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
std::unique_ptr< IAlignment >	read (const std::string &description)
	Read a IAlignment object from a string. More...
std::unique_ptr< IProbabilisticAlignment >	readProbabilistic (const std::string &description)
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 21 of file BppOAlignmentReaderFormat.h.

Constructor & Destructor Documentation

BppOAlignmentReaderFormat()

bpp::BppOAlignmentReaderFormat::BppOAlignmentReaderFormat ( int  warningLevel )

inline

Definition at line 29 of file BppOAlignmentReaderFormat.h.

~BppOAlignmentReaderFormat()

virtual bpp::BppOAlignmentReaderFormat::~BppOAlignmentReaderFormat ( )

inlinevirtual

Definition at line 31 of file BppOAlignmentReaderFormat.h.

Member Function Documentation

getDataType()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 38 of file BppOAlignmentReaderFormat.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 36 of file BppOAlignmentReaderFormat.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 34 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 54 of file BppOAlignmentReaderFormat.h.

References unparsedArguments_.

Referenced by bpp::SequenceApplicationTools::getProbabilisticSiteContainer(), and bpp::SequenceApplicationTools::getSiteContainer().

read()

unique_ptr< IAlignment > BppOAlignmentReaderFormat::read

(

const std::string &

description

)

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 occurred.

Definition at line 21 of file BppOAlignmentReaderFormat.cpp.

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

Referenced by bpp::SequenceApplicationTools::getProbabilisticSiteContainer(), and bpp::SequenceApplicationTools::getSiteContainer().

readProbabilistic()

unique_ptr< IProbabilisticAlignment > BppOAlignmentReaderFormat::readProbabilistic

(

const std::string &

description

)

Definition at line 90 of file BppOAlignmentReaderFormat.cpp.

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

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

Member Data Documentation

unparsedArguments_

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

private

Definition at line 25 of file BppOAlignmentReaderFormat.h.

Referenced by getUnparsedArguments().

warningLevel_

int bpp::BppOAlignmentReaderFormat::warningLevel_

private

Definition at line 26 of file BppOAlignmentReaderFormat.h.

---

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

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