Replication between to nucleic acids. More...

#include <Bpp/Seq/NucleicAcidsReplication.h>

Inheritance diagram for bpp::NucleicAcidsReplication:

Collaboration diagram for bpp::NucleicAcidsReplication:

Public Member Functions
	NucleicAcidsReplication (std::shared_ptr< const NucleicAlphabet > nuc1, std::shared_ptr< const NucleicAlphabet > nuc2)

	NucleicAcidsReplication (const NucleicAcidsReplication &nar)

NucleicAcidsReplication &	operator= (const NucleicAcidsReplication &nar)

virtual	~NucleicAcidsReplication ()

std::shared_ptr< const Alphabet >	getSourceAlphabet () const override
	Get the source alphabet. More...

const Alphabet &	sourceAlphabet () const override
	Get the source alphabet. More...

std::shared_ptr< const Alphabet >	getTargetAlphabet () const override
	Get the target alphabet. More...

const Alphabet &	targetAlphabet () const override
	Get the target alphabet. More...

int	translate (int state) const override
	Translate a given state coded as a int from source alphabet to target alphabet. More...

std::string	translate (const std::string &state) const override
	Translate a given state coded as a string from source alphabet to target alphabet. More...

std::unique_ptr< Sequence >	translate (const SequenceInterface &sequence) const override
	Translate a whole sequence from source alphabet to target alphabet. More...

int	reverse (int state) const override
	Translate a given state coded as a int from target alphabet to source alphabet. More...

std::string	reverse (const std::string &state) const override
	Translate a given state coded as a string from target alphabet to source alphabet. More...

std::unique_ptr< Sequence >	reverse (const SequenceInterface &sequence) const override
	Translate a whole sequence from target alphabet to source alphabet. More...

Private Attributes
std::shared_ptr< const NucleicAlphabet >	nuc1_

std::shared_ptr< const NucleicAlphabet >	nuc2_

std::map< int, int >	trans_

Detailed Description

Replication between to nucleic acids.

Example of use:

DNA -> DNA: DNA Replication
RNA -> RNA: RNA Replication
DNA -> RNA: Transcription
RNA -> DNA: Reverse transcription

Since this is an instance of the ReverseIterator interface, transcription and reverse transcription may be achieved from the same instance of the object by using the translate and reverse methods.

Definition at line 31 of file NucleicAcidsReplication.h.

Constructor & Destructor Documentation

◆ NucleicAcidsReplication() [1/2]

NucleicAcidsReplication::NucleicAcidsReplication	(	std::shared_ptr< const NucleicAlphabet >	nuc1,
		std::shared_ptr< const NucleicAlphabet >	nuc2
	)

Definition at line 11 of file NucleicAcidsReplication.cpp.

References trans_.

◆ NucleicAcidsReplication() [2/2]

bpp::NucleicAcidsReplication::NucleicAcidsReplication ( const NucleicAcidsReplication & nar )

inline

Definition at line 43 of file NucleicAcidsReplication.h.

◆ ~NucleicAcidsReplication()

virtual bpp::NucleicAcidsReplication::~NucleicAcidsReplication ( )

inlinevirtual

Definition at line 57 of file NucleicAcidsReplication.h.

Member Function Documentation

◆ getSourceAlphabet()

std::shared_ptr<const Alphabet> bpp::NucleicAcidsReplication::getSourceAlphabet ( ) const

inlineoverridevirtual

Get the source alphabet.

Returns: A pointer toward the source alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 60 of file NucleicAcidsReplication.h.

References nuc1_.

Referenced by reverse(), and translate().

◆ getTargetAlphabet()

std::shared_ptr<const Alphabet> bpp::NucleicAcidsReplication::getTargetAlphabet ( ) const

inlineoverridevirtual

Get the target alphabet.

Returns: A pointer toward the target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 64 of file NucleicAcidsReplication.h.

References nuc2_.

Referenced by reverse(), and translate().

◆ operator=()

NucleicAcidsReplication& bpp::NucleicAcidsReplication::operator= ( const NucleicAcidsReplication & nar )

inline

Definition at line 48 of file NucleicAcidsReplication.h.

References nuc1_, nuc2_, and trans_.

◆ reverse() [1/3]

unique_ptr< Sequence > NucleicAcidsReplication::reverse ( const SequenceInterface & sequence ) const

overridevirtual

Translate a whole sequence from target alphabet to source alphabet.

Parameters

sequence A sequence in target alphabet.

Returns: The corresponding sequence in source alphabet.

Implements bpp::ReverseTransliteratorInterface.

Definition at line 75 of file NucleicAcidsReplication.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), bpp::Commentable::getComments(), bpp::CoreSequenceInterface::getName(), getSourceAlphabet(), getTargetAlphabet(), bpp::TemplateCoreSymbolListInterface< T >::getValue(), reverse(), and bpp::CruxSymbolListInterface::size().

◆ reverse() [2/3]

std::string NucleicAcidsReplication::reverse ( const std::string & state ) const

overridevirtual

Translate a given state coded as a string from target alphabet to source alphabet.

Parameters

state A state in target alphabet.

Returns: The corresponding state in source alphabet.

Implements bpp::ReverseTransliteratorInterface.

Definition at line 69 of file NucleicAcidsReplication.cpp.

References nuc1_, nuc2_, and trans_.

◆ reverse() [3/3]

int NucleicAcidsReplication::reverse ( int state ) const

overridevirtual

Translate a given state coded as a int from target alphabet to source alphabet.

Parameters

state A state in target alphabet.

Returns: The corresponding state in source alphabet.

Implements bpp::ReverseTransliteratorInterface.

Definition at line 63 of file NucleicAcidsReplication.cpp.

References nuc2_, and trans_.

Referenced by reverse().

◆ sourceAlphabet()

const Alphabet& bpp::NucleicAcidsReplication::sourceAlphabet ( ) const

inlineoverridevirtual

Get the source alphabet.

Returns: A reference toward the source alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 62 of file NucleicAcidsReplication.h.

References nuc1_.

◆ targetAlphabet()

const Alphabet& bpp::NucleicAcidsReplication::targetAlphabet ( ) const

inlineoverridevirtual

Get the target alphabet.

Returns: A reference toward the target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 66 of file NucleicAcidsReplication.h.

References nuc2_.

◆ translate() [1/3]

unique_ptr< Sequence > NucleicAcidsReplication::translate ( const SequenceInterface & sequence ) const

overridevirtual

Translate a whole sequence from source alphabet to target alphabet.

Parameters

sequence A sequence in source alphabet.

Returns: The corresponding sequence in target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 49 of file NucleicAcidsReplication.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), bpp::Commentable::getComments(), bpp::CoreSequenceInterface::getName(), getSourceAlphabet(), getTargetAlphabet(), bpp::TemplateCoreSymbolListInterface< T >::getValue(), bpp::CruxSymbolListInterface::size(), and translate().

◆ translate() [2/3]

std::string NucleicAcidsReplication::translate ( const std::string & state ) const

overridevirtual

Translate a given state coded as a string from source alphabet to target alphabet.

Parameters

state A state in source alphabet.

Returns: The corresponding state in target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 43 of file NucleicAcidsReplication.cpp.

References nuc1_, nuc2_, and trans_.

◆ translate() [3/3]

int NucleicAcidsReplication::translate ( int state ) const

overridevirtual

Translate a given state coded as a int from source alphabet to target alphabet.

Parameters

state A state in source alphabet.

Returns: The corresponding state in target alphabet.

Implements bpp::TransliteratorInterface.

Definition at line 37 of file NucleicAcidsReplication.cpp.

References nuc1_, and trans_.

Referenced by bpp::SequenceWithQualityTools::complement(), bpp::SequenceTools::complement(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::invertComplement(), and translate().

Member Data Documentation

◆ nuc1_

std::shared_ptr<const NucleicAlphabet> bpp::NucleicAcidsReplication::nuc1_

private

Definition at line 35 of file NucleicAcidsReplication.h.

Referenced by getSourceAlphabet(), operator=(), reverse(), sourceAlphabet(), and translate().

◆ nuc2_

std::shared_ptr<const NucleicAlphabet> bpp::NucleicAcidsReplication::nuc2_

private

Definition at line 35 of file NucleicAcidsReplication.h.

Referenced by getTargetAlphabet(), operator=(), reverse(), targetAlphabet(), and translate().

◆ trans_

std::map<int, int> bpp::NucleicAcidsReplication::trans_

mutableprivate

Definition at line 36 of file NucleicAcidsReplication.h.

Referenced by NucleicAcidsReplication(), operator=(), reverse(), and translate().

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

Bpp/Seq/NucleicAcidsReplication.h
Bpp/Seq/NucleicAcidsReplication.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NucleicAcidsReplication() [1/2]

◆ NucleicAcidsReplication() [2/2]

◆ ~NucleicAcidsReplication()

Member Function Documentation

◆ getSourceAlphabet()

◆ getTargetAlphabet()

◆ operator=()

◆ reverse() [1/3]

◆ reverse() [2/3]

◆ reverse() [3/3]

◆ sourceAlphabet()

◆ targetAlphabet()

◆ translate() [1/3]

◆ translate() [2/3]

◆ translate() [3/3]

Member Data Documentation

◆ nuc1_

◆ nuc2_

◆ trans_