bpp-seq  2.2.0
bpp::BppOAlphabetIndex1Format Class Reference

AlphabetIndex1 I/O in BppO format. More...

#include <Bpp/Seq/Io/BppOAlphabetIndex1Format.h>

+ Inheritance diagram for bpp::BppOAlphabetIndex1Format:
+ Collaboration diagram for bpp::BppOAlphabetIndex1Format:

Public Member Functions

 BppOAlphabetIndex1Format (const Alphabet *alphabet, const std::string &message, bool verbose=true)
 
 BppOAlphabetIndex1Format (const BppOAlphabetIndex1Format &format)
 
BppOAlphabetIndex1Formatoperator= (const BppOAlphabetIndex1Format &format)
 
virtual ~BppOAlphabetIndex1Format ()
 
const std::string getFormatName () const
 
const std::string getFormatDescription () const
 
const std::string getDataType () const
 
AlphabetIndex1read (const std::string &description) throw (Exception)
 Read a AlphabetIndex1 object from a string. More...
 

Private Attributes

const Alphabetalphabet_
 
std::string message_
 
bool verbose_
 

Detailed Description

AlphabetIndex1 I/O in BppO format.

Enables the instanciation of AlphabetIndex1 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 BppOAlphabetIndex1Format.h.

Constructor & Destructor Documentation

◆ BppOAlphabetIndex1Format() [1/2]

bpp::BppOAlphabetIndex1Format::BppOAlphabetIndex1Format ( const Alphabet alphabet,
const std::string &  message,
bool  verbose = true 
)
inline
Parameters
alphabetThe alphabet for which indices should be built. The alphabet will be used to check that the instanciated index is compatible.
messageSome text describing what the index is intended for.
verboseTell if some messages should be printed while parsing.

Definition at line 75 of file BppOAlphabetIndex1Format.h.

◆ BppOAlphabetIndex1Format() [2/2]

bpp::BppOAlphabetIndex1Format::BppOAlphabetIndex1Format ( const BppOAlphabetIndex1Format format)
inline

Definition at line 78 of file BppOAlphabetIndex1Format.h.

◆ ~BppOAlphabetIndex1Format()

virtual bpp::BppOAlphabetIndex1Format::~BppOAlphabetIndex1Format ( )
inlinevirtual

Definition at line 91 of file BppOAlphabetIndex1Format.h.

Member Function Documentation

◆ getDataType()

const std::string bpp::BppOAlphabetIndex1Format::getDataType ( ) const
inline

Definition at line 98 of file BppOAlphabetIndex1Format.h.

◆ getFormatDescription()

const std::string bpp::BppOAlphabetIndex1Format::getFormatDescription ( ) const
inline

Definition at line 96 of file BppOAlphabetIndex1Format.h.

◆ getFormatName()

const std::string bpp::BppOAlphabetIndex1Format::getFormatName ( ) const
inline

Definition at line 94 of file BppOAlphabetIndex1Format.h.

◆ operator=()

BppOAlphabetIndex1Format& bpp::BppOAlphabetIndex1Format::operator= ( const BppOAlphabetIndex1Format format)
inline

Definition at line 83 of file BppOAlphabetIndex1Format.h.

References alphabet_, message_, and verbose_.

◆ read()

AlphabetIndex1 * BppOAlphabetIndex1Format::read ( const std::string &  description)
throw (Exception
)

Read a AlphabetIndex1 object from a string.

Parameters
descriptionA string describing the index in the keyval syntax.
Returns
A new AlphabetIndex1 object according to options specified.
Exceptions
Exceptionif an error occured.

Definition at line 67 of file BppOAlphabetIndex1Format.cpp.

References bpp::AlphabetTools::isProteicAlphabet().

Referenced by bpp::SequenceApplicationTools::getAlphabetIndex1(), and bpp::BppOAlphabetIndex2Format::read().

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::BppOAlphabetIndex1Format::alphabet_
private

Definition at line 64 of file BppOAlphabetIndex1Format.h.

Referenced by operator=().

◆ message_

std::string bpp::BppOAlphabetIndex1Format::message_
private

Definition at line 65 of file BppOAlphabetIndex1Format.h.

Referenced by operator=().

◆ verbose_

bool bpp::BppOAlphabetIndex1Format::verbose_
private

Definition at line 66 of file BppOAlphabetIndex1Format.h.

Referenced by operator=().


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