std::string > &	getUnparsedArguments () const

Private Attributes
std::map< std::string, std::string >	unparsedArguments_
int	warningLevel_

Detailed Description

Sequence I/O in BppO format.

Creates a new OAlignment object according to distribution description syntax (see the Bio++ Program Suite manual for a detailed description of this syntax).

Definition at line 21 of file BppOAlignmentWriterFormat.h.

Constructor & Destructor Documentation

BppOAlignmentWriterFormat()

bpp::BppOAlignmentWriterFormat::BppOAlignmentWriterFormat ( int  warningLevel )

inline

Definition at line 29 of file BppOAlignmentWriterFormat.h.

~BppOAlignmentWriterFormat()

virtual bpp::BppOAlignmentWriterFormat::~BppOAlignmentWriterFormat ( )

inlinevirtual

Definition at line 33 of file BppOAlignmentWriterFormat.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 40 of file BppOAlignmentWriterFormat.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 38 of file BppOAlignmentWriterFormat.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 36 of file BppOAlignmentWriterFormat.h.

getUnparsedArguments()

virtual const std::map<std::string, std::string>& bpp::BppOAlignmentWriterFormat::getUnparsedArguments ( ) const

inlinevirtual

Returns

The arguments and their unparsed values from the last call of the read function, if there are any.

Definition at line 54 of file BppOAlignmentWriterFormat.h.

References unparsedArguments_.

read()

unique_ptr< OAlignment > BppOAlignmentWriterFormat::read

(

const std::string &

description

)

Read a OAlignment object from a string.

Parameters

description

A string describing the reader in the keyval syntax.

Returns

A new OAlignment object according to options specified.

Exceptions

Exception

if an error occurred.

Definition at line 19 of file BppOAlignmentWriterFormat.cpp.

References bpp::ApplicationTools::getStringParameter(), bpp::KeyvalTools::parseProcedure(), and split().

Referenced by bpp::SequenceApplicationTools::writeAlignmentFile().

Member Data Documentation

unparsedArguments_

std::map<std::string, std::string> bpp::BppOAlignmentWriterFormat::unparsedArguments_

private

Definition at line 25 of file BppOAlignmentWriterFormat.h.

Referenced by getUnparsedArguments().

warningLevel_

int bpp::BppOAlignmentWriterFormat::warningLevel_

private

Definition at line 26 of file BppOAlignmentWriterFormat.h.

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

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