bpp::BppOSequenceReaderFormat Class Reference

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

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

Inheritance diagram for bpp::BppOSequenceReaderFormat:

Collaboration diagram for bpp::BppOSequenceReaderFormat:

Public Member Functions
	BppOSequenceReaderFormat (int warningLevel)
virtual	~BppOSequenceReaderFormat ()
const std::string	getFormatName () const
const std::string	getFormatDescription () const
const std::string	getDataType () const
std::unique_ptr< ISequence >	read (const std::string &description)
	Read a ISequence 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 ISequence 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 BppOSequenceReaderFormat.h.

Constructor & Destructor Documentation

BppOSequenceReaderFormat()

bpp::BppOSequenceReaderFormat::BppOSequenceReaderFormat ( int  warningLevel )

inline

Definition at line 29 of file BppOSequenceReaderFormat.h.

~BppOSequenceReaderFormat()

virtual bpp::BppOSequenceReaderFormat::~BppOSequenceReaderFormat ( )

inlinevirtual

Definition at line 32 of file BppOSequenceReaderFormat.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 39 of file BppOSequenceReaderFormat.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 37 of file BppOSequenceReaderFormat.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 35 of file BppOSequenceReaderFormat.h.

getUnparsedArguments()

virtual const std::map<std::string, std::string>& bpp::BppOSequenceReaderFormat::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 53 of file BppOSequenceReaderFormat.h.

References unparsedArguments_.

read()

unique_ptr< ISequence > BppOSequenceReaderFormat::read

(

const std::string &

description

)

Read a ISequence object from a string.

Parameters

description

A string describing the reader in the keyval syntax.

Returns

A new ISequence object according to options specified.

Exceptions

Exception

if an error occurred.

Definition at line 21 of file BppOSequenceReaderFormat.cpp.

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

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

Member Data Documentation

unparsedArguments_

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

private

Definition at line 25 of file BppOSequenceReaderFormat.h.

Referenced by getUnparsedArguments().

warningLevel_

int bpp::BppOSequenceReaderFormat::warningLevel_

private

Definition at line 26 of file BppOSequenceReaderFormat.h.

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

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