A event-driven IntSymbolList object. More...

#include <Bpp/Seq/IntSymbolList.h>

Inheritance diagram for bpp::EdIntSymbolList:

Collaboration diagram for bpp::EdIntSymbolList:

Public Member Functions
	EdIntSymbolList (const Alphabet *alpha)
	Build a new void EdIntSymbolList object with the specified alphabet. More...

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

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

	EdIntSymbolList (const IntSymbolList &list)
	The generic copy constructor. More...

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

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

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

	~EdIntSymbolList ()

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

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

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

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

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

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

virtual std::string	getChar (size_t pos) const

void	addIntSymbolListListener (IntSymbolListListener *listener)

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 int &v)
	Add a character to the end of the list. More...

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

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

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

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

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

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

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

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

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

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

virtual double	getStateValueAt (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

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

The Clonable interface
EdIntSymbolList *	clone () const

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

Edition methods.
virtual void	addElement (const T &c)=0
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, const T &c)=0
	Add a character at a certain position in the list. More...

virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...

Protected Member Functions
virtual void	beforeSequenceChanged (const IntSymbolListEditionEvent &event)

virtual void	afterSequenceChanged (const IntSymbolListEditionEvent &event)

virtual void	beforeSequenceInserted (const IntSymbolListInsertionEvent &event)

virtual void	afterSequenceInserted (const IntSymbolListInsertionEvent &event)

virtual void	beforeSequenceDeleted (const IntSymbolListDeletionEvent &event)

virtual void	afterSequenceDeleted (const IntSymbolListDeletionEvent &event)

virtual void	beforeSequenceSubstituted (const IntSymbolListSubstitutionEvent &event)

virtual void	afterSequenceSubstituted (const IntSymbolListSubstitutionEvent &event)

void	propagateEvents (bool yn)

bool	propagateEvents () const

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

std::vector< int >	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 size_t	getNumberOfListeners () const

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

virtual CoreSymbolListListener< int > &	getListener (size_t i)

virtual void	addCoreSymbolListListener (CoreSymbolListListener< int > *listener)

virtual void	removeCoreSymbolListListener (CoreSymbolListListener< int > *listener)

void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< int > &event)

void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< int > &event)

void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< int > &event)

void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< int > &event)

void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< int > &event)

void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< int > &event)

void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< int > &event)

void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< int > &event)

Events handling
virtual void	addCoreSymbolListListener (CoreSymbolListListener< T > *listener)=0

virtual void	removeCoreSymbolListListener (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 254 of file IntSymbolList.h.

Constructor & Destructor Documentation

◆ EdIntSymbolList() [1/5]

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

inline

Build a new void EdIntSymbolList object with the specified alphabet.

Parameters

alpha The alphabet to use.

Definition at line 263 of file IntSymbolList.h.

Referenced by clone().

◆ EdIntSymbolList() [2/5]

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

Build a new EdIntSymbolList 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 178 of file IntSymbolList.cpp.

References setContent().

◆ EdIntSymbolList() [3/5]

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

Build a new EdIntSymbolList 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 184 of file IntSymbolList.cpp.

◆ EdIntSymbolList() [4/5]

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

The generic copy constructor.

◆ EdIntSymbolList() [5/5]

EdIntSymbolList::EdIntSymbolList ( const EdIntSymbolList & list )

The copy constructor.

Definition at line 190 of file IntSymbolList.cpp.

◆ ~EdIntSymbolList()

bpp::EdIntSymbolList::~EdIntSymbolList ( )

inline

Definition at line 312 of file IntSymbolList.h.

Member Function Documentation

◆ addCoreSymbolListListener() [1/2]

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

inlinevirtualinherited

Definition at line 439 of file SymbolList.h.

◆ addCoreSymbolListListener() [2/2]

template<class T >

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

pure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ addElement() [1/6]

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

inlinevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 394 of file SymbolList.h.

◆ addElement() [2/6]

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

virtual

Definition at line 243 of file IntSymbolList.cpp.

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

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

◆ addElement() [3/6]

template<class T >

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

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

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

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

◆ addElement() [4/6]

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

inlinevirtualinherited

Add a character at a certain position in the list.

Parameters

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

Definition at line 402 of file SymbolList.h.

◆ addElement() [5/6]

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

virtual

Definition at line 250 of file IntSymbolList.cpp.

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

◆ addElement() [6/6]

template<class T >

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

pure virtualinherited

Add a character at a certain position in the list.

Parameters

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

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

◆ addIntSymbolListListener()

void bpp::EdIntSymbolList::addIntSymbolListListener ( IntSymbolListListener * listener )

inline

Definition at line 333 of file IntSymbolList.h.

References bpp::EdSymbolList< int >::addCoreSymbolListListener().

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

◆ afterSequenceChanged() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ afterSequenceChanged() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 340 of file IntSymbolList.h.

◆ afterSequenceDeleted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ afterSequenceDeleted() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 344 of file IntSymbolList.h.

◆ afterSequenceInserted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ afterSequenceInserted() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 342 of file IntSymbolList.h.

◆ afterSequenceSubstituted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ afterSequenceSubstituted() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 346 of file IntSymbolList.h.

◆ beforeSequenceChanged() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ beforeSequenceChanged() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 339 of file IntSymbolList.h.

◆ beforeSequenceDeleted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ beforeSequenceDeleted() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 343 of file IntSymbolList.h.

◆ beforeSequenceInserted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ beforeSequenceInserted() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 341 of file IntSymbolList.h.

◆ beforeSequenceSubstituted() [1/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ beforeSequenceSubstituted() [2/2]

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

inlineprotectedvirtual

Reimplemented from bpp::EdSymbolList< int >.

Definition at line 345 of file IntSymbolList.h.

◆ clone()

EdIntSymbolList* bpp::EdIntSymbolList::clone ( ) const

inlinevirtual

Implements bpp::EdCoreSymbolList< T >.

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

Definition at line 309 of file IntSymbolList.h.

References EdIntSymbolList().

◆ deleteElement()

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

inlinevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Reimplemented from bpp::SymbolList< int >.

Definition at line 377 of file SymbolList.h.

◆ deleteElements()

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

inlinevirtualinherited

Remove the elements at position 'pos'.

Parameters

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

Reimplemented from bpp::SymbolList< int >.

Definition at line 386 of file SymbolList.h.

◆ fireAfterSequenceChanged() [1/2]

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

inlineprotectedinherited

Definition at line 472 of file SymbolList.h.

◆ fireAfterSequenceChanged() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireAfterSequenceDeleted() [1/2]

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

inlineprotectedinherited

Definition at line 512 of file SymbolList.h.

◆ fireAfterSequenceDeleted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireAfterSequenceInserted() [1/2]

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

inlineprotectedinherited

Definition at line 492 of file SymbolList.h.

◆ fireAfterSequenceInserted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireAfterSequenceSubstituted() [1/2]

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

inlineprotectedinherited

Definition at line 532 of file SymbolList.h.

◆ fireAfterSequenceSubstituted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireBeforeSequenceChanged() [1/2]

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

inlineprotectedinherited

Definition at line 462 of file SymbolList.h.

◆ fireBeforeSequenceChanged() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireBeforeSequenceDeleted() [1/2]

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

inlineprotectedinherited

Definition at line 502 of file SymbolList.h.

◆ fireBeforeSequenceDeleted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireBeforeSequenceInserted() [1/2]

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

inlineprotectedinherited

Definition at line 482 of file SymbolList.h.

◆ fireBeforeSequenceInserted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ fireBeforeSequenceSubstituted() [1/2]

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

inlineprotectedinherited

Definition at line 522 of file SymbolList.h.

◆ fireBeforeSequenceSubstituted() [2/2]

template<class T >

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

protectedpure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ getAlphabet()

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

inlinevirtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolList.

Definition at line 169 of file SymbolList.h.

◆ getChar()

string EdIntSymbolList::getChar ( size_t pos ) const

virtual

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 264 of file IntSymbolList.cpp.

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

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

◆ getContent()

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

inlinevirtualinherited

Implements bpp::CoreSymbolList< T >.

Definition at line 178 of file SymbolList.h.

◆ getElement()

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

inlinevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::CoreSymbolList< T >.

Definition at line 220 of file SymbolList.h.

◆ getListener() [1/2]

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

inlinevirtualinherited

Implements bpp::EdCoreSymbolList< T >.

Definition at line 432 of file SymbolList.h.

◆ getListener() [2/2]

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

inlinevirtualinherited

Implements bpp::EdCoreSymbolList< T >.

Definition at line 425 of file SymbolList.h.

◆ getNumberOfListeners()

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

inlinevirtualinherited

Implements bpp::EdCoreSymbolList< T >.

Definition at line 423 of file SymbolList.h.

◆ 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()

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

inlinevirtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::CoreSymbolList< T >.

Definition at line 227 of file SymbolList.h.

◆ operator()() [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]

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

The assignment operator.

Definition at line 194 of file IntSymbolList.cpp.

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

◆ operator=() [2/2]

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

The generic assignment operator.

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

◆ operator[]() [1/2]

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

inlinevirtualinherited

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

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::CoreSymbolList< T >.

Definition at line 236 of file SymbolList.h.

◆ operator[]() [2/2]

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

inlinevirtualinherited

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

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

Implements bpp::CoreSymbolList< T >.

Definition at line 234 of file SymbolList.h.

◆ propagateEvents() [1/2]

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

inlineprotectedvirtualinherited

Implements bpp::EdCoreSymbolList< T >.

Definition at line 545 of file SymbolList.h.

◆ propagateEvents() [2/2]

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

inlineprotectedvirtualinherited

Implements bpp::EdCoreSymbolList< T >.

Definition at line 544 of file SymbolList.h.

◆ removeCoreSymbolListListener() [1/2]

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

inlinevirtualinherited

Definition at line 444 of file SymbolList.h.

◆ removeCoreSymbolListListener() [2/2]

template<class T >

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

pure virtualinherited

Implemented in bpp::EdSymbolList< T >.

◆ setContent() [1/3]

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

virtual

Reimplemented from bpp::EdSymbolList< int >.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 222 of file IntSymbolList.cpp.

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

◆ setContent() [2/3]

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

virtual

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 202 of file IntSymbolList.cpp.

References bpp::SymbolList< int >::getAlphabet().

Referenced by EdIntSymbolList(), and bpp::SequenceWithAnnotation::setContent().

◆ setContent() [3/3]

template<class T >

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

pure virtualinherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internaly stored.

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

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

◆ setElement() [1/3]

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

inlinevirtualinherited

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 410 of file SymbolList.h.

◆ setElement() [2/3]

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

virtual

Definition at line 257 of file IntSymbolList.cpp.

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

◆ setElement() [3/3]

template<class T >

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

pure virtualinherited

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

Parameters

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

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

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

◆ shuffle()

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

inlinevirtualinherited

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

Implements bpp::CruxSymbolList.

Definition at line 238 of file SymbolList.h.

◆ size()

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

inlinevirtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::CruxSymbolList.

Definition at line 171 of file SymbolList.h.

◆ toString()

string EdIntSymbolList::toString ( ) const

virtual

Convert the list as a string.

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

Returns: The whole list as a string.

Reimplemented from bpp::SymbolList< int >.

Definition at line 236 of file IntSymbolList.cpp.

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

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::SymbolList< int >::alphabet_

privateinherited

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

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

Definition at line 79 of file SymbolList.h.

◆ content_

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

protectedinherited

The list content.

Definition at line 85 of file SymbolList.h.

◆ listeners_

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

protectedinherited

Contains the listeners.

Definition at line 257 of file SymbolList.h.

◆ propagateEvents_

bool bpp::EdSymbolList< int >::propagateEvents_

privateinherited

Definition at line 251 of file SymbolList.h.

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Events handling

Events handling

Detailed Description

Constructor & Destructor Documentation

◆ EdIntSymbolList() [1/5]

◆ EdIntSymbolList() [2/5]

◆ EdIntSymbolList() [3/5]

◆ EdIntSymbolList() [4/5]

◆ EdIntSymbolList() [5/5]

◆ ~EdIntSymbolList()

Member Function Documentation

◆ addCoreSymbolListListener() [1/2]

◆ addCoreSymbolListListener() [2/2]

◆ addElement() [1/6]

◆ addElement() [2/6]

◆ addElement() [3/6]

◆ addElement() [4/6]

◆ addElement() [5/6]

◆ addElement() [6/6]

◆ addIntSymbolListListener()

◆ afterSequenceChanged() [1/2]

◆ afterSequenceChanged() [2/2]

◆ afterSequenceDeleted() [1/2]

◆ afterSequenceDeleted() [2/2]

◆ afterSequenceInserted() [1/2]

◆ afterSequenceInserted() [2/2]

◆ afterSequenceSubstituted() [1/2]

◆ afterSequenceSubstituted() [2/2]

◆ beforeSequenceChanged() [1/2]

◆ beforeSequenceChanged() [2/2]

◆ beforeSequenceDeleted() [1/2]

◆ beforeSequenceDeleted() [2/2]

◆ beforeSequenceInserted() [1/2]

◆ beforeSequenceInserted() [2/2]

◆ beforeSequenceSubstituted() [1/2]

◆ beforeSequenceSubstituted() [2/2]

◆ clone()

◆ deleteElement()

◆ deleteElements()

◆ fireAfterSequenceChanged() [1/2]

◆ fireAfterSequenceChanged() [2/2]

◆ fireAfterSequenceDeleted() [1/2]

◆ fireAfterSequenceDeleted() [2/2]

◆ fireAfterSequenceInserted() [1/2]

◆ fireAfterSequenceInserted() [2/2]

◆ fireAfterSequenceSubstituted() [1/2]

◆ fireAfterSequenceSubstituted() [2/2]

◆ fireBeforeSequenceChanged() [1/2]

◆ fireBeforeSequenceChanged() [2/2]

◆ fireBeforeSequenceDeleted() [1/2]

◆ fireBeforeSequenceDeleted() [2/2]

◆ fireBeforeSequenceInserted() [1/2]

◆ fireBeforeSequenceInserted() [2/2]

◆ fireBeforeSequenceSubstituted() [1/2]

◆ fireBeforeSequenceSubstituted() [2/2]

◆ getAlphabet()

◆ getChar()

◆ 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() [1/2]

◆ removeCoreSymbolListListener() [2/2]

◆ setContent() [1/3]