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

#include <Bpp/Seq/Sequence.h>

Inheritance diagram for bpp::BasicSequence:

Collaboration diagram for bpp::BasicSequence:

Public Member Functions
	BasicSequence (const Alphabet *alpha)
	Empty constructor: build a void Sequence with just an Alphabet. More...

	BasicSequence (const std::string &name, const std::string &sequence, 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...

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

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

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

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

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

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

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

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

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

virtual	~BasicSequence ()

virtual const Alphabet *	getAlphabet () 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	getStateValueAt (size_t siteIndex, int state) const

virtual double	operator() (size_t siteIndex, int state) const

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

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

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

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

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

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

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

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

virtual double	getStateValueAt (size_t siteIndex, int state) const

virtual double	operator() (size_t siteIndex, int state) const

const Alphabet *	getAlphabet () const
	Get the alphabet associated to the list. More...

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

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

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

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

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

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

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

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

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

The Clonable interface
BasicSequence *	clone () const

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

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

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

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

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

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

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

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

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

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

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

void	clearComments ()
	Clear the comments. 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

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 modifiy 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...

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 modifiy 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...

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...

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

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

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

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

Protected Attributes
Comments	comments_

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

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

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 objets also contain a name attribute and potentially several comment lines.

See also: Alphabet

Definition at line 151 of file Sequence.h.

Constructor & Destructor Documentation

◆ BasicSequence() [1/9]

BasicSequence::BasicSequence ( const Alphabet * alpha )

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 57 of file Sequence.cpp.

Referenced by clone().

◆ BasicSequence() [2/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::string &	sequence,
		const Alphabet *	alpha
	)

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 63 of file Sequence.cpp.

References setContent().

◆ BasicSequence() [3/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::string &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)

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 76 of file Sequence.cpp.

References setContent().

◆ BasicSequence() [4/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< std::string > &	sequence,
		const Alphabet *	alpha
	)

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 90 of file Sequence.cpp.

◆ BasicSequence() [5/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< std::string > &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)

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 100 of file Sequence.cpp.

◆ BasicSequence() [6/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< int > &	sequence,
		const Alphabet *	alpha
	)

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 111 of file Sequence.cpp.

◆ BasicSequence() [7/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< int > &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)

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 121 of file Sequence.cpp.

◆ BasicSequence() [8/9]

BasicSequence::BasicSequence ( const Sequence & s )

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

Definition at line 134 of file Sequence.cpp.

◆ BasicSequence() [9/9]

BasicSequence::BasicSequence ( const BasicSequence & s )

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

Definition at line 140 of file Sequence.cpp.

◆ ~BasicSequence()

virtual bpp::BasicSequence::~BasicSequence ( )

inlinevirtual

Definition at line 265 of file Sequence.h.

Member Function Documentation

◆ addElement() [1/6]

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

inlineinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 199 of file SymbolList.h.

◆ addElement() [2/6]

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

virtualinherited

Implements bpp::IntSymbolList.

Definition at line 135 of file IntSymbolList.cpp.

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

Referenced by bpp::NucleicAcidsReplication::reverse(), and bpp::NucleicAcidsReplication::translate().

◆ addElement() [3/6]

template<class T >

virtual void bpp::CoreSymbolList< 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::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::addSite(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractReverseTransliterator::reverse(), and bpp::AbstractTransliterator::translate().

◆ addElement() [4/6]

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

inlineinherited

Add a character at a certain position in the list.

Parameters

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

Definition at line 204 of file SymbolList.h.

◆ addElement() [5/6]

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

virtualinherited

Add a character at a certain position in the list.

Parameters

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

Implements bpp::IntSymbolList.

Definition at line 142 of file IntSymbolList.cpp.

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

◆ addElement() [6/6]

template<class T >

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

pure virtualinherited

Add a character at a certain position in the list.

Parameters

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

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

◆ append() [1/4]

void BasicSequence::append ( const Sequence & seq )

virtual

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::Sequence.

Definition at line 217 of file Sequence.cpp.

References bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), bpp::CruxSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), and bpp::CruxSymbolList::size().

Referenced by append(), and bpp::SequenceContainerTools::merge().

◆ append() [2/4]

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

virtual

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::Sequence.

Definition at line 259 of file Sequence.cpp.

References append(), bpp::StringSequenceTools::codeSequence(), and bpp::SymbolList< int >::getAlphabet().

◆ append() [3/4]

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

virtual

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::Sequence.

Definition at line 228 of file Sequence.cpp.

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

◆ append() [4/4]

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

virtual

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::Sequence.

Definition at line 243 of file Sequence.cpp.

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

◆ clearComments()

void bpp::BasicSequence::clearComments ( )

inlinevirtual

Clear the comments.

Implements bpp::CoreSequence.

Definition at line 318 of file Sequence.h.

References bpp::Commentable::clearComments().

◆ clone()

BasicSequence* bpp::BasicSequence::clone ( ) const

inlinevirtual

Implements bpp::AbstractCoreSequence.

Definition at line 273 of file Sequence.h.

References BasicSequence().

◆ deleteElement() [1/2]

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

inlinevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolList.

Reimplemented in bpp::EdSymbolList< int >.

Definition at line 185 of file SymbolList.h.

◆ deleteElement() [2/2]

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

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implemented in bpp::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::deleteSite(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), bpp::VectorSiteContainer::removeSequence(), bpp::AlignedSequenceContainer::removeSite(), and bpp::SequenceTools::removeStops().

◆ deleteElements() [1/2]

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

inlinevirtualinherited

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::CruxSymbolList.

Reimplemented in bpp::EdSymbolList< int >.

Definition at line 192 of file SymbolList.h.

◆ deleteElements() [2/2]

virtual void bpp::CruxSymbolList::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::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::deleteSites().

◆ getAlphabet() [1/2]

const Alphabet* bpp::SymbolList< int >::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolList.

Definition at line 169 of file SymbolList.h.

◆ getAlphabet() [2/2]

virtual const Alphabet* bpp::CruxSymbolList::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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

◆ getChar()

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

inlinevirtual

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

Parameters

pos	The position of the character to retrieve.

Reimplemented from bpp::BasicIntSymbolList.

Definition at line 301 of file Sequence.h.

References bpp::BasicIntSymbolList::getChar().

◆ getComments() [1/2]

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

inlinevirtualinherited

Get the comments.

Returns: The comments.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithQuality, and bpp::SequenceWithAnnotation.

Definition at line 235 of file CoreSequence.h.

References bpp::Commentable::getComments().

◆ getComments() [2/2]

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

pure virtualinherited

Get the comments.

Returns: The comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::getComments(), bpp::AbstractSequenceContainer::getComments(), bpp::VectorProbabilisticSequenceContainer::getComments(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getContent() [1/2]

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

inlinevirtualinherited

Implements bpp::CoreSymbolList< T >.

Definition at line 178 of file SymbolList.h.

◆ getContent() [2/2]

template<class T >

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

pure virtualinherited

Implemented in bpp::ProbabilisticSequence, bpp::SymbolList< T >, bpp::SymbolList< int >, bpp::BasicProbabilisticSymbolList, and bpp::BasicProbabilisticSequence.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::BasicProbabilisticSymbolList::operator=(), operator=(), and bpp::SequenceWithAnnotation::operator=().

◆ getElement() [1/2]

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

inlinevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::CoreSymbolList< T >.

Definition at line 220 of file SymbolList.h.

◆ getElement() [2/2]

template<class T >

virtual const T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

◆ getName() [1/2]

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

inlinevirtualinherited

Get the name of this sequence.

Returns: This sequence name.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 231 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::SequenceWithAnnotation::getName().

◆ getName() [2/2]

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

pure virtualinherited

Get the name of this sequence.

Returns: This sequence name.

Implemented in bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::VectorSequenceContainer::deleteSequenceByName(), bpp::AbstractProbabilisticSequenceContainer::getName(), bpp::AbstractSequenceContainer::getName(), bpp::VectorProbabilisticSequenceContainer::getName(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::VectorSequenceContainer::getSequenceByName(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::VectorSequenceContainer::removeSequenceByName(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getStateValueAt() [1/2]

virtual double bpp::CruxSymbolList::getStateValueAt	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtualinherited

Reimplemented in bpp::BasicProbabilisticSymbolList, bpp::BasicIntSymbolList, and bpp::EdCoreSymbolList< T >.

Definition at line 147 of file CoreSymbolList.h.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::BasicProbabilisticSymbolList::BasicProbabilisticSymbolList(), bpp::VectorProbabilisticSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::EdCoreSymbolList< T >::getStateValueAt(), and bpp::Pasta::writeSequence().

◆ getStateValueAt() [2/2]

virtual double bpp::BasicIntSymbolList::getStateValueAt	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtualinherited

Reimplemented from bpp::CruxSymbolList.

Definition at line 217 of file IntSymbolList.h.

References bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), and bpp::Alphabet::isResolvedIn().

◆ getValue() [1/2]

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

inlinevirtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::CoreSymbolList< T >.

Definition at line 227 of file SymbolList.h.

◆ getValue() [2/2]

template<class T >

virtual const T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorSiteContainer::addSequence(), 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::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

◆ operator()() [1/2]

virtual double bpp::CruxSymbolList::operator()	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtualinherited

Reimplemented in bpp::BasicProbabilisticSymbolList, bpp::BasicIntSymbolList, and bpp::EdCoreSymbolList< T >.

Definition at line 154 of file CoreSymbolList.h.

Referenced by bpp::EdCoreSymbolList< T >::operator()().

◆ operator()() [2/2]

virtual double bpp::BasicIntSymbolList::operator()	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtualinherited

Reimplemented from bpp::CruxSymbolList.

Definition at line 225 of file IntSymbolList.h.

References bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), and bpp::Alphabet::isResolvedIn().

◆ operator=() [1/2]

BasicSequence & BasicSequence::operator= ( const BasicSequence & s )

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 156 of file Sequence.cpp.

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

◆ operator=() [2/2]

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

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 149 of file Sequence.cpp.

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

◆ operator[]() [1/4]

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

inlinevirtualinherited

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::CoreSymbolList< T >.

Definition at line 236 of file SymbolList.h.

◆ operator[]() [2/4]

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

inlinevirtualinherited

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::CoreSymbolList< T >.

Definition at line 234 of file SymbolList.h.

◆ operator[]() [3/4]

template<class T >

virtual const T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

◆ operator[]() [4/4]

template<class T >

virtual T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

◆ setComments() [1/2]

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

inlinevirtualinherited

Set the comments.

Parameters

comments The new comments.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithQuality, and bpp::SequenceWithAnnotation.

Definition at line 240 of file CoreSequence.h.

References bpp::Commentable::setComments().

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet().

◆ setComments() [2/2]

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

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setComments(), bpp::VectorSequenceContainer::setComments(), and bpp::SequenceTools::subseq().

◆ setContent() [1/4]

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

virtual

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 internaly stored.

Implements bpp::Sequence.

Definition at line 165 of file Sequence.cpp.

References bpp::StringSequenceTools::codeSequence(), bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), and bpp::TextTools::removeWhiteSpaces().

Referenced by BasicSequence(), and operator=().

◆ setContent() [2/4]

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

inlinevirtual

Reimplemented from bpp::BasicIntSymbolList.

Definition at line 291 of file Sequence.h.

References bpp::BasicIntSymbolList::setContent().

◆ setContent() [3/4]

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

inlinevirtual

Reimplemented from bpp::BasicIntSymbolList.

Definition at line 286 of file Sequence.h.

References bpp::BasicIntSymbolList::setContent().

◆ setContent() [4/4]

template<class T >

virtual void bpp::CoreSymbolList< 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 internaly stored.

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

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

◆ setElement() [1/3]

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

inlineinherited

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 212 of file SymbolList.h.

◆ setElement() [2/3]

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

virtualinherited

Implements bpp::IntSymbolList.

Definition at line 151 of file IntSymbolList.cpp.

References bpp::Alphabet::charToInt(), bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), and bpp::SymbolList< int >::size().

Referenced by bpp::VectorSiteContainer::setSequence().

◆ setElement() [3/3]

template<class T >

virtual void bpp::CoreSymbolList< 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::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

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

◆ setName() [1/2]

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

inlinevirtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 233 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet(), and bpp::SequenceWithAnnotation::setName().

◆ setName() [2/2]

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

pure virtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::SequenceTools::getPutativeHaplotypes(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::PhredPhd::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setSequenceNames(), bpp::VectorSequenceContainer::setSequenceNames(), and bpp::SequenceTools::subseq().

◆ setToSizeL()

void BasicSequence::setToSizeL ( size_t newSize )

virtual

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::CoreSequence.

Definition at line 195 of file Sequence.cpp.

References bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

◆ setToSizeR()

void BasicSequence::setToSizeR ( size_t newSize )

virtual

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::CoreSequence.

Definition at line 174 of file Sequence.cpp.

References bpp::SymbolList< int >::content_, bpp::SymbolList< int >::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

◆ shuffle() [1/2]

virtual void bpp::SymbolList< int >::shuffle ( )

inlinevirtualinherited

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

Implements bpp::CruxSymbolList.

Definition at line 238 of file SymbolList.h.

◆ shuffle() [2/2]

virtual void bpp::CruxSymbolList::shuffle ( )

pure virtualinherited

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

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

◆ size() [1/2]

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

inlinevirtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::CruxSymbolList.

Definition at line 171 of file SymbolList.h.

◆ size() [2/2]

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

pure virtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

◆ toString()

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

inlinevirtual

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::BasicIntSymbolList.

Definition at line 296 of file Sequence.h.

References bpp::BasicIntSymbolList::toString().

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::SymbolList< 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 79 of file SymbolList.h.

◆ comments_

Comments bpp::Commentable::comments_

protectedinherited

Definition at line 63 of file Commentable.h.

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

◆ content_

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

protectedinherited

The list content.

Definition at line 85 of file SymbolList.h.

◆ name_

std::string bpp::AbstractCoreSequence::name_

privateinherited

The sequence name.

Definition at line 163 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 Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BasicSequence() [1/9]

◆ BasicSequence() [2/9]

◆ BasicSequence() [3/9]

◆ BasicSequence() [4/9]

◆ BasicSequence() [5/9]

◆ BasicSequence() [6/9]

◆ BasicSequence() [7/9]

◆ BasicSequence() [8/9]

◆ BasicSequence() [9/9]

◆ ~BasicSequence()

Member Function Documentation

◆ addElement() [1/6]

◆ addElement() [2/6]

◆ addElement() [3/6]

◆ addElement() [4/6]

◆ addElement() [5/6]

◆ addElement() [6/6]

◆ append() [1/4]

◆ append() [2/4]

◆ append() [3/4]

◆ append() [4/4]

◆ clearComments()

◆ 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() [1/2]

◆ getStateValueAt() [2/2]

◆ 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() [1/4]

◆ setContent() [2/4]

◆ setContent() [3/4]

◆ setContent() [4/4]

◆ setElement() [1/3]

◆ setElement() [2/3]

◆ setElement() [3/3]

◆ setName() [1/2]

◆ setName() [2/2]

◆ setToSizeL()

◆ setToSizeR()

◆ shuffle() [1/2]

◆ shuffle() [2/2]

◆ size() [1/2]

◆ size() [2/2]

◆ toString()

Member Data Documentation

◆ alphabet_

◆ comments_

◆ content_

◆ name_