#include <Bpp/Seq/IntSymbolList.h>

Inheritance diagram for bpp::BasicIntSymbolList:

Collaboration diagram for bpp::BasicIntSymbolList:

Public Member Functions
	BasicIntSymbolList (const Alphabet *alpha)

	BasicIntSymbolList (const std::vector< std::string > &list, const Alphabet *alpha)
	Build a new BasicIntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters. More...

	BasicIntSymbolList (const std::vector< int > &list, const Alphabet *alpha)
	Build a new BasicIntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers. More...

	BasicIntSymbolList (const BasicIntSymbolList &list)
	The copy constructor. More...

BasicIntSymbolList &	operator= (const IntSymbolList &list)
	The generic assignment operator. More...

BasicIntSymbolList &	operator= (const BasicIntSymbolList &list)
	The assignment operator. More...

virtual	~BasicIntSymbolList ()

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

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

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

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

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

virtual double	getStateValueAt (size_t siteIndex, int state) const

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

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...

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

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
BasicIntSymbolList *	clone () const

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

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

Private Attributes
const Alphabet *	alphabet_
	The Alphabet attribute must be initialized in constructor and then can never be changed. More...

Detailed Description

A basic IntSymbolList object.

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

See also: Alphabet

Definition at line 150 of file IntSymbolList.h.

Constructor & Destructor Documentation

◆ BasicIntSymbolList() [1/4]

bpp::BasicIntSymbolList::BasicIntSymbolList ( const Alphabet * alpha )

inline

Definition at line 154 of file IntSymbolList.h.

Referenced by clone().

◆ BasicIntSymbolList() [2/4]

BasicIntSymbolList::BasicIntSymbolList	(	const std::vector< std::string > &	list,
		const Alphabet *	alpha
	)

Build a new BasicIntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters.

Parameters

list	The content of the site.
alpha	The alphabet to use.

Definition at line 51 of file IntSymbolList.cpp.

References setContent().

◆ BasicIntSymbolList() [3/4]

BasicIntSymbolList::BasicIntSymbolList	(	const std::vector< int > &	list,
		const Alphabet *	alpha
	)

Build a new BasicIntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers.

Parameters

list	The content of the site.
alpha	The alphabet to use.

Definition at line 57 of file IntSymbolList.cpp.

References setContent().

◆ BasicIntSymbolList() [4/4]

BasicIntSymbolList::BasicIntSymbolList ( const BasicIntSymbolList & list )

The copy constructor.

Definition at line 72 of file IntSymbolList.cpp.

◆ ~BasicIntSymbolList()

virtual bpp::BasicIntSymbolList::~BasicIntSymbolList ( )

inlinevirtual

Definition at line 200 of file IntSymbolList.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 )

virtual

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
	)

virtual

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.

◆ clone()

BasicIntSymbolList* bpp::BasicIntSymbolList::clone ( ) const

inlinevirtual

Implements bpp::SymbolList< int >.

Reimplemented in bpp::Site, and bpp::BasicSequence.

Definition at line 196 of file IntSymbolList.h.

References BasicIntSymbolList().

◆ deleteElement()

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.

◆ deleteElements()

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.

◆ getAlphabet()

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.

◆ getChar()

string BasicIntSymbolList::getChar ( size_t pos ) const

virtual

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::IntSymbolList.

Reimplemented in bpp::BasicSequence.

Definition at line 160 of file IntSymbolList.cpp.

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

Referenced by bpp::BasicSequence::getChar(), and bpp::SiteContainerTools::resolveDottedAlignment().

◆ getContent()

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

inlinevirtualinherited

Implements bpp::CoreSymbolList< T >.

Definition at line 178 of file SymbolList.h.

◆ getElement()

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.

◆ getStateValueAt()

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

inlinevirtual

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()

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.

◆ operator()()

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

inlinevirtual

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]

BasicIntSymbolList & BasicIntSymbolList::operator= ( const BasicIntSymbolList & list )

The assignment operator.

Definition at line 84 of file IntSymbolList.cpp.

References bpp::SymbolList< T >::operator=().

◆ operator=() [2/2]

BasicIntSymbolList& bpp::BasicIntSymbolList::operator= ( const IntSymbolList & list )

The generic assignment operator.

Referenced by bpp::BasicSequence::operator=(), and bpp::Site::operator=().

◆ operator[]() [1/2]

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[]() [2/2]

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.

◆ setContent() [1/3]

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

virtual

Reimplemented from bpp::SymbolList< int >.

Reimplemented in bpp::BasicSequence.

Definition at line 113 of file IntSymbolList.cpp.

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

Referenced by BasicIntSymbolList(), and bpp::BasicSequence::setContent().

◆ setContent() [2/3]

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

virtual

Implements bpp::IntSymbolList.

Reimplemented in bpp::BasicSequence.

Definition at line 92 of file IntSymbolList.cpp.

References bpp::Alphabet::charToInt(), bpp::SymbolList< int >::getAlphabet(), and bpp::SymbolList< T >::setContent().

◆ setContent() [3/3]

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
	)

virtual

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().

◆ shuffle()

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.

◆ size()

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.

◆ toString()

string BasicIntSymbolList::toString ( ) const

virtual

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::SymbolList< int >.

Reimplemented in bpp::BasicSequence.

Definition at line 128 of file IntSymbolList.cpp.

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

Referenced by bpp::BasicSequence::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.

◆ content_

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

protectedinherited

The list content.

Definition at line 85 of file SymbolList.h.

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

Bpp/Seq/IntSymbolList.h
Bpp/Seq/IntSymbolList.cpp

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BasicIntSymbolList() [1/4]

◆ BasicIntSymbolList() [2/4]

◆ BasicIntSymbolList() [3/4]

◆ BasicIntSymbolList() [4/4]

◆ ~BasicIntSymbolList()

Member Function Documentation

◆ addElement() [1/6]

◆ addElement() [2/6]

◆ addElement() [3/6]

◆ addElement() [4/6]

◆ addElement() [5/6]

◆ addElement() [6/6]

◆ clone()

◆ deleteElement()

◆ deleteElements()

◆ getAlphabet()

◆ getChar()

◆ getContent()

◆ getElement()

◆ getStateValueAt()

◆ getValue()

◆ operator()()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setContent() [1/3]

◆ setContent() [2/3]

◆ setContent() [3/3]

◆ setElement() [1/3]

◆ setElement() [2/3]

◆ setElement() [3/3]

◆ shuffle()

◆ size()

◆ toString()

Member Data Documentation

◆ alphabet_

◆ content_