#include <Bpp/Seq/SymbolList.h>

Inheritance diagram for bpp::EdSymbolList< T >:

Collaboration diagram for bpp::EdSymbolList< T >:

Public Member Functions
virtual void	setContent (const std::vector< T > &list)
	Set the whole content of the list. More...

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

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

virtual void	setElement (size_t pos, const T &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< T > &	getContent () const

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

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

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

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

virtual T &	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...

virtual double	getStateValueAt (size_t siteIndex, int state) const

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

virtual double	getStateValueAt (size_t siteIndex, int state) const
	From CruxSymbolList. More...

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

Protected Member Functions
	EdSymbolList (const Alphabet *alpha)
	Build a new void CoreSymbolList object with the specified alphabet. More...

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

	EdSymbolList (const CoreSymbolList< T > &list)
	The generic copy constructor. More...

	EdSymbolList (const EdSymbolList< T > &list)
	The copy constructor. More...

EdSymbolList< T > &	operator= (const CoreSymbolList< T > &list)
	The generic assignment operator. More...

EdSymbolList< T > &	operator= (const EdSymbolList &list)
	The assignment operator. More...

virtual	~EdSymbolList ()

void	propagateEvents (bool yn)

bool	propagateEvents () const

The Clonable interface
EdSymbolList *	clone () const

Protected Attributes
std::vector< CoreSymbolListListener< T > * >	listeners_
	Contains the listeners. More...

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

Private Attributes
bool	propagateEvents_

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

Events handling
virtual void	beforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event)

virtual void	afterSequenceChanged (const CoreSymbolListEditionEvent< T > &event)

virtual void	beforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)

virtual void	afterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)

virtual void	beforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)

virtual void	afterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)

virtual void	beforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)

virtual void	afterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)

void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event)

void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< T > &event)

void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)

void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)

void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)

void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)

void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)

void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)

virtual size_t	getNumberOfListeners () const

virtual const CoreSymbolListListener< T > &	getListener (size_t i) const

virtual CoreSymbolListListener< T > &	getListener (size_t i)

virtual void	addCoreSymbolListListener (CoreSymbolListListener< T > *listener)

virtual void	removeCoreSymbolListListener (CoreSymbolListListener< T > *listener)

Detailed Description

template<class T>
class bpp::EdSymbolList< T >

Definition at line 246 of file SymbolList.h.

Constructor & Destructor Documentation

◆ EdSymbolList() [1/4]

template<class T >

bpp::EdSymbolList< T >::EdSymbolList ( const Alphabet * alpha )

inlineprotected

Build a new void CoreSymbolList object with the specified alphabet.

Parameters

alpha The alphabet to use.

Definition at line 265 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::clone().

◆ EdSymbolList() [2/4]

template<class T >

bpp::EdSymbolList< T >::EdSymbolList	(	const std::vector< T > &	list,
		const Alphabet *	alpha
	)

inlineprotected

Build a new CoreSymbolList 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.

Exceptions

BadIntException If the content does not match the specified alphabet.

Definition at line 276 of file SymbolList.h.

◆ EdSymbolList() [3/4]

template<class T >

bpp::EdSymbolList< T >::EdSymbolList ( const CoreSymbolList< T > & list )

inlineprotected

The generic copy constructor.

Definition at line 283 of file SymbolList.h.

◆ EdSymbolList() [4/4]

template<class T >

bpp::EdSymbolList< T >::EdSymbolList ( const EdSymbolList< T > & list )

inlineprotected

The copy constructor.

Definition at line 291 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_.

◆ ~EdSymbolList()

template<class T >

virtual bpp::EdSymbolList< T >::~EdSymbolList ( )

inlineprotectedvirtual

Definition at line 355 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_.

Member Function Documentation

◆ addCoreSymbolListListener()

template<class T >

virtual void bpp::EdSymbolList< T >::addCoreSymbolListListener ( CoreSymbolListListener< T > * listener )

inlinevirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 439 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_.

◆ addElement() [1/2]

template<class T >

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

inlinevirtual

Add a character to the end of the list.

Parameters

c	The character to add.

Reimplemented from bpp::SymbolList< T >.

Definition at line 394 of file SymbolList.h.

References bpp::SymbolList< T >::addElement(), bpp::EdSymbolList< T >::fireAfterSequenceInserted(), and bpp::EdSymbolList< T >::fireBeforeSequenceInserted().

Referenced by bpp::EdIntSymbolList::addElement(), and bpp::SequenceWithQuality::addElement().

◆ addElement() [2/2]

template<class T >

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

inlinevirtual

Add a character at a certain position in the list.

Parameters

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

Reimplemented from bpp::SymbolList< T >.

Definition at line 402 of file SymbolList.h.

References bpp::SymbolList< T >::addElement(), bpp::EdSymbolList< T >::fireAfterSequenceInserted(), and bpp::EdSymbolList< T >::fireBeforeSequenceInserted().

◆ afterSequenceChanged()

template<class T >

virtual void bpp::EdSymbolList< T >::afterSequenceChanged ( const CoreSymbolListEditionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 454 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireAfterSequenceChanged().

◆ afterSequenceDeleted()

template<class T >

virtual void bpp::EdSymbolList< T >::afterSequenceDeleted ( const CoreSymbolListDeletionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 458 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireAfterSequenceDeleted().

◆ afterSequenceInserted()

template<class T >

virtual void bpp::EdSymbolList< T >::afterSequenceInserted ( const CoreSymbolListInsertionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 456 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireAfterSequenceInserted().

◆ afterSequenceSubstituted()

template<class T >

virtual void bpp::EdSymbolList< T >::afterSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 460 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireAfterSequenceSubstituted().

◆ beforeSequenceChanged()

template<class T >

virtual void bpp::EdSymbolList< T >::beforeSequenceChanged ( const CoreSymbolListEditionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 453 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireBeforeSequenceChanged().

◆ beforeSequenceDeleted()

template<class T >

virtual void bpp::EdSymbolList< T >::beforeSequenceDeleted ( const CoreSymbolListDeletionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 457 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireBeforeSequenceDeleted().

◆ beforeSequenceInserted()

template<class T >

virtual void bpp::EdSymbolList< T >::beforeSequenceInserted ( const CoreSymbolListInsertionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 455 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireBeforeSequenceInserted().

◆ beforeSequenceSubstituted()

template<class T >

virtual void bpp::EdSymbolList< T >::beforeSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Reimplemented in bpp::EdIntSymbolList.

Definition at line 459 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireBeforeSequenceSubstituted().

◆ clone()

template<class T >

EdSymbolList* bpp::EdSymbolList< T >::clone ( ) const

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 351 of file SymbolList.h.

References bpp::EdSymbolList< T >::EdSymbolList().

◆ deleteElement()

template<class T >

void bpp::EdSymbolList< T >::deleteElement ( size_t pos )

inlinevirtual

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Reimplemented from bpp::SymbolList< T >.

Definition at line 377 of file SymbolList.h.

References bpp::SymbolList< T >::deleteElement(), bpp::EdSymbolList< T >::fireAfterSequenceDeleted(), and bpp::EdSymbolList< T >::fireBeforeSequenceDeleted().

◆ deleteElements()

template<class T >

void bpp::EdSymbolList< T >::deleteElements	(	size_t	pos,
		size_t	len
	)

inlinevirtual

Remove the elements at position 'pos'.

Parameters

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

Reimplemented from bpp::SymbolList< T >.

Definition at line 386 of file SymbolList.h.

References bpp::SymbolList< T >::deleteElements(), bpp::EdSymbolList< T >::fireAfterSequenceDeleted(), and bpp::EdSymbolList< T >::fireBeforeSequenceDeleted().

◆ fireAfterSequenceChanged()

template<class T >

void bpp::EdSymbolList< T >::fireAfterSequenceChanged ( const CoreSymbolListEditionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 472 of file SymbolList.h.

References bpp::EdSymbolList< T >::afterSequenceChanged(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::setContent().

◆ fireAfterSequenceDeleted()

template<class T >

void bpp::EdSymbolList< T >::fireAfterSequenceDeleted ( const CoreSymbolListDeletionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 512 of file SymbolList.h.

References bpp::EdSymbolList< T >::afterSequenceDeleted(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::deleteElement(), and bpp::EdSymbolList< T >::deleteElements().

◆ fireAfterSequenceInserted()

template<class T >

void bpp::EdSymbolList< T >::fireAfterSequenceInserted ( const CoreSymbolListInsertionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 492 of file SymbolList.h.

References bpp::EdSymbolList< T >::afterSequenceInserted(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::addElement().

◆ fireAfterSequenceSubstituted()

template<class T >

void bpp::EdSymbolList< T >::fireAfterSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 532 of file SymbolList.h.

References bpp::EdSymbolList< T >::afterSequenceSubstituted(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::setElement().

◆ fireBeforeSequenceChanged()

template<class T >

void bpp::EdSymbolList< T >::fireBeforeSequenceChanged ( const CoreSymbolListEditionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 462 of file SymbolList.h.

References bpp::EdSymbolList< T >::beforeSequenceChanged(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::setContent().

◆ fireBeforeSequenceDeleted()

template<class T >

void bpp::EdSymbolList< T >::fireBeforeSequenceDeleted ( const CoreSymbolListDeletionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 502 of file SymbolList.h.

References bpp::EdSymbolList< T >::beforeSequenceDeleted(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::deleteElement(), and bpp::EdSymbolList< T >::deleteElements().

◆ fireBeforeSequenceInserted()

template<class T >

void bpp::EdSymbolList< T >::fireBeforeSequenceInserted ( const CoreSymbolListInsertionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 482 of file SymbolList.h.

References bpp::EdSymbolList< T >::beforeSequenceInserted(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::addElement().

◆ fireBeforeSequenceSubstituted()

template<class T >

void bpp::EdSymbolList< T >::fireBeforeSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > & event )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 522 of file SymbolList.h.

References bpp::EdSymbolList< T >::beforeSequenceSubstituted(), bpp::EdSymbolList< T >::listeners_, and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdSymbolList< T >::setElement().

◆ getAlphabet()

template<class T >

const Alphabet* bpp::SymbolList< T >::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.

References bpp::SymbolList< T >::alphabet_.

Referenced by bpp::SequenceWithQualityTools::complement(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithAnnotation::merge(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceWithQualityTools::reverseTranscript(), bpp::SequenceWithQualityTools::subseq(), and bpp::SequenceWithQualityTools::transcript().

◆ getContent()

template<class T >

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

inlinevirtualinherited

Implements bpp::CoreSymbolList< T >.

Definition at line 178 of file SymbolList.h.

References bpp::SymbolList< T >::content_.

◆ getElement()

template<class T >

virtual const T& bpp::SymbolList< T >::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.

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

◆ getListener() [1/2]

template<class T >

virtual CoreSymbolListListener<T>& bpp::EdSymbolList< T >::getListener ( size_t i )

inlinevirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 432 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_.

◆ getListener() [2/2]

template<class T >

virtual const CoreSymbolListListener<T>& bpp::EdSymbolList< T >::getListener ( size_t i ) const

inlinevirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 425 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_.

◆ getNumberOfListeners()

template<class T >

virtual size_t bpp::EdSymbolList< T >::getNumberOfListeners ( ) const

inlinevirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 423 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_.

◆ 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]

template<class T >

virtual double bpp::EdCoreSymbolList< T >::getStateValueAt	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtualinherited

From CruxSymbolList.

Reimplemented from bpp::CruxSymbolList.

Definition at line 416 of file CoreSymbolList.h.

References bpp::CruxSymbolList::getStateValueAt().

◆ getValue()

template<class T >

virtual const T& bpp::SymbolList< T >::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.

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

Referenced by bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::CodonSiteTools::isFourFoldDegenerated(), and bpp::CodonSiteTools::numberOfSubstitutions().

◆ 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]

template<class T >

virtual double bpp::EdCoreSymbolList< T >::operator()	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtualinherited

Reimplemented from bpp::CruxSymbolList.

Definition at line 421 of file CoreSymbolList.h.

References bpp::CruxSymbolList::operator()().

◆ operator=() [1/2]

template<class T >

EdSymbolList<T>& bpp::EdSymbolList< T >::operator= ( const CoreSymbolList< T > & list )

inlineprotected

The generic assignment operator.

Definition at line 307 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_, bpp::SymbolList< T >::operator=(), and bpp::EdSymbolList< T >::propagateEvents_.

Referenced by bpp::EdIntSymbolList::operator=().

◆ operator=() [2/2]

template<class T >

EdSymbolList<T>& bpp::EdSymbolList< T >::operator= ( const EdSymbolList< T > & list )

inlineprotected

The assignment operator.

Definition at line 324 of file SymbolList.h.

References bpp::EdSymbolList< T >::listeners_, bpp::SymbolList< T >::operator=(), and bpp::EdSymbolList< T >::propagateEvents_.

◆ operator[]() [1/2]

template<class T >

virtual T& bpp::SymbolList< T >::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.

References bpp::SymbolList< T >::content_.

◆ operator[]() [2/2]

template<class T >

virtual const T& bpp::SymbolList< T >::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.

References bpp::SymbolList< T >::content_.

◆ propagateEvents() [1/2]

template<class T >

bool bpp::EdSymbolList< T >::propagateEvents ( ) const

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 545 of file SymbolList.h.

References bpp::EdSymbolList< T >::propagateEvents_.

◆ propagateEvents() [2/2]

template<class T >

void bpp::EdSymbolList< T >::propagateEvents ( bool yn )

inlineprotectedvirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 544 of file SymbolList.h.

References bpp::EdSymbolList< T >::propagateEvents_.

◆ removeCoreSymbolListListener()

template<class T >

virtual void bpp::EdSymbolList< T >::removeCoreSymbolListListener ( CoreSymbolListListener< T > * listener )

inlinevirtual

Implements bpp::EdCoreSymbolList< T >.

Definition at line 444 of file SymbolList.h.

References bpp::CoreSymbolListListener< T >::isRemovable(), and bpp::EdSymbolList< T >::listeners_.

◆ setContent()

template<class T >

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

inlinevirtual

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.

Reimplemented from bpp::SymbolList< T >.

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

Definition at line 367 of file SymbolList.h.

References bpp::EdSymbolList< T >::fireAfterSequenceChanged(), bpp::EdSymbolList< T >::fireBeforeSequenceChanged(), and bpp::SymbolList< T >::setContent().

Referenced by bpp::EdIntSymbolList::setContent().

◆ setElement()

template<class T >

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

inlinevirtual

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

Parameters

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

Reimplemented from bpp::SymbolList< T >.

Definition at line 410 of file SymbolList.h.

References bpp::EdSymbolList< T >::fireAfterSequenceSubstituted(), bpp::EdSymbolList< T >::fireBeforeSequenceSubstituted(), and bpp::SymbolList< T >::setElement().

Referenced by bpp::EdIntSymbolList::setElement().

◆ shuffle()

template<class T >

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

inlinevirtualinherited

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

Implements bpp::CruxSymbolList.

Definition at line 238 of file SymbolList.h.

References bpp::SymbolList< T >::content_.

◆ size()

template<class T >

size_t bpp::SymbolList< T >::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.

References bpp::SymbolList< T >::content_.

Referenced by bpp::SymbolList< T >::addElement(), bpp::SymbolList< T >::deleteElement(), bpp::SymbolList< T >::deleteElements(), bpp::SymbolList< T >::getElement(), bpp::SymbolList< T >::getValue(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SymbolList< T >::setElement(), and bpp::SequenceWithQualityTools::subseq().

◆ toString()

template<class T >

virtual std::string bpp::SymbolList< T >::toString ( ) const

inlinevirtualinherited

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.

Implements bpp::CruxSymbolList.

Reimplemented in bpp::BasicSequence, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

Definition at line 180 of file SymbolList.h.

Member Data Documentation

◆ alphabet_

template<class T >

const Alphabet* bpp::SymbolList< T >::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.

Referenced by bpp::SymbolList< T >::getAlphabet(), and bpp::SymbolList< T >::operator=().

◆ content_

template<class T >

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

protectedinherited

The list content.

Definition at line 85 of file SymbolList.h.

Referenced by bpp::SymbolList< T >::addElement(), bpp::SymbolList< T >::deleteElement(), bpp::SymbolList< T >::deleteElements(), bpp::SymbolList< T >::getContent(), bpp::SymbolList< T >::getElement(), bpp::SymbolList< T >::getValue(), bpp::SymbolList< T >::operator=(), bpp::SymbolList< T >::operator[](), bpp::SymbolList< T >::setContent(), bpp::SymbolList< T >::setElement(), bpp::SymbolList< T >::shuffle(), bpp::SymbolList< T >::size(), and bpp::SymbolList< T >::SymbolList().

◆ listeners_

template<class T >

std::vector<CoreSymbolListListener<T>* > bpp::EdSymbolList< T >::listeners_

protected

Contains the listeners.

Definition at line 257 of file SymbolList.h.

◆ propagateEvents_

template<class T >

bool bpp::EdSymbolList< T >::propagateEvents_

private

Definition at line 251 of file SymbolList.h.

Referenced by bpp::EdSymbolList< T >::fireAfterSequenceChanged(), bpp::EdSymbolList< T >::fireAfterSequenceDeleted(), bpp::EdSymbolList< T >::fireAfterSequenceInserted(), bpp::EdSymbolList< T >::fireAfterSequenceSubstituted(), bpp::EdSymbolList< T >::fireBeforeSequenceChanged(), bpp::EdSymbolList< T >::fireBeforeSequenceDeleted(), bpp::EdSymbolList< T >::fireBeforeSequenceInserted(), bpp::EdSymbolList< T >::fireBeforeSequenceSubstituted(), bpp::EdSymbolList< T >::operator=(), and bpp::EdSymbolList< T >::propagateEvents().

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

Bpp/Seq/SymbolList.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Events handling

Detailed Description

template<class T> class bpp::EdSymbolList< T >

Constructor & Destructor Documentation

◆ EdSymbolList() [1/4]

◆ EdSymbolList() [2/4]

◆ EdSymbolList() [3/4]

◆ EdSymbolList() [4/4]

◆ ~EdSymbolList()

Member Function Documentation

◆ addCoreSymbolListListener()

◆ addElement() [1/2]

◆ addElement() [2/2]

◆ afterSequenceChanged()

◆ afterSequenceDeleted()

◆ afterSequenceInserted()

◆ afterSequenceSubstituted()

◆ beforeSequenceChanged()

◆ beforeSequenceDeleted()

◆ beforeSequenceInserted()

◆ beforeSequenceSubstituted()

◆ clone()

◆ deleteElement()

◆ deleteElements()

◆ fireAfterSequenceChanged()

◆ fireAfterSequenceDeleted()

◆ fireAfterSequenceInserted()

◆ fireAfterSequenceSubstituted()

◆ fireBeforeSequenceChanged()

◆ fireBeforeSequenceDeleted()

◆ fireBeforeSequenceInserted()

◆ fireBeforeSequenceSubstituted()

◆ getAlphabet()

◆ getContent()

◆ getElement()

◆ getListener() [1/2]

◆ getListener() [2/2]

◆ getNumberOfListeners()

◆ getStateValueAt() [1/2]

◆ getStateValueAt() [2/2]

◆ getValue()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ propagateEvents() [1/2]

◆ propagateEvents() [2/2]

◆ removeCoreSymbolListListener()

◆ setContent()

◆ setElement()

◆ shuffle()

◆ size()

◆ toString()

Member Data Documentation

◆ alphabet_

◆ content_

◆ listeners_

◆ propagateEvents_

template<class T>
class bpp::EdSymbolList< T >