bpp::EventDrivenIntSymbolList Class Reference

A event-driven IntSymbolList object. More...

#include <Bpp/Seq/IntSymbolList.h>

Inheritance diagram for bpp::EventDrivenIntSymbolList:

Collaboration diagram for bpp::EventDrivenIntSymbolList:

Public Types
typedef int	SymbolType

Public Member Functions
	EventDrivenIntSymbolList (std::shared_ptr< const Alphabet > alpha)
	Build a new void EventDrivenIntSymbolList object with the specified alphabet. More...
	EventDrivenIntSymbolList (const std::vector< std::string > &list, std::shared_ptr< const Alphabet > alpha)
	Build a new EventDrivenIntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters. More...
	EventDrivenIntSymbolList (const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)
	Build a new EventDrivenIntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers. More...
	EventDrivenIntSymbolList (const IntSymbolList &list)
	The generic copy constructor. More...
	EventDrivenIntSymbolList (const EventDrivenIntSymbolList &list)
	The copy constructor. More...
EventDrivenIntSymbolList &	operator= (const IntSymbolList &list)
	The generic assignment operator. More...
EventDrivenIntSymbolList &	operator= (const EventDrivenIntSymbolList &list)
	The assignment operator. More...
virtual	~EventDrivenIntSymbolList ()
virtual void	setContent (const std::vector< std::string > &list) override
	Set the whole content of the list. More...
void	setContent (const std::vector< int > &list) override
virtual std::string	toString () const override
	Convert the list as a string. More...
virtual void	addElement (const std::string &c) override
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const std::string &c) override
	Add a character at a certain position in the list. More...
virtual void	setElement (size_t pos, const std::string &c) override
	Set the element at position 'pos' to character 'c'. More...
virtual std::string	getChar (size_t pos) const override
	Get the element at position 'pos' as a character. More...
void	addIntSymbolListListener (std::shared_ptr< IntSymbolListListener > listener)
void	addElement (const T &v) override
void	addElement (const int &v) override
	Add a character to the end of the list. More...
void	addElement (size_t pos, const int &v) override
	Add a character at a certain position in the list. More...
void	setElement (size_t pos, const T &v) override
void	setElement (size_t pos, const int &v) override
	Set the element at position 'pos' to character 'c'. More...
double	getStateValueAt (size_t siteIndex, int state) const override
	get value of a state at a position More...
double	operator() (size_t siteIndex, int state) const override
	get value of a state at a position More...
virtual const std::vector< int > &	getContent () const override
const int &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...
const int &	getValue (size_t pos) const override
	checked access to a character in list. More...
const int &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...
int &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. More...
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the list. More...
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the list. More...
virtual const Alphabet &	alphabet () const =0
	Get the alphabet associated to the list. More...
const Alphabet &	alphabet () const override
	Get the alphabet associated to the list. More...
virtual size_t	size () const =0
	Get the number of elements in the list. More...
size_t	size () const override
	Get the number of elements in the list. More...
void	deleteElement (size_t pos) override
	Remove the element at position 'pos'. More...
void	deleteElements (size_t pos, size_t len) override
	Remove the elements at position 'pos'. More...
void	shuffle () override
	Randomly shuffle the content of the list, with linear complexity. More...
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 int &v) override
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const int &v) override
	Add a character at a certain position in the list. More...
virtual void	setElement (size_t pos, const int &v) override
	Set the element at position 'pos' to character 'c'. More...
The Clonable interface
EventDrivenIntSymbolList *	clone () const override
Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
virtual const std::vector< T > &	getContent () const =0
Edition methods.
virtual void	addElement (const T &c)=0
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const T &c)=0
	Add a character at a certain position in the list. More...
virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...
virtual const T &	getElement (size_t pos) const =0
	Get the element at position 'pos' as a character. More...
Provide direct access to the list content.
Warning These operators allow you to modify the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual const T &	getValue (size_t pos) const =0
	checked access to a character in list. More...
virtual const T &	operator[] (size_t pos) const =0
	Operator [] overloaded for quick access to a character in list. More...
virtual T &	operator[] (size_t pos)=0
	Operator [] overloaded for quick access to a character in list. More...
Edition methods.
virtual void	deleteElement (size_t pos)=0
	Remove the element at position 'pos'. More...
virtual void	deleteElements (size_t pos, size_t len)=0
	Remove the elements at position 'pos'. More...
Provide direct access to the list content.
Warning These operators allow you to modify the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

Protected Member Functions
virtual void	beforeSequenceChanged (const IntSymbolListEditionEvent &event) override
virtual void	afterSequenceChanged (const IntSymbolListEditionEvent &event) override
virtual void	beforeSequenceInserted (const IntSymbolListInsertionEvent &event) override
virtual void	afterSequenceInserted (const IntSymbolListInsertionEvent &event) override
virtual void	beforeSequenceDeleted (const IntSymbolListDeletionEvent &event) override
virtual void	afterSequenceDeleted (const IntSymbolListDeletionEvent &event) override
virtual void	beforeSequenceSubstituted (const IntSymbolListSubstitutionEvent &event) override
virtual void	afterSequenceSubstituted (const IntSymbolListSubstitutionEvent &event) override
void	propagateEvents (bool yn) override
bool	propagateEvents () const override

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

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

Events handling
virtual size_t	getNumberOfListeners () const override
virtual const CoreSymbolListListener< int > &	listener (size_t i) const override
virtual CoreSymbolListListener< int > &	listener (size_t i) override
virtual std::shared_ptr< const CoreSymbolListListener< int > >	getListener (size_t i) const override
virtual std::shared_ptr< CoreSymbolListListener< int > >	getListener (size_t i) override
virtual void	addCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< int >> listener) override
virtual void	removeCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< int >> listener) override
void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< int > &event) override
void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< int > &event) override
void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< int > &event) override
void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< int > &event) override
void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< int > &event) override
void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< int > &event) override
void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< int > &event) override
void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< int > &event) override

Events handling
virtual void	addCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< T >> listener)=0
virtual void	removeCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< T >> listener)=0
virtual void	beforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	afterSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	beforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	afterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	beforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	afterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	beforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0
virtual void	afterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0
virtual void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0
virtual void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0

Detailed Description

A event-driven 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 247 of file IntSymbolList.h.

Member Typedef Documentation

SymbolType

typedef int bpp::IntSymbolListInterface::SymbolType

inherited

Definition at line 31 of file IntSymbolList.h.

Constructor & Destructor Documentation

EventDrivenIntSymbolList() [1/5]

bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList ( std::shared_ptr< const Alphabet >  alpha )

inline

Build a new void EventDrivenIntSymbolList object with the specified alphabet.

Parameters

alpha

The alphabet to use.

Definition at line 257 of file IntSymbolList.h.

Referenced by clone().

EventDrivenIntSymbolList() [2/5]

bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList ( const std::vector< std::string > &  list, std::shared_ptr< const Alphabet >  alpha  )

inline

Build a new EventDrivenIntSymbolList 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 270 of file IntSymbolList.h.

References bpp::IntSymbolListInterface::setContent().

EventDrivenIntSymbolList() [3/5]

bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList ( const std::vector< int > &  list, std::shared_ptr< const Alphabet >  alpha  )

inline

Build a new EventDrivenIntSymbolList 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 288 of file IntSymbolList.h.

EventDrivenIntSymbolList() [4/5]

bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList ( const IntSymbolList &  list )

inline

The generic copy constructor.

Definition at line 300 of file IntSymbolList.h.

EventDrivenIntSymbolList() [5/5]

bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList ( const EventDrivenIntSymbolList &  list )

inline

The copy constructor.

Definition at line 309 of file IntSymbolList.h.

~EventDrivenIntSymbolList()

virtual bpp::EventDrivenIntSymbolList::~EventDrivenIntSymbolList ( )

inlinevirtual

Definition at line 347 of file IntSymbolList.h.

Member Function Documentation

addCoreSymbolListListener() [1/2]

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

inlineoverridevirtualinherited

Definition at line 391 of file SymbolList.h.

addCoreSymbolListListener() [2/2]

template<class T >

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

pure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

addElement() [1/9]

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

inlineoverrideinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 152 of file SymbolList.h.

addElement() [2/9]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::addElement ( const int &  v )

inlineoverridevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 336 of file SymbolList.h.

addElement() [3/9]

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

overridevirtual

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Reimplemented from bpp::IntSymbolList.

Definition at line 113 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::addElement().

addElement() [4/9]

template<class T >

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

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

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

addElement() [5/9]

void bpp::AbstractTemplateSymbolList< T >::addElement

inlineoverrideinherited

Definition at line 152 of file SymbolList.h.

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

addElement() [6/9]

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

inlineoverrideinherited

Add a character at a certain position in the list.

Parameters

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

Definition at line 157 of file SymbolList.h.

addElement() [7/9]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::addElement ( size_t  pos, const int &  v  )

inlineoverridevirtualinherited

Add a character at a certain position in the list.

Parameters

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

Definition at line 344 of file SymbolList.h.

addElement() [8/9]

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

overridevirtual

Add a character at a certain position in the list.

Parameters

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

Reimplemented from bpp::IntSymbolList.

Definition at line 120 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::addElement().

addElement() [9/9]

template<class T >

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

pure virtualinherited

Add a character at a certain position in the list.

Parameters

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

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

addIntSymbolListListener()

void bpp::EventDrivenIntSymbolList::addIntSymbolListListener ( std::shared_ptr< IntSymbolListListener >  listener )

inline

Definition at line 368 of file IntSymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< int >::addCoreSymbolListListener(), and bpp::AbstractTemplateEventDrivenSymbolList< int >::listener().

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

afterSequenceChanged() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceChanged() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceChanged ( const IntSymbolListEditionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 375 of file IntSymbolList.h.

afterSequenceDeleted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceDeleted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceDeleted ( const IntSymbolListDeletionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 379 of file IntSymbolList.h.

afterSequenceInserted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceInserted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceInserted ( const IntSymbolListInsertionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 377 of file IntSymbolList.h.

afterSequenceSubstituted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceSubstituted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceSubstituted ( const IntSymbolListSubstitutionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 381 of file IntSymbolList.h.

alphabet() [1/2]

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

pure virtualinherited

Get the alphabet associated to the list.

Returns

A const reference to the alphabet.

See also

Alphabet class.

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

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::concatenate(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::invertComplement(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), and bpp::AbstractTransliterator::translate().

alphabet() [2/2]

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

inlineoverridevirtualinherited

Get the alphabet associated to the list.

Returns

A const reference to the alphabet.

See also

Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 122 of file SymbolList.h.

beforeSequenceChanged() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceChanged() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceChanged ( const IntSymbolListEditionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 374 of file IntSymbolList.h.

beforeSequenceDeleted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceDeleted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceDeleted ( const IntSymbolListDeletionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 378 of file IntSymbolList.h.

beforeSequenceInserted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceInserted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceInserted ( const IntSymbolListInsertionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 376 of file IntSymbolList.h.

beforeSequenceSubstituted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceSubstituted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceSubstituted ( const IntSymbolListSubstitutionEvent &  event )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 380 of file IntSymbolList.h.

clone()

EventDrivenIntSymbolList* bpp::EventDrivenIntSymbolList::clone ( ) const

inlineoverridevirtual

Reimplemented from bpp::IntSymbolList.

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

Definition at line 344 of file IntSymbolList.h.

References EventDrivenIntSymbolList().

deleteElement() [1/3]

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

inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 138 of file SymbolList.h.

deleteElement() [2/3]

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

inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

Definition at line 319 of file SymbolList.h.

deleteElement() [3/3]

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

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

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

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

deleteElements() [1/3]

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

inlineoverridevirtualinherited

Remove the elements at position 'pos'.

Parameters

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

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 145 of file SymbolList.h.

deleteElements() [2/3]

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

inlineoverridevirtualinherited

Remove the elements at position 'pos'.

Parameters

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

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

Definition at line 328 of file SymbolList.h.

deleteElements() [3/3]

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

pure virtualinherited

Remove the elements at position 'pos'.

Parameters

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

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

fireAfterSequenceChanged() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 424 of file SymbolList.h.

fireAfterSequenceChanged() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireAfterSequenceDeleted() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 464 of file SymbolList.h.

fireAfterSequenceDeleted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireAfterSequenceInserted() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 444 of file SymbolList.h.

fireAfterSequenceInserted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireAfterSequenceSubstituted() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 484 of file SymbolList.h.

fireAfterSequenceSubstituted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceChanged() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 414 of file SymbolList.h.

fireBeforeSequenceChanged() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceDeleted() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 454 of file SymbolList.h.

fireBeforeSequenceDeleted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceInserted() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 434 of file SymbolList.h.

fireBeforeSequenceInserted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceSubstituted() [1/2]

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

inlineoverrideprotectedinherited

Definition at line 474 of file SymbolList.h.

fireBeforeSequenceSubstituted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

getAlphabet() [1/2]

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

pure virtualinherited

Get the alphabet associated to the list.

Returns

A const pointer to the alphabet.

See also

Alphabet class.

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

Referenced by bpp::Sequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceWithQualityTools::complement(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::getComplement(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::jointEntropy(), bpp::SequenceWithAnnotation::merge(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::ProbabilisticSymbolList::operator=(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::SequenceWithQualityTools::reverseTranscript(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SequenceWithQualityTools::transcript(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::WordAlphabet::translate(), and bpp::SymbolListTools::variabilityShannon().

getAlphabet() [2/2]

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

inlineoverridevirtualinherited

Get the alphabet associated to the list.

Returns

A const pointer to the alphabet.

See also

Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 120 of file SymbolList.h.

getChar()

string EventDrivenIntSymbolList::getChar ( size_t  pos ) const

overridevirtual

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

Parameters

pos	The position of the character to retrieve.

Reimplemented from bpp::IntSymbolList.

Definition at line 134 of file IntSymbolList.cpp.

getContent() [1/2]

template<class T >

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

pure virtualinherited

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

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

getContent() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 131 of file SymbolList.h.

getElement() [1/2]

template<class T >

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

pure virtualinherited

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

Parameters

pos	The position of the character to retrieve.

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

getElement() [2/2]

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

inlineoverridevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 173 of file SymbolList.h.

getListener() [1/2]

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

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 374 of file SymbolList.h.

getListener() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 386 of file SymbolList.h.

getNumberOfListeners()

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

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 365 of file SymbolList.h.

getStateValueAt()

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

inlineoverridevirtualinherited

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.

Implements bpp::CruxSymbolListInterface.

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

Definition at line 210 of file IntSymbolList.h.

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

getValue() [1/2]

template<class T >

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

pure virtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

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

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

getValue() [2/2]

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

inlineoverridevirtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 180 of file SymbolList.h.

listener() [1/2]

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

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 367 of file SymbolList.h.

listener() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 379 of file SymbolList.h.

operator()()

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

inlineoverridevirtualinherited

get value of a state at a position

Short-cut for getStateValueAt.

Parameters

position	position in the list
state	state in the alphabet

Returns

The state value at the given position.

Implements bpp::CruxSymbolListInterface.

Definition at line 218 of file IntSymbolList.h.

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

operator=() [1/2]

EventDrivenIntSymbolList& bpp::EventDrivenIntSymbolList::operator= ( const EventDrivenIntSymbolList &  list )

inline

The assignment operator.

Definition at line 331 of file IntSymbolList.h.

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

operator=() [2/2]

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

inline

The generic assignment operator.

Definition at line 319 of file IntSymbolList.h.

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

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

operator[]() [1/4]

template<class T >

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

pure virtualinherited

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

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

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

operator[]() [2/4]

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

inlineoverridevirtualinherited

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

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 187 of file SymbolList.h.

operator[]() [3/4]

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

inlineoverridevirtualinherited

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

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 189 of file SymbolList.h.

operator[]() [4/4]

template<class T >

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

pure virtualinherited

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

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

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

propagateEvents() [1/2]

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

inlineoverrideprotectedvirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 497 of file SymbolList.h.

propagateEvents() [2/2]

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

inlineoverrideprotectedvirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 496 of file SymbolList.h.

removeCoreSymbolListListener() [1/2]

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

inlineoverridevirtualinherited

Definition at line 396 of file SymbolList.h.

removeCoreSymbolListListener() [2/2]

template<class T >

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

pure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

setContent() [1/4]

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

overridevirtual

Reimplemented from bpp::IntSymbolList.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 91 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::setContent().

setContent() [2/4]

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

overridevirtual

Set the whole content of the list.

Parameters

list	The new content of the list.

See also

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

Reimplemented from bpp::IntSymbolList.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 70 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::setContent().

setContent() [3/4]

template<class T >

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

pure virtualinherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also

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

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

setContent() [4/4]

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

inherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also

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

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

setElement() [1/5]

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

inlineoverrideinherited

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

Parameters

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

Definition at line 165 of file SymbolList.h.

setElement() [2/5]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::setElement ( size_t  pos, const int &  v  )

inlineoverridevirtualinherited

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

Parameters

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

Definition at line 352 of file SymbolList.h.

setElement() [3/5]

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

overridevirtual

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

Parameters

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

Reimplemented from bpp::IntSymbolList.

Definition at line 127 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::setElement().

setElement() [4/5]

template<class T >

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

pure virtualinherited

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

Parameters

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

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

setElement() [5/5]

void bpp::AbstractTemplateSymbolList< T >::setElement

inlineoverrideinherited

Definition at line 165 of file SymbolList.h.

shuffle() [1/2]

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

inlineoverridevirtualinherited

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

Implements bpp::CruxSymbolListInterface.

Definition at line 191 of file SymbolList.h.

shuffle() [2/2]

virtual void bpp::CruxSymbolListInterface::shuffle ( )

pure virtualinherited

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

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

size() [1/2]

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

pure virtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

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

Referenced by bpp::AbstractTemplateSymbolList< T >::AbstractTemplateSymbolList(), bpp::SequenceWithQuality::addElement(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getFrequencies(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getMajorAllele(), bpp::SymbolListTools::getMajorAlleleFrequency(), bpp::SymbolListTools::getMinorAllele(), bpp::SymbolListTools::getMinorAlleleFrequency(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SymbolListTools::getNumberOfDistinctCharacters(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasSingleton(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SymbolListTools::heterozygosity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isDoubleton(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::isParsimonyInformativeSite(), bpp::SymbolListTools::isTriplet(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), bpp::SymbolListTools::jointEntropy(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SiteInterface::operator==(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceWalker::SequenceWalker(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::SymbolListTools::variabilityFactorial(), and bpp::SymbolListTools::variabilityShannon().

size() [2/2]

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

inlineoverridevirtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implements bpp::CruxSymbolListInterface.

Definition at line 124 of file SymbolList.h.

toString()

string EventDrivenIntSymbolList::toString ( ) const

overridevirtual

Convert the list as a string.

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

Returns

The whole list as a string.

Reimplemented from bpp::IntSymbolList.

Definition at line 105 of file IntSymbolList.cpp.

References bpp::StringSequenceTools::decodeSequence().

Member Data Documentation

alphabet_

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

privateinherited

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

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

Definition at line 41 of file SymbolList.h.

content_

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

protectedinherited

The list content.

Definition at line 47 of file SymbolList.h.

listeners_

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

protectedinherited

Contains the listeners.

Definition at line 218 of file SymbolList.h.

propagateEvents_

bool bpp::AbstractTemplateEventDrivenSymbolList< int >::propagateEvents_

privateinherited

Definition at line 212 of file SymbolList.h.

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

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