bpp::BppOAlignmentReaderFormat Class Reference

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

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

Inheritance diagram for bpp::BppOAlignmentReaderFormat:

Collaboration diagram for bpp::BppOAlignmentReaderFormat:

Public Member Functions
	BppOAlignmentReaderFormat (int warningLevel)
virtual	~BppOAlignmentReaderFormat ()
const std::string	getFormatName () const
const std::string	getFormatDescription () const
const std::string	getDataType () const
IAlignment *	read (const std::string &description) throw (Exception)
	Read a IAlignment 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 IAlignment object according to distribution description syntax (see the Bio++ Program Suite manual for a detailed description of this syntax).

Definition at line 56 of file BppOAlignmentReaderFormat.h.

Constructor & Destructor Documentation

BppOAlignmentReaderFormat()

bpp::BppOAlignmentReaderFormat::BppOAlignmentReaderFormat ( int  warningLevel )

inline

Definition at line 64 of file BppOAlignmentReaderFormat.h.

~BppOAlignmentReaderFormat()

virtual bpp::BppOAlignmentReaderFormat::~BppOAlignmentReaderFormat ( )

inlinevirtual

Definition at line 66 of file BppOAlignmentReaderFormat.h.

Member Function Documentation

getDataType()

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

inline

Definition at line 73 of file BppOAlignmentReaderFormat.h.

getFormatDescription()

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

inline

Definition at line 71 of file BppOAlignmentReaderFormat.h.

getFormatName()

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

inline

Definition at line 69 of file BppOAlignmentReaderFormat.h.

getUnparsedArguments()

virtual const std::map<std::string, std::string>& bpp::BppOAlignmentReaderFormat::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 87 of file BppOAlignmentReaderFormat.h.

References unparsedArguments_.

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

read()

IAlignment * BppOAlignmentReaderFormat::read	(	const std::string &	description	)
throw	(	Exception
	)

Read a IAlignment object from a string.

Parameters

description

A string describing the reader in the keyval syntax.

Returns

A new IAlignment object according to options specified.

Exceptions

Exception

if an error occured.

Definition at line 56 of file BppOAlignmentReaderFormat.cpp.

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

Member Data Documentation

unparsedArguments_

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

private

Definition at line 60 of file BppOAlignmentReaderFormat.h.

Referenced by getUnparsedArguments().

warningLevel_

int bpp::BppOAlignmentReaderFormat::warningLevel_

private

Definition at line 61 of file BppOAlignmentReaderFormat.h.

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

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