bpp::AbstractTemplateEventDrivenSymbolList< T > Class Template Reference

A partial implementation of a EventDrivenSymbolList object. More...

#include <Bpp/Seq/SymbolList.h>

Inheritance diagram for bpp::AbstractTemplateEventDrivenSymbolList< T >:

Collaboration diagram for bpp::AbstractTemplateEventDrivenSymbolList< T >:

Public Member Functions
virtual void	setContent (const std::vector< T > &list) override
	Set the whole content of 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...
virtual void	addElement (const T &c) override
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const T &c) override
	Add a character at a certain position in the list. More...
virtual void	setElement (size_t pos, const T &c) override
	Set the element at position 'pos' to character 'c'. 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...
virtual const std::vector< T > &	getContent () const override
virtual std::string	toString () const override
	Convert the list as a string. More...
const T &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...
const T &	getValue (size_t pos) const override
	checked access to a character in list. More...
const T &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...
T &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. More...
void	shuffle () override
	Randomly shuffle the content of the list, with linear complexity. More...
virtual double	getStateValueAt (size_t position, int state) const =0
	get value of a state at a position More...
virtual double	operator() (size_t position, int state) const =0
	get value of a state at a position More...
The Clonable interface
TemplateCoreSymbolListInterface *	clone () const override=0
The Clonable interface
virtual TemplateEventDrivenCoreSymbolListInterface *	clone () const override=0

Protected Member Functions
	AbstractTemplateEventDrivenSymbolList (std::shared_ptr< const Alphabet > alpha)
	Build a new void EventDrivenSymbolList object with the specified alphabet. More...
	AbstractTemplateEventDrivenSymbolList (const std::vector< T > &list, std::shared_ptr< const Alphabet > alpha)
	Build a new EventDrivenSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers. More...
	AbstractTemplateEventDrivenSymbolList (const TemplateCoreSymbolListInterface< T > &list)
	The generic copy constructor. More...
	AbstractTemplateEventDrivenSymbolList (const AbstractTemplateEventDrivenSymbolList< T > &list)
	The copy constructor. More...
AbstractTemplateEventDrivenSymbolList< T > &	operator= (const TemplateCoreSymbolListInterface< T > &list)
	The generic assignment operator. More...
AbstractTemplateEventDrivenSymbolList< T > &	operator= (const AbstractTemplateEventDrivenSymbolList &list)
	The assignment operator. More...
virtual	~AbstractTemplateEventDrivenSymbolList ()=default
void	propagateEvents (bool yn) override
bool	propagateEvents () const override

Protected Attributes
std::vector< std::shared_ptr< CoreSymbolListListener< T > > >	listeners_
	Contains the listeners. More...
std::vector< T >	content_
	The list content. More...

Private Attributes
bool	propagateEvents_
std::shared_ptr< 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) override
virtual void	afterSequenceChanged (const CoreSymbolListEditionEvent< T > &event) override
virtual void	beforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event) override
virtual void	afterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event) override
virtual void	beforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event) override
virtual void	afterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event) override
virtual void	beforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event) override
virtual void	afterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event) override
void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event) override
void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< T > &event) override
void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event) override
void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event) override
void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event) override
void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event) override
void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event) override
void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event) override
virtual size_t	getNumberOfListeners () const override
virtual const CoreSymbolListListener< T > &	listener (size_t i) const override
virtual std::shared_ptr< const CoreSymbolListListener< T > >	getListener (size_t i) const override
virtual CoreSymbolListListener< T > &	listener (size_t i) override
virtual std::shared_ptr< CoreSymbolListListener< T > >	getListener (size_t i) override
virtual void	addCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< T >> listener) override
virtual void	removeCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< T >> listener) override

Detailed Description

template<class T>
class bpp::AbstractTemplateEventDrivenSymbolList< T >

A partial implementation of a EventDrivenSymbolList object.

This class implements most of the CoreSymbolList interface, with the exception of the getStateValueAt function, which depend on the template type.

See also

Alphabet

Definition at line 206 of file SymbolList.h.

Constructor & Destructor Documentation

AbstractTemplateEventDrivenSymbolList() [1/4]

template<class T >

bpp::AbstractTemplateEventDrivenSymbolList< T >::AbstractTemplateEventDrivenSymbolList ( std::shared_ptr< const Alphabet >  alpha )

inlineprotected

Build a new void EventDrivenSymbolList object with the specified alphabet.

Parameters

alpha

The alphabet to use.

Definition at line 225 of file SymbolList.h.

AbstractTemplateEventDrivenSymbolList() [2/4]

template<class T >

bpp::AbstractTemplateEventDrivenSymbolList< T >::AbstractTemplateEventDrivenSymbolList ( const std::vector< T > &  list, std::shared_ptr< const Alphabet >  alpha  )

inlineprotected

Build a new EventDrivenSymbolList 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 236 of file SymbolList.h.

AbstractTemplateEventDrivenSymbolList() [3/4]

template<class T >

bpp::AbstractTemplateEventDrivenSymbolList< T >::AbstractTemplateEventDrivenSymbolList ( const TemplateCoreSymbolListInterface< T > &  list )

inlineprotected

The generic copy constructor.

Definition at line 243 of file SymbolList.h.

AbstractTemplateEventDrivenSymbolList() [4/4]

template<class T >

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

inlineprotected

The copy constructor.

Definition at line 253 of file SymbolList.h.

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

~AbstractTemplateEventDrivenSymbolList()

template<class T >

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

protectedvirtualdefault

Member Function Documentation

addCoreSymbolListListener()

template<class T >

virtual void bpp::AbstractTemplateEventDrivenSymbolList< T >::addCoreSymbolListListener ( std::shared_ptr< CoreSymbolListListener< T >>  listener )

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 391 of file SymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::listener(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::listeners_.

addElement() [1/2]

template<class T >

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

inlineoverridevirtual

Add a character to the end of the list.

Parameters

c	The character to add.

Reimplemented from bpp::AbstractTemplateSymbolList< T >.

Definition at line 336 of file SymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::addElement(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceInserted(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceInserted().

Referenced by bpp::EventDrivenIntSymbolList::addElement().

addElement() [2/2]

template<class T >

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

inlineoverridevirtual

Add a character at a certain position in the list.

Parameters

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

Reimplemented from bpp::AbstractTemplateSymbolList< T >.

Definition at line 344 of file SymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::addElement(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceInserted(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceInserted().

afterSequenceChanged()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 406 of file SymbolList.h.

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

afterSequenceDeleted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 410 of file SymbolList.h.

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

afterSequenceInserted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 408 of file SymbolList.h.

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

afterSequenceSubstituted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 412 of file SymbolList.h.

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

alphabet()

template<class T >

const Alphabet& bpp::AbstractTemplateSymbolList< T >::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.

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

Referenced by bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::CodonSiteTools::hasGapOrStop(), bpp::CodonSiteTools::hasStop(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SequenceTools::reverseTranscript(), and bpp::SequenceTools::transcript().

beforeSequenceChanged()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 405 of file SymbolList.h.

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

beforeSequenceDeleted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 409 of file SymbolList.h.

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

beforeSequenceInserted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 407 of file SymbolList.h.

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

beforeSequenceSubstituted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 411 of file SymbolList.h.

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

clone() [1/2]

template<class T >

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

overridepure virtualinherited

Implements bpp::CruxSymbolListInterface.

Implemented in bpp::SiteInterface, bpp::SequenceInterface, bpp::TemplateEventDrivenCoreSymbolListInterface< T >, bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::Sequence, bpp::ProbabilisticSymbolList, bpp::ProbabilisticSequence, bpp::EventDrivenIntSymbolList, bpp::IntSymbolList, bpp::ProbabilisticSiteInterface, bpp::ProbabilisticSequenceInterface, bpp::Site, and bpp::ProbabilisticSite.

clone() [2/2]

template<class T >

virtual TemplateEventDrivenCoreSymbolListInterface* bpp::TemplateEventDrivenCoreSymbolListInterface< T >::clone ( ) const

overridepure virtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

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

deleteElement()

template<class T >

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

inlineoverridevirtual

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Reimplemented from bpp::AbstractTemplateSymbolList< T >.

Definition at line 319 of file SymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::deleteElement(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceDeleted(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceDeleted().

deleteElements()

template<class T >

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

inlineoverridevirtual

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::AbstractTemplateSymbolList< T >.

Definition at line 328 of file SymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::deleteElements(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceDeleted(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceDeleted().

fireAfterSequenceChanged()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 424 of file SymbolList.h.

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

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

fireAfterSequenceDeleted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 464 of file SymbolList.h.

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

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

fireAfterSequenceInserted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 444 of file SymbolList.h.

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

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

fireAfterSequenceSubstituted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 484 of file SymbolList.h.

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

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

fireBeforeSequenceChanged()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 414 of file SymbolList.h.

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

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

fireBeforeSequenceDeleted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 454 of file SymbolList.h.

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

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

fireBeforeSequenceInserted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 434 of file SymbolList.h.

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

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

fireBeforeSequenceSubstituted()

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 474 of file SymbolList.h.

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

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

getAlphabet()

template<class T >

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< T >::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.

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

Referenced by bpp::CompressedVectorSiteContainer::addSite(), bpp::SiteContainerTools::alignNW(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SiteContainerTools::getAlignmentPositions(), bpp::SiteContainerTools::getSequencePositions(), bpp::CodonSiteTools::hasGapOrStop(), bpp::CodonSiteTools::hasStop(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::PhredPoly::nextSequence(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SequenceTools::reverseTranscript(), bpp::CompressedVectorSiteContainer::setSite(), bpp::SequenceTools::transcript(), bpp::SiteContainerTools::translateAlignment(), and bpp::Pasta::writeSequence().

getContent()

template<class T >

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

inlineoverridevirtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 131 of file SymbolList.h.

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

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

getElement()

template<class T >

const T& bpp::AbstractTemplateSymbolList< T >::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.

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

getListener() [1/2]

template<class T >

virtual std::shared_ptr<const CoreSymbolListListener<T> > bpp::AbstractTemplateEventDrivenSymbolList< T >::getListener ( size_t  i ) const

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 374 of file SymbolList.h.

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

getListener() [2/2]

template<class T >

virtual std::shared_ptr<CoreSymbolListListener<T> > bpp::AbstractTemplateEventDrivenSymbolList< T >::getListener ( size_t  i )

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 386 of file SymbolList.h.

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

getNumberOfListeners()

template<class T >

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

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 365 of file SymbolList.h.

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

getStateValueAt()

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

pure virtualinherited

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.

Implemented in bpp::Sequence, bpp::ProbabilisticSequence, bpp::ProbabilisticSymbolList, bpp::IntSymbolList, bpp::CoreSiteInterface, bpp::Site, and bpp::ProbabilisticSite.

Referenced by bpp::ProbabilisticSymbolList::ProbabilisticSymbolList().

getValue()

template<class T >

const T& bpp::AbstractTemplateSymbolList< T >::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.

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

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

listener() [1/2]

template<class T >

virtual const CoreSymbolListListener<T>& bpp::AbstractTemplateEventDrivenSymbolList< T >::listener ( size_t  i ) const

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 367 of file SymbolList.h.

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

Referenced by bpp::AbstractTemplateEventDrivenSymbolList< T >::addCoreSymbolListListener(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::removeCoreSymbolListListener().

listener() [2/2]

template<class T >

virtual CoreSymbolListListener<T>& bpp::AbstractTemplateEventDrivenSymbolList< T >::listener ( size_t  i )

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 379 of file SymbolList.h.

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

operator()()

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=() [1/2]

template<class T >

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

inlineprotected

The assignment operator.

Definition at line 286 of file SymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::listeners_, bpp::AbstractTemplateSymbolList< T >::operator=(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::propagateEvents_.

operator=() [2/2]

template<class T >

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

inlineprotected

The generic assignment operator.

Definition at line 274 of file SymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::listeners_, bpp::AbstractTemplateSymbolList< T >::operator=(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::propagateEvents_.

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

operator[]() [1/2]

template<class T >

const T& bpp::AbstractTemplateSymbolList< T >::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.

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

operator[]() [2/2]

template<class T >

T& bpp::AbstractTemplateSymbolList< T >::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.

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

propagateEvents() [1/2]

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 497 of file SymbolList.h.

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

propagateEvents() [2/2]

template<class T >

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

inlineoverrideprotectedvirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 496 of file SymbolList.h.

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

removeCoreSymbolListListener()

template<class T >

virtual void bpp::AbstractTemplateEventDrivenSymbolList< T >::removeCoreSymbolListListener ( std::shared_ptr< CoreSymbolListListener< T >>  listener )

inlineoverridevirtual

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 396 of file SymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::listener(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::listeners_.

setContent()

template<class T >

virtual void bpp::AbstractTemplateEventDrivenSymbolList< T >::setContent ( const std::vector< T > &  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::AbstractTemplateSymbolList< T >.

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

Definition at line 309 of file SymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceChanged(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceChanged(), and bpp::AbstractTemplateSymbolList< T >::setContent().

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

setElement()

template<class T >

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

inlineoverridevirtual

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::AbstractTemplateSymbolList< T >.

Definition at line 352 of file SymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceSubstituted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceSubstituted(), and bpp::AbstractTemplateSymbolList< T >::setElement().

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

shuffle()

template<class T >

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

inlineoverridevirtualinherited

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

Implements bpp::CruxSymbolListInterface.

Definition at line 191 of file SymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::content_, and bpp::RandomTools::DEFAULT_GENERATOR.

size()

template<class T >

size_t bpp::AbstractTemplateSymbolList< T >::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.

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

Referenced by bpp::AbstractTemplateSymbolList< T >::addElement(), bpp::CompressedVectorSiteContainer::addSite(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::checkSize_(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractTemplateSymbolList< T >::deleteElement(), bpp::AbstractTemplateSymbolList< T >::deleteElements(), bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SiteContainerTools::getAlignmentPositions(), bpp::SequenceContainerTools::getCounts(), bpp::AbstractTemplateSymbolList< T >::getElement(), bpp::SequenceContainerTools::getFrequencies(), bpp::SiteContainerTools::getSequencePositions(), bpp::CompressedVectorSiteContainer::getSiteIndex_(), bpp::AbstractTemplateSymbolList< T >::getValue(), bpp::CodonAlphabet::getWord(), bpp::WordAlphabet::getWord(), bpp::CodonSiteTools::hasGapOrStop(), bpp::SimpleSequencePositionIterator::hasMorePositions(), bpp::CodonSiteTools::hasStop(), bpp::SequenceMask::init(), bpp::SequenceQuality::init(), bpp::CodonSiteTools::isFourFoldDegenerated(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::AbstractTemplateSymbolList< T >::setElement(), bpp::CompressedVectorSiteContainer::setSite(), bpp::SiteContainerTools::translateAlignment(), bpp::Fasta::writeSequence(), and bpp::Pasta::writeSequence().

toString()

template<class T >

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

inlineoverridevirtualinherited

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::CruxSymbolListInterface.

Reimplemented in bpp::Sequence, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

Definition at line 133 of file SymbolList.h.

Member Data Documentation

alphabet_

template<class T >

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< 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 41 of file SymbolList.h.

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

content_

template<class T >

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

protectedinherited

The list content.

Definition at line 47 of file SymbolList.h.

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

listeners_

template<class T >

std::vector<std::shared_ptr<CoreSymbolListListener<T> > > bpp::AbstractTemplateEventDrivenSymbolList< T >::listeners_

protected

Contains the listeners.

Definition at line 218 of file SymbolList.h.

Referenced by bpp::AbstractTemplateEventDrivenSymbolList< T >::AbstractTemplateEventDrivenSymbolList(), bpp::AbstractTemplateEventDrivenSymbolList< T >::addCoreSymbolListListener(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceChanged(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceDeleted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceInserted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireAfterSequenceSubstituted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceChanged(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceDeleted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceInserted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::fireBeforeSequenceSubstituted(), bpp::AbstractTemplateEventDrivenSymbolList< T >::getListener(), bpp::AbstractTemplateEventDrivenSymbolList< T >::getNumberOfListeners(), bpp::AbstractTemplateEventDrivenSymbolList< T >::listener(), bpp::AbstractTemplateEventDrivenSymbolList< T >::operator=(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::removeCoreSymbolListListener().

propagateEvents_

template<class T >

bool bpp::AbstractTemplateEventDrivenSymbolList< T >::propagateEvents_

private

Definition at line 212 of file SymbolList.h.

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

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

• Bpp/Seq/SymbolList.h