A basic implementation of the Sequence interface. More...

#include <Bpp/Seq/Sequence.h>

Inheritance diagram for bpp::Sequence:

Collaboration diagram for bpp::Sequence:

Public Types
typedef int	ElementType

typedef int	SymbolType

Public Member Functions
	Sequence (std::shared_ptr< const Alphabet > &alpha)
	Empty constructor: build a void Sequence with just an Alphabet. More...

	Sequence (const std::string &name, const std::string &sequence, std::shared_ptr< const Alphabet > &alpha)
	Direct constructor: build a Sequence object from a std::string You can use it safely for RNA, DNA and protein sequences. More...

	Sequence (const std::string &name, const std::string &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	Direct constructor: build a Sequence object from a std::string. More...

	Sequence (const std::string &name, const std::vector< std::string > &sequence, std::shared_ptr< const Alphabet > &alpha)
	General purpose constructor, can be used with any alphabet. More...

	Sequence (const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	General purpose constructor, can be used with any alphabet. More...

	Sequence (const std::string &name, const std::vector< int > &sequence, std::shared_ptr< const Alphabet > &alpha)
	General purpose constructor, can be used with any alphabet. More...

	Sequence (const std::string &name, const std::vector< int > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	General purpose constructor, can be used with any alphabet. More...

	Sequence (const SequenceInterface &s)
	The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object. More...

	Sequence (const Sequence &s)
	The Sequence copy constructor. This does not perform a hard copy of the alphabet object. More...

Sequence &	operator= (const SequenceInterface &s)
	The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object. More...

Sequence &	operator= (const Sequence &s)
	The Sequence assignment operator. This does not perform a hard copy of the alphabet object. More...

virtual	~Sequence ()

double	getStateValueAt (size_t sitePosition, int state) const override
	get value of a state at a position More...

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the list. More...

virtual const Alphabet &	alphabet () const =0
	Get the alphabet associated to the list. More...

virtual size_t	size () const =0
	Get the number of elements in the list. More...

virtual double	operator() (size_t position, int state) const =0
	get value of a state at a position More...

virtual const Comments &	getComments () const =0
	Get the comments. More...

virtual void	setComments (const Comments &comments)=0
	Set the comments. More...

virtual void	clearComments ()=0

const Comments &	getComments () const override
	Get the comments. More...

void	setComments (const Comments &comments) override
	Set the comments. More...

void	clearComments () override

void	addElement (const std::string &c) override
	Add a character to the end of the list. More...

void	addElement (size_t pos, const std::string &c) override
	Add a character at a certain position in the list. More...

void	addElement (const int &v) override
	Add a character to the end of the list. More...

void	addElement (size_t pos, const int &v) override
	Add a character at a certain position in the list. More...

void	setElement (size_t pos, const std::string &c) override
	Set the element at position 'pos' to character 'c'. More...

void	setElement (size_t pos, const T &v) override

void	setElement (size_t pos, const int &v) override
	Set the element at position 'pos' to character 'c'. More...

double	operator() (size_t siteIndex, int state) const override
	get value of a state at a position More...

virtual const std::vector< int > &	getContent () const override

const int &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...

const int &	getValue (size_t pos) const override
	checked access to a character in list. More...

const int &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...

int &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. More...

std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the list. More...

const Alphabet &	alphabet () const override
	Get the alphabet associated to the list. More...

size_t	size () const override
	Get the number of elements in the list. More...

void	deleteElement (size_t pos) override
	Remove the element at position 'pos'. More...

void	deleteElements (size_t pos, size_t len) override
	Remove the elements at position 'pos'. More...

void	shuffle () override
	Randomly shuffle the content of the list, with linear complexity. More...

The Clonable interface
Sequence *	clone () const override

Adjusting the size of the sequence.
void	setContent (const std::string &sequence) override
	Set the whole content of the sequence. More...

void	setContent (const std::vector< std::string > &list) override
	Set the whole content of the list. More...

void	setContent (const std::vector< int > &list) override

std::string	toString () const override
	Convert the list as a string. More...

std::string	getChar (size_t pos) const override
	Get the element at position 'pos' as a character. More...

void	setToSizeR (size_t newSize) override
	Set up the size of a sequence from the right side. More...

void	setToSizeL (size_t newSize) override
	Set up the size of a sequence from the left side. More...

void	append (const SequenceInterface &seq) override
	Append the content of the sequence. More...

void	append (const std::vector< int > &content) override
	Append the specified content to the sequence. More...

void	append (const std::vector< std::string > &content) override
	Append the specified content to the sequence. More...

void	append (const std::string &content) override
	Append the specified content to the sequence. More...

void	addElement (const std::string &c) override

void	addElement (size_t pos, const std::string &c) override

void	addElement (const T &v) override

void	addElement (size_t pos, const T &v) override

Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...

Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...

virtual const std::vector< T > &	getContent () const =0

Setting/getting the name of the sequence.
virtual const std::string &	getName () const =0
	Get the name of this sequence. More...

virtual void	setName (const std::string &name)=0
	Set the name of this sequence. More...

Edition methods.
virtual void	deleteElement (size_t pos)=0
	Remove the element at position 'pos'. More...

virtual void	deleteElements (size_t pos, size_t len)=0
	Remove the elements at position 'pos'. More...

Provide direct access to the list content.
Warning These operators allow you to modify the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

Edition methods.
virtual void	addElement (const std::string &c)=0
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, const std::string &c)=0
	Add a character at a certain position in the list. More...

virtual void	setElement (size_t pos, const std::string &c)=0
	Set the element at position 'pos' to character 'c'. More...

virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...

Edition methods.
virtual void	addElement (const T &c)=0
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, const T &c)=0
	Add a character at a certain position in the list. More...

virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...

virtual const T &	getElement (size_t pos) const =0
	Get the element at position 'pos' as a character. More...

Provide direct access to the list content.
Warning These operators allow you to modify the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual const T &	getValue (size_t pos) const =0
	checked access to a character in list. More...

virtual const T &	operator[] (size_t pos) const =0
	Operator [] overloaded for quick access to a character in list. More...

virtual T &	operator[] (size_t pos)=0
	Operator [] overloaded for quick access to a character in list. More...

Setting/getting the name of the sequence.
const std::string &	getName () const override
	Get the name of this sequence. More...

void	setName (const std::string &name) override
	Set the name of this sequence. More...

Protected Attributes
Comments	comments_

std::vector< int >	content_
	The list content. More...

Private Attributes
std::string	name_
	The sequence name. More...

std::shared_ptr< const Alphabet >	alphabet_
	The Alphabet attribute must be initialized in constructor and then can never be changed. More...

Detailed Description

A basic implementation of the Sequence interface.

This is a general purpose container, containing an ordered list of states. The states that allowed to be present in the sequence are defined by an alphabet object, which is passed to the sequence constructor by a pointer.

For programming convenience, the states are stored as integers, but the translation toward and from a char description is easily performed with the Alphabet classes.

Sequence objects also contain a name attribute and potentially several comment lines.

See also: Alphabet

Definition at line 113 of file Sequence.h.

Member Typedef Documentation

◆ ElementType

typedef int bpp::SequenceInterface::ElementType

inherited

Definition at line 36 of file Sequence.h.

◆ SymbolType

typedef int bpp::IntSymbolListInterface::SymbolType

inherited

Definition at line 31 of file IntSymbolList.h.

Constructor & Destructor Documentation

◆ Sequence() [1/9]

bpp::Sequence::Sequence ( std::shared_ptr< const Alphabet > & alpha )

inline

Empty constructor: build a void Sequence with just an Alphabet.

You can use it safely for all type of Alphabet in order to build an empty Sequence i.e. without name nor sequence data.

Parameters

alpha A pointer toward the Alphabet to be used with this Sequence.

Definition at line 127 of file Sequence.h.

Referenced by clone().

◆ Sequence() [2/9]

bpp::Sequence::Sequence	(	const std::string &	name,
		const std::string &	sequence,
		std::shared_ptr< const Alphabet > &	alpha
	)

inline

Direct constructor: build a Sequence object from a std::string You can use it safely for RNA, DNA and protein sequences.

It can be used with codon sequences too, the std::string will be cut into parts of size 3. But for more complicated alphabets, you should use one complete constructors.

Parameters

name	The sequence name.
sequence	The whole sequence to be parsed as a std::string.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 146 of file Sequence.h.

References bpp::IntSymbolListInterface::setContent().

◆ Sequence() [3/9]

bpp::Sequence::Sequence	(	const std::string &	name,
		const std::string &	sequence,
		const Comments &	comments,
		std::shared_ptr< const Alphabet > &	alpha
	)

inline

Direct constructor: build a Sequence object from a std::string.

You can use it safely for RNA, DNA and protein sequences.

It can be used with codon sequences too, the std::string will be cut into tokens of size 3. But for more complicated alphabets, you should use one complete constructors.

Parameters

name	The sequence name.
sequence	The whole sequence to be parsed as a std::string.
comments	Comments to add to the sequence.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 173 of file Sequence.h.

References bpp::IntSymbolListInterface::setContent().

◆ Sequence() [4/9]

bpp::Sequence::Sequence	(	const std::string &	name,
		const std::vector< std::string > &	sequence,
		std::shared_ptr< const Alphabet > &	alpha
	)

inline

General purpose constructor, can be used with any alphabet.

You should note that the sequence is stored as a std::vector of int. Hence each std::string in the std::vector will be translated using the alphabet object.

Parameters

name	The sequence name.
sequence	The sequence content.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 197 of file Sequence.h.

◆ Sequence() [5/9]

bpp::Sequence::Sequence	(	const std::string &	name,
		const std::vector< std::string > &	sequence,
		const Comments &	comments,
		std::shared_ptr< const Alphabet > &	alpha
	)

inline

General purpose constructor, can be used with any alphabet.

You should note that the sequence is stored as a std::vector of int. Hence each std::string in the std::vector will be translated using the alphabet object.

Parameters

name	The sequence name.
sequence	The sequence content.
comments	Comments to add to the sequence.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 218 of file Sequence.h.

◆ Sequence() [6/9]

bpp::Sequence::Sequence	(	const std::string &	name,
		const std::vector< int > &	sequence,
		std::shared_ptr< const Alphabet > &	alpha
	)

inline

General purpose constructor, can be used with any alphabet.

Parameters

name	The sequence name.
sequence	The sequence content.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 236 of file Sequence.h.

◆ Sequence() [7/9]

bpp::Sequence::Sequence	(	const std::string &	name,
		const std::vector< int > &	sequence,
		const Comments &	comments,
		std::shared_ptr< const Alphabet > &	alpha
	)

inline

General purpose constructor, can be used with any alphabet.

Parameters

name	The sequence name.
sequence	The sequence content.
comments	Comments to add to the sequence.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 254 of file Sequence.h.

◆ Sequence() [8/9]

bpp::Sequence::Sequence ( const SequenceInterface & s )

inline

The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object.

Definition at line 268 of file Sequence.h.

◆ Sequence() [9/9]

bpp::Sequence::Sequence ( const Sequence & s )

inline

The Sequence copy constructor. This does not perform a hard copy of the alphabet object.

Definition at line 278 of file Sequence.h.

◆ ~Sequence()

virtual bpp::Sequence::~Sequence ( )

inlinevirtual

Definition at line 311 of file Sequence.h.

Member Function Documentation

◆ addElement() [1/12]

void bpp::AbstractTemplateSymbolList< int >::addElement ( const T & c )

inlineoverrideinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 152 of file SymbolList.h.

◆ addElement() [2/12]

void bpp::IntSymbolList::addElement ( const std::string & c )

inlineoverridevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 185 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

◆ addElement() [3/12]

void bpp::IntSymbolList::addElement

inlineoverride

Definition at line 185 of file IntSymbolList.h.

◆ addElement() [4/12]

virtual void bpp::IntSymbolListInterface::addElement ( const std::string & c )

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Implemented in bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

◆ addElement() [5/12]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement ( const T & c )

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.

◆ addElement() [6/12]

void bpp::AbstractTemplateSymbolList< T >::addElement

inlineoverride

Definition at line 190 of file SymbolList.h.

◆ addElement() [7/12]

void bpp::AbstractTemplateSymbolList< int >::addElement	(	size_t	pos,
		const T &	c
	)

inlineoverrideinherited

Add a character at a certain position in the list.

Parameters

pos	The position where to insert the element.
c	The character to add.

Definition at line 157 of file SymbolList.h.

◆ addElement() [8/12]

void bpp::IntSymbolList::addElement	(	size_t	pos,
		const std::string &	c
	)

inlineoverridevirtualinherited

Add a character at a certain position in the list.

Parameters

pos	The position where to insert the element.
c	The character to add, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 192 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, bpp::AbstractTemplateSymbolList< int >::getAlphabet(), and bpp::AbstractTemplateSymbolList< int >::size().

◆ addElement() [9/12]

void bpp::IntSymbolList::addElement

inlineoverride

Definition at line 192 of file IntSymbolList.h.

◆ addElement() [10/12]

virtual void bpp::IntSymbolListInterface::addElement	(	size_t	pos,
		const std::string &	c
	)

pure virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The position where to insert the element.
c	The character to add, given as a string.

Implemented in bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

◆ addElement() [11/12]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement	(	size_t	pos,
		const T &	c
	)

pure virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The position where to insert the element.
c	The character to add.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.

◆ addElement() [12/12]

void bpp::AbstractTemplateSymbolList< T >::addElement

inlineoverride

Definition at line 190 of file SymbolList.h.

◆ alphabet() [1/2]

virtual const Alphabet& bpp::CruxSymbolListInterface::alphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns: A const reference to the alphabet.

See also: Alphabet class.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ alphabet() [2/2]

const Alphabet& bpp::AbstractTemplateSymbolList< int >::alphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to the list.

Returns: A const reference to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 122 of file SymbolList.h.

◆ append() [1/4]

void Sequence::append ( const SequenceInterface & seq )

overridevirtual

Append the content of the sequence.

Parameters

seq	The sequence to append.

Exceptions

AlphabetMismatchException If the alphabet of the specified sequence does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 73 of file Sequence.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), and bpp::TemplateCoreSymbolListInterface< T >::getContent().

◆ append() [2/4]

void Sequence::append ( const std::string & content )

overridevirtual

Append the specified content to the sequence.

Parameters

content The content to append to the sequence.

Exceptions

BadCharException If the content does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 115 of file Sequence.cpp.

References bpp::StringSequenceTools::codeSequence().

◆ append() [3/4]

void Sequence::append ( const std::vector< int > & content )

overridevirtual

Append the specified content to the sequence.

Parameters

content The content to append to the sequence.

Exceptions

BadIntException If the content does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 84 of file Sequence.cpp.

◆ append() [4/4]

void Sequence::append ( const std::vector< std::string > & content )

overridevirtual

Append the specified content to the sequence.

Parameters

content The content to append to the sequence.

Exceptions

BadCharException If the content does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 99 of file Sequence.cpp.

◆ clearComments() [1/2]

void bpp::SimpleCommentable::clearComments ( )

inlineoverridevirtualinherited

Implements bpp::Commentable.

Definition at line 88 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

◆ clearComments() [2/2]

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

◆ clone()

Sequence* bpp::Sequence::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractCoreSequence.

Definition at line 319 of file Sequence.h.

References Sequence().

Referenced by bpp::SiteContainerTools::alignNW().

◆ deleteElement() [1/2]

void bpp::AbstractTemplateSymbolList< int >::deleteElement ( size_t pos )

inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 138 of file SymbolList.h.

◆ deleteElement() [2/2]

virtual void bpp::CruxSymbolListInterface::deleteElement ( size_t pos )

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), and bpp::SequenceTools::removeStops().

◆ deleteElements() [1/2]

void bpp::AbstractTemplateSymbolList< int >::deleteElements	(	size_t	pos,
		size_t	len
	)

inlineoverridevirtualinherited

Remove the elements at position 'pos'.

Parameters

pos	The position of the first element to remove.
len	The length of the region to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 145 of file SymbolList.h.

◆ deleteElements() [2/2]

virtual void bpp::CruxSymbolListInterface::deleteElements	(	size_t	pos,
		size_t	len
	)

pure virtualinherited

Remove the elements at position 'pos'.

Parameters

pos	The position of the first element to remove.
len	The length of the region to remove.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ getAlphabet() [1/2]

virtual std::shared_ptr<const Alphabet> bpp::CruxSymbolListInterface::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ getAlphabet() [2/2]

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< int >::getAlphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 120 of file SymbolList.h.

◆ getChar()

std::string bpp::Sequence::getChar ( size_t pos ) const

inlineoverridevirtual

Get the element at position 'pos' as a character.

Parameters

pos	The position of the character to retrieve.

Reimplemented from bpp::IntSymbolList.

Definition at line 346 of file Sequence.h.

References bpp::IntSymbolList::getChar().

Referenced by bpp::SiteContainerTools::resolveDottedAlignment(), and bpp::Fasta::writeSequence().

◆ getComments() [1/2]

virtual const Comments& bpp::Commentable::getComments ( ) const

pure virtualinherited

Get the comments.

Returns: The comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Mase::appendSequencesFromStream(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractCoreSequence::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

◆ getComments() [2/2]

const Comments& bpp::SimpleCommentable::getComments ( ) const

inlineoverridevirtualinherited

Get the comments.

Returns: The comments.

Implements bpp::Commentable.

Definition at line 79 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::createEmptyContainer(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getContent() [1/2]

template<class T >

virtual const std::vector<T>& bpp::TemplateCoreSymbolListInterface< T >::getContent ( ) const

pure virtualinherited

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by append(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::SequenceWithAnnotation::merge(), bpp::ProbabilisticSymbolList::operator=(), and operator=().

◆ getContent() [2/2]

virtual const std::vector<int >& bpp::AbstractTemplateSymbolList< int >::getContent ( ) const

inlineoverridevirtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 131 of file SymbolList.h.

◆ getElement() [1/2]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< T >::getElement ( size_t pos ) const

pure virtualinherited

Get the element at position 'pos' as a character.

Parameters

pos	The position of the character to retrieve.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ getElement() [2/2]

const int & bpp::AbstractTemplateSymbolList< int >::getElement ( size_t pos ) const

inlineoverridevirtualinherited

Get the element at position 'pos' as a character.

Parameters

pos	The position of the character to retrieve.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 173 of file SymbolList.h.

◆ getName() [1/2]

virtual const std::string& bpp::CoreSequenceInterface::getName ( ) const

pure virtualinherited

Get the name of this sequence.

Returns: This sequence name.

Implemented in bpp::AbstractCoreSequence.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractCoreSequence::operator=(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), and bpp::WordAlphabet::translate().

◆ getName() [2/2]

const std::string& bpp::AbstractCoreSequence::getName ( ) const

inlineoverridevirtualinherited

Get the name of this sequence.

Returns: This sequence name.

Implements bpp::CoreSequenceInterface.

Definition at line 170 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::merge(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getStateValueAt()

double bpp::Sequence::getStateValueAt	(	size_t	position,
		int	state
	)		const

inlineoverridevirtual

get value of a state at a position

Parameters

position	position in the list
state	state in the alphabet

Returns: The state value at the given position.

Reimplemented from bpp::IntSymbolList.

Definition at line 366 of file Sequence.h.

References bpp::AbstractTemplateSymbolList< int >::getAlphabet(), and bpp::AbstractTemplateSymbolList< int >::size().

Referenced by bpp::Pasta::writeSequence().

◆ getValue() [1/2]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< T >::getValue ( size_t pos ) const

pure virtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::findFirstOf(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

◆ getValue() [2/2]

const int & bpp::AbstractTemplateSymbolList< int >::getValue ( size_t pos ) const

inlineoverridevirtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 180 of file SymbolList.h.

◆ operator()() [1/2]

virtual double bpp::CruxSymbolListInterface::operator()	(	size_t	position,
		int	state
	)		const

pure virtualinherited

get value of a state at a position

Short-cut for getStateValueAt.

Parameters

position	position in the list
state	state in the alphabet

Returns: The state value at the given position.

Implemented in bpp::ProbabilisticSymbolList, and bpp::IntSymbolList.

◆ operator()() [2/2]

double bpp::IntSymbolList::operator()	(	size_t	position,
		int	state
	)		const

inlineoverridevirtualinherited

get value of a state at a position

Short-cut for getStateValueAt.

Parameters

position	position in the list
state	state in the alphabet

Returns: The state value at the given position.

Implements bpp::CruxSymbolListInterface.

Definition at line 218 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

◆ operator=() [1/2]

Sequence& bpp::Sequence::operator= ( const Sequence & s )

inline

The Sequence assignment operator. This does not perform a hard copy of the alphabet object.

Returns: A ref toward the assigned Sequence.

Definition at line 303 of file Sequence.h.

References bpp::AbstractCoreSequence::operator=(), and bpp::IntSymbolList::operator=().

◆ operator=() [2/2]

Sequence& bpp::Sequence::operator= ( const SequenceInterface & s )

inline

The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object.

Returns: A ref toward the assigned Sequence.

Definition at line 290 of file Sequence.h.

References bpp::TemplateCoreSymbolListInterface< T >::getContent(), bpp::AbstractCoreSequence::operator=(), and bpp::IntSymbolListInterface::setContent().

◆ operator[]() [1/4]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< T >::operator[] ( size_t pos ) const

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ operator[]() [2/4]

const int & bpp::AbstractTemplateSymbolList< int >::operator[] ( size_t pos ) const

inlineoverridevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 187 of file SymbolList.h.

◆ operator[]() [3/4]

int & bpp::AbstractTemplateSymbolList< int >::operator[] ( size_t pos )

inlineoverridevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 189 of file SymbolList.h.

◆ operator[]() [4/4]

template<class T >

virtual T& bpp::TemplateCoreSymbolListInterface< T >::operator[] ( size_t pos )

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ setComments() [1/2]

void bpp::SimpleCommentable::setComments ( const Comments & comments )

inlineoverridevirtualinherited

Set the comments.

Parameters

comments The new comments.

Implements bpp::Commentable.

Definition at line 86 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), and bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer().

◆ setComments() [2/2]

virtual void bpp::Commentable::setComments ( const Comments & comments )

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Pasta::appendAlignmentFromStream(), bpp::Clustal::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), and bpp::Mase::appendSequencesFromStream().

◆ setContent() [1/5]

void Sequence::setContent ( const std::string & sequence )

overridevirtual

Set the whole content of the sequence.

Parameters

sequence The new content of the sequence.

See also: The Sequence constructor for information about the way sequences are internally stored.

Implements bpp::SequenceInterface.

Definition at line 20 of file Sequence.cpp.

References bpp::StringSequenceTools::codeSequence(), and bpp::TextTools::removeWhiteSpaces().

Referenced by bpp::PhredPoly::nextSequence(), bpp::Fasta::nextSequence(), and bpp::PhredPhd::nextSequence().

◆ setContent() [2/5]

void bpp::Sequence::setContent ( const std::vector< int > & list )

inlineoverridevirtual

Reimplemented from bpp::IntSymbolList.

Definition at line 336 of file Sequence.h.

References bpp::IntSymbolListInterface::setContent().

◆ setContent() [3/5]

void bpp::Sequence::setContent ( const std::vector< std::string > & list )

inlineoverridevirtual

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internally stored.

Reimplemented from bpp::IntSymbolList.

Definition at line 331 of file Sequence.h.

References bpp::IntSymbolListInterface::setContent().

◆ setContent() [4/5]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::setContent ( const std::vector< T > & list )

pure virtualinherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internally stored.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.

◆ setContent() [5/5]

virtual void bpp::TemplateCoreSymbolListInterface< T >::setContent

inherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internally stored.

Referenced by bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList(), bpp::IntSymbolList::IntSymbolList(), bpp::SequenceWithAnnotation::operator=(), operator=(), Sequence(), bpp::SequenceWithAnnotation::SequenceWithAnnotation(), setContent(), and bpp::SequenceWithAnnotation::setContent().

◆ setElement() [1/6]

void bpp::AbstractTemplateSymbolList< int >::setElement	(	size_t	pos,
		const T &	c
	)

inlineoverrideinherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element.

Definition at line 165 of file SymbolList.h.

◆ setElement() [2/6]

void bpp::IntSymbolList::setElement	(	size_t	pos,
		const std::string &	c
	)

inlineoverridevirtualinherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 201 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, bpp::AbstractTemplateSymbolList< int >::getAlphabet(), and bpp::AbstractTemplateSymbolList< int >::size().

◆ setElement() [3/6]

virtual void bpp::IntSymbolListInterface::setElement	(	size_t	pos,
		const std::string &	c
	)

pure virtualinherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element, given as a string.

Implemented in bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

Referenced by bpp::SequenceTools::complement(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), and bpp::SequenceTools::replaceStopsWithGaps().

◆ setElement() [4/6]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::setElement	(	size_t	pos,
		const T &	c
	)

pure virtualinherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateSymbolList< T >.

◆ setElement() [5/6]

virtual void bpp::TemplateCoreSymbolListInterface< T >::setElement

inherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element.

◆ setElement() [6/6]

void bpp::AbstractTemplateSymbolList< T >::setElement

inlineoverrideinherited

Definition at line 165 of file SymbolList.h.

◆ setName() [1/2]

void bpp::AbstractCoreSequence::setName ( const std::string & name )

inlineoverridevirtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::CoreSequenceInterface.

Definition at line 172 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::Pasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPhd::nextSequence(), and bpp::SequenceWithAnnotation::operator=().

◆ setName() [2/2]

virtual void bpp::CoreSequenceInterface::setName ( const std::string & name )

pure virtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::AbstractCoreSequence.

◆ setToSizeL()

void Sequence::setToSizeL ( size_t newSize )

overridevirtual

Set up the size of a sequence from the left side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize The new size of the sequence.

Implements bpp::CoreSequenceInterface.

Definition at line 51 of file Sequence.cpp.

◆ setToSizeR()

void Sequence::setToSizeR ( size_t newSize )

overridevirtual

Set up the size of a sequence from the right side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize The new size of the sequence.

Implements bpp::CoreSequenceInterface.

Definition at line 30 of file Sequence.cpp.

◆ shuffle() [1/2]

void bpp::AbstractTemplateSymbolList< int >::shuffle ( )

inlineoverridevirtualinherited

Randomly shuffle the content of the list, with linear complexity.

Implements bpp::CruxSymbolListInterface.

Definition at line 191 of file SymbolList.h.

◆ shuffle() [2/2]

virtual void bpp::CruxSymbolListInterface::shuffle ( )

pure virtualinherited

Randomly shuffle the content of the list, with linear complexity.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ size() [1/2]

virtual size_t bpp::CruxSymbolListInterface::size ( ) const

pure virtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

◆ size() [2/2]

size_t bpp::AbstractTemplateSymbolList< int >::size ( ) const

inlineoverridevirtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::CruxSymbolListInterface.

Definition at line 124 of file SymbolList.h.

◆ toString()

std::string bpp::Sequence::toString ( ) const

inlineoverridevirtual

Convert the list as a string.

This method is useful for dumping a list to a file or to the screen for display.

Returns: The whole list as a string.

Reimplemented from bpp::IntSymbolList.

Definition at line 341 of file Sequence.h.

References bpp::IntSymbolList::toString().

Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< int >::alphabet_

privateinherited

The Alphabet attribute must be initialized in constructor and then can never be changed.

To apply another alphabet to a list you'll have to create a new list.

Definition at line 41 of file SymbolList.h.

◆ comments_

Comments bpp::SimpleCommentable::comments_

protectedinherited

Definition at line 50 of file Commentable.h.

Referenced by bpp::SimpleCommentable::clearComments(), bpp::SimpleCommentable::getComments(), bpp::SimpleCommentable::operator=(), and bpp::SimpleCommentable::setComments().

◆ content_

std::vector<int > bpp::AbstractTemplateSymbolList< int >::content_

protectedinherited

The list content.

Definition at line 47 of file SymbolList.h.

◆ name_

std::string bpp::AbstractCoreSequence::name_

privateinherited

The sequence name.

Definition at line 103 of file CoreSequence.h.

Referenced by bpp::AbstractCoreSequence::getName(), bpp::AbstractCoreSequence::operator=(), and bpp::AbstractCoreSequence::setName().

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

Bpp/Seq/Sequence.h
Bpp/Seq/Sequence.cpp

Public Types

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ElementType

◆ SymbolType

Constructor & Destructor Documentation

◆ Sequence() [1/9]

◆ Sequence() [2/9]

◆ Sequence() [3/9]

◆ Sequence() [4/9]

◆ Sequence() [5/9]

◆ Sequence() [6/9]

◆ Sequence() [7/9]

◆ Sequence() [8/9]

◆ Sequence() [9/9]

◆ ~Sequence()

Member Function Documentation

◆ addElement() [1/12]

◆ addElement() [2/12]

◆ addElement() [3/12]

◆ addElement() [4/12]

◆ addElement() [5/12]

◆ addElement() [6/12]

◆ addElement() [7/12]

◆ addElement() [8/12]

◆ addElement() [9/12]

◆ addElement() [10/12]

◆ addElement() [11/12]

◆ addElement() [12/12]

◆ alphabet() [1/2]

◆ alphabet() [2/2]

◆ append() [1/4]

◆ append() [2/4]

◆ append() [3/4]

◆ append() [4/4]

◆ clearComments() [1/2]

◆ clearComments() [2/2]

◆ clone()

◆ deleteElement() [1/2]

◆ deleteElement() [2/2]

◆ deleteElements() [1/2]

◆ deleteElements() [2/2]

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getChar()

◆ getComments() [1/2]

◆ getComments() [2/2]

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getElement() [1/2]

◆ getElement() [2/2]

◆ getName() [1/2]

◆ getName() [2/2]

◆ getStateValueAt()

◆ getValue() [1/2]

◆ getValue() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/4]

◆ operator[]() [2/4]

◆ operator[]() [3/4]

◆ operator[]() [4/4]

◆ setComments() [1/2]

◆ setComments() [2/2]

◆ setContent() [1/5]

◆ setContent() [2/5]

◆ setContent() [3/5]

◆ setContent() [4/5]

◆ setContent() [5/5]

◆ setElement() [1/6]

◆ setElement() [2/6]

◆ setElement() [3/6]

◆ setElement() [4/6]

◆ setElement() [5/6]

◆ setElement() [6/6]