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 (std::shared_ptr< const Alphabet > &alphabet, const std::string &message, bool verbose=true)
	BppOAlphabetIndex2Format (std::shared_ptr< const CodonAlphabet > &alphabet, std::shared_ptr< const GeneticCode > &gencode, 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
std::unique_ptr< AlphabetIndex2 >	read (const std::string &description)
	Read a AlphabetIndex2 object from a string. More...

Private Attributes
std::shared_ptr< const Alphabet >	alphabet_
std::shared_ptr< const GeneticCode >	gencode_
std::string	message_
bool	verbose_

Detailed Description

AlphabetIndex2 I/O in BppO format.

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

Definition at line 26 of file BppOAlphabetIndex2Format.h.

Constructor & Destructor Documentation

BppOAlphabetIndex2Format() [1/3]

bpp::BppOAlphabetIndex2Format::BppOAlphabetIndex2Format ( std::shared_ptr< 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 instantiated 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 43 of file BppOAlphabetIndex2Format.h.

BppOAlphabetIndex2Format() [2/3]

bpp::BppOAlphabetIndex2Format::BppOAlphabetIndex2Format ( std::shared_ptr< const CodonAlphabet > &  alphabet, std::shared_ptr< const GeneticCode > &  gencode, const std::string &  message, bool  verbose = true  )

inline

Definition at line 53 of file BppOAlphabetIndex2Format.h.

BppOAlphabetIndex2Format() [3/3]

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

inline

Definition at line 64 of file BppOAlphabetIndex2Format.h.

~BppOAlphabetIndex2Format()

virtual bpp::BppOAlphabetIndex2Format::~BppOAlphabetIndex2Format ( )

inlinevirtual

Definition at line 79 of file BppOAlphabetIndex2Format.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 86 of file BppOAlphabetIndex2Format.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 84 of file BppOAlphabetIndex2Format.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 82 of file BppOAlphabetIndex2Format.h.

operator=()

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

inline

Definition at line 70 of file BppOAlphabetIndex2Format.h.

References alphabet_, gencode_, message_, and verbose_.

read()

unique_ptr< AlphabetIndex2 > BppOAlphabetIndex2Format::read

(

const std::string &

description

)

Read a AlphabetIndex2 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 occurred.

Definition at line 24 of file BppOAlphabetIndex2Format.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getAFilePath(), bpp::ApplicationTools::getBooleanParameter(), bpp::ApplicationTools::getStringParameter(), bpp::AlphabetTools::isCodonAlphabet(), bpp::AlphabetTools::isProteicAlphabet(), bpp::KeyvalTools::parseProcedure(), bpp::BppOAlphabetIndex1Format::read(), and read().

Referenced by bpp::SequenceApplicationTools::getAlphabetIndex2(), and read().

Member Data Documentation

alphabet_

std::shared_ptr<const Alphabet> bpp::BppOAlphabetIndex2Format::alphabet_

private

Definition at line 30 of file BppOAlphabetIndex2Format.h.

Referenced by operator=().

gencode_

std::shared_ptr<const GeneticCode> bpp::BppOAlphabetIndex2Format::gencode_

private

Definition at line 31 of file BppOAlphabetIndex2Format.h.

Referenced by operator=().

message_

std::string bpp::BppOAlphabetIndex2Format::message_

private

Definition at line 33 of file BppOAlphabetIndex2Format.h.

Referenced by operator=().

verbose_

bool bpp::BppOAlphabetIndex2Format::verbose_

private

Definition at line 34 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