bpp::BppOAlphabetIndex2Format Class Reference

AlphabetIndex2 I/O in BppO format. More...

#include <Bpp/Seq/Io/BppOAlphabetIndex2Format.h>

Inheritance diagram for bpp::BppOAlphabetIndex2Format:

Collaboration diagram for bpp::BppOAlphabetIndex2Format:

Public Member Functions
	BppOAlphabetIndex2Format (const Alphabet *alphabet, const std::string &message, bool verbose=true)
	BppOAlphabetIndex2Format (const BppOAlphabetIndex2Format &format)
BppOAlphabetIndex2Format &	operator= (const BppOAlphabetIndex2Format &format)
virtual	~BppOAlphabetIndex2Format ()
const std::string	getFormatName () const
const std::string	getFormatDescription () const
const std::string	getDataType () const
AlphabetIndex2 *	read (const std::string &description) throw (Exception)
	Read a AlphabetIndex1 object from a string. More...

Private Attributes
const Alphabet *	alphabet_
std::string	message_
bool	verbose_

Detailed Description

AlphabetIndex2 I/O in BppO format.

Enables the instanciation of AlphabetIndex2 objects according to the BppO syntax (see the Bio++ Program Suite manual for a detailed description of this syntax).

Definition at line 60 of file BppOAlphabetIndex2Format.h.

Constructor & Destructor Documentation

BppOAlphabetIndex2Format() [1/2]

bpp::BppOAlphabetIndex2Format::BppOAlphabetIndex2Format ( const Alphabet *  alphabet, const std::string &  message, bool  verbose = true  )

inline

Parameters

alphabet	The alphabet for which indices should be built. The alphabet will be used to check that the instanciated index is compatible.
message	Some text describing what the index is intended for.
verbose	Tell if some messages should be printed while parsing.

Definition at line 75 of file BppOAlphabetIndex2Format.h.

BppOAlphabetIndex2Format() [2/2]

bpp::BppOAlphabetIndex2Format::BppOAlphabetIndex2Format ( const BppOAlphabetIndex2Format &  format )

inline

Definition at line 78 of file BppOAlphabetIndex2Format.h.

~BppOAlphabetIndex2Format()

virtual bpp::BppOAlphabetIndex2Format::~BppOAlphabetIndex2Format ( )

inlinevirtual

Definition at line 91 of file BppOAlphabetIndex2Format.h.

Member Function Documentation

getDataType()

const std::string bpp::BppOAlphabetIndex2Format::getDataType ( ) const

inline

Definition at line 98 of file BppOAlphabetIndex2Format.h.

getFormatDescription()

const std::string bpp::BppOAlphabetIndex2Format::getFormatDescription ( ) const

inline

Definition at line 96 of file BppOAlphabetIndex2Format.h.

getFormatName()

const std::string bpp::BppOAlphabetIndex2Format::getFormatName ( ) const

inline

Definition at line 94 of file BppOAlphabetIndex2Format.h.

operator=()

BppOAlphabetIndex2Format& bpp::BppOAlphabetIndex2Format::operator= ( const BppOAlphabetIndex2Format &  format )

inline

Definition at line 83 of file BppOAlphabetIndex2Format.h.

References alphabet_, message_, and verbose_.

read()

AlphabetIndex2 * BppOAlphabetIndex2Format::read	(	const std::string &	description	)
throw	(	Exception
	)

Read a AlphabetIndex1 object from a string.

Parameters

description

A string describing the index in the keyval syntax.

Returns

A new AlphabetIndex2 object according to options specified.

Exceptions

Exception

if an error occured.

Definition at line 59 of file BppOAlphabetIndex2Format.cpp.

References bpp::AlphabetTools::isProteicAlphabet(), bpp::BppOAlphabetIndex1Format::read(), bpp::GranthamAAChemicalDistance::setPC1Sign(), bpp::MiyataAAChemicalDistance::setSymmetric(), bpp::SimpleIndexDistance::setSymmetric(), and bpp::GranthamAAChemicalDistance::setSymmetric().

Referenced by bpp::SequenceApplicationTools::getAlphabetIndex2().

Member Data Documentation

alphabet_

const Alphabet* bpp::BppOAlphabetIndex2Format::alphabet_

private

Definition at line 64 of file BppOAlphabetIndex2Format.h.

Referenced by operator=().

message_

std::string bpp::BppOAlphabetIndex2Format::message_

private

Definition at line 65 of file BppOAlphabetIndex2Format.h.

Referenced by operator=().

verbose_

bool bpp::BppOAlphabetIndex2Format::verbose_

private

Definition at line 66 of file BppOAlphabetIndex2Format.h.

Referenced by operator=().

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

• Bpp/Seq/Io/BppOAlphabetIndex2Format.h
• Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp