#include <Bpp/Seq/ProbabilisticSymbolList.h>

Inheritance diagram for bpp::ProbabilisticSymbolList:

Collaboration diagram for bpp::ProbabilisticSymbolList:

Public Types
typedef std::vector< double >	SymbolType

typedef Table< double >	DTable

Public Member Functions
	ProbabilisticSymbolList (std::shared_ptr< const Alphabet > &alpha)
	Build a new void ProbabilisticSymbolList object with the specified alphabet. More...

	ProbabilisticSymbolList (const DTable &list, std::shared_ptr< const Alphabet > &alpha)
	Build a new ProbabilisticSymbolList object with the specified alphabet and constant as a DataTable. More...

	ProbabilisticSymbolList (const std::vector< std::vector< double >> &list, std::shared_ptr< const Alphabet > &alpha)
	Build a new ProbabilisticSymbolList object with the specified alphabet and constant as a VVdouble. More...

	ProbabilisticSymbolList (const ProbabilisticSymbolListInterface &list)
	The generic copy constructor. More...

	ProbabilisticSymbolList (const CruxSymbolListInterface &list)

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

ProbabilisticSymbolList &	operator= (const ProbabilisticSymbolListInterface &list)
	The generic assignment operator. More...

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

virtual	~ProbabilisticSymbolList ()

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...

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

void	setContent (const DTable &list) override

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

void	addElement (const std::vector< double > &element) override

void	addElement (size_t pos, const std::vector< double > &element) override

void	setElement (size_t pos, const std::vector< double > &element) override

const std::vector< double > &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...

virtual void	deleteElement (size_t pos) override
	Remove the element at position 'pos'. More...

virtual void	deleteElements (size_t pos, size_t len) override
	Remove the elements at position 'pos'. More...

const std::vector< std::vector< double > > &	getContent () const override

const DTable &	getTable () const override

const std::vector< double > &	getValue (size_t pos) const override
	checked access to a character in list. More...

const std::vector< double > &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...

std::vector< double > &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. 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...

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

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

The Clonable interface
ProbabilisticSymbolList *	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...

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

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

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

Protected Attributes
DTable	content_
	The list content. More...

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

Detailed Description

ProbabilisticSymbolList object.

This is a general purpose container, containing an ordered list of elements. The states represented by the elements are defined by an alphabet object, which is passed to the list constructor by a pointer.

See also: Alphabet

Definition at line 61 of file ProbabilisticSymbolList.h.

Member Typedef Documentation

◆ DTable

typedef Table<double> bpp::ProbabilisticSymbolListInterface::DTable

inherited

Definition at line 35 of file ProbabilisticSymbolList.h.

◆ SymbolType

typedef std::vector<double> bpp::ProbabilisticSymbolListInterface::SymbolType

inherited

Definition at line 34 of file ProbabilisticSymbolList.h.

Constructor & Destructor Documentation

◆ ProbabilisticSymbolList() [1/6]

ProbabilisticSymbolList::ProbabilisticSymbolList ( std::shared_ptr< const Alphabet > & alpha )

Build a new void ProbabilisticSymbolList object with the specified alphabet.

Parameters

alpha the alphabet to use.

Definition at line 15 of file ProbabilisticSymbolList.cpp.

References alphabet_, content_, and bpp::Table< class >::setRowNames().

Referenced by clone().

◆ ProbabilisticSymbolList() [2/6]

ProbabilisticSymbolList::ProbabilisticSymbolList	(	const DTable &	list,
		std::shared_ptr< const Alphabet > &	alpha
	)

Build a new ProbabilisticSymbolList object with the specified alphabet and constant as a DataTable.

Parameters

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

Exceptions

If	the content is internally inconsistent, or is inconsistent with the specified alphabet.

Definition at line 21 of file ProbabilisticSymbolList.cpp.

References content_, bpp::ProbabilisticSymbolListInterface::setContent(), and bpp::Table< class >::setRowNames().

◆ ProbabilisticSymbolList() [3/6]

ProbabilisticSymbolList::ProbabilisticSymbolList	(	const std::vector< std::vector< double >> &	list,
		std::shared_ptr< const Alphabet > &	alpha
	)

Build a new ProbabilisticSymbolList object with the specified alphabet and constant as a VVdouble.

Parameters

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

Exceptions

If	the content is internally inconsistent, or is inconsistent with the specified alphabet.

Definition at line 28 of file ProbabilisticSymbolList.cpp.

References content_, bpp::ProbabilisticSymbolListInterface::setContent(), and bpp::Table< class >::setRowNames().

◆ ProbabilisticSymbolList() [4/6]

ProbabilisticSymbolList::ProbabilisticSymbolList ( const ProbabilisticSymbolListInterface & list )

The generic copy constructor.

Definition at line 37 of file ProbabilisticSymbolList.cpp.

◆ ProbabilisticSymbolList() [5/6]

ProbabilisticSymbolList::ProbabilisticSymbolList ( const CruxSymbolListInterface & list )

Definition at line 45 of file ProbabilisticSymbolList.cpp.

References alphabet_, content_, getAlphabet(), bpp::CruxSymbolListInterface::getStateValueAt(), bpp::Table< class >::setRowNames(), and size().

◆ ProbabilisticSymbolList() [6/6]

ProbabilisticSymbolList::ProbabilisticSymbolList ( const ProbabilisticSymbolList & list )

The copy constructor.

Definition at line 41 of file ProbabilisticSymbolList.cpp.

◆ ~ProbabilisticSymbolList()

virtual bpp::ProbabilisticSymbolList::~ProbabilisticSymbolList ( )

inlinevirtual

Definition at line 139 of file ProbabilisticSymbolList.h.

Member Function Documentation

◆ addElement() [1/4]

void ProbabilisticSymbolList::addElement ( const std::vector< double > & element )

override

Definition at line 146 of file ProbabilisticSymbolList.cpp.

References bpp::Table< class >::addColumn(), content_, and bpp::Table< class >::getNumberOfRows().

◆ addElement() [2/4]

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() [3/4]

void ProbabilisticSymbolList::addElement	(	size_t	pos,
		const std::vector< double > &	element
	)

override

Definition at line 171 of file ProbabilisticSymbolList.cpp.

References bpp::Table< class >::addColumn(), content_, and bpp::Table< class >::getNumberOfRows().

◆ addElement() [4/4]

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 >.

◆ alphabet()

const Alphabet& bpp::ProbabilisticSymbolList::alphabet ( ) const

inlineoverridevirtual

Get the alphabet associated to the list.

Returns: A const reference to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 144 of file ProbabilisticSymbolList.h.

References alphabet_.

◆ clone()

ProbabilisticSymbolList* bpp::ProbabilisticSymbolList::clone ( ) const

inlineoverridevirtual

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 132 of file ProbabilisticSymbolList.h.

References ProbabilisticSymbolList().

◆ deleteElement()

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

inlineoverridevirtual

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Definition at line 172 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::deleteColumn().

◆ deleteElements()

virtual void bpp::ProbabilisticSymbolList::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.

Implements bpp::CruxSymbolListInterface.

Definition at line 177 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::deleteColumns().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::ProbabilisticSymbolList::getAlphabet ( ) const

inlineoverridevirtual

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 142 of file ProbabilisticSymbolList.h.

References alphabet_.

Referenced by getStateValueAt(), bpp::Pasta::nextSequence(), operator()(), ProbabilisticSymbolList(), and bpp::Pasta::writeSequence().

◆ getContent()

const std::vector<std::vector<double> >& bpp::ProbabilisticSymbolList::getContent ( ) const

inlineoverridevirtual

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 182 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::getData().

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

◆ getElement()

const std::vector<double>& bpp::ProbabilisticSymbolList::getElement ( size_t pos ) const

inlineoverridevirtual

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 167 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::getColumn().

Referenced by getValue().

◆ getStateValueAt()

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

inlineoverridevirtual

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.

Definition at line 207 of file ProbabilisticSymbolList.h.

References content_, getAlphabet(), bpp::Table< class >::getColumn(), and bpp::Table< class >::getNumberOfColumns().

◆ getTable()

const DTable& bpp::ProbabilisticSymbolList::getTable ( ) const

inlineoverridevirtual

Implements bpp::ProbabilisticSymbolListInterface.

Definition at line 187 of file ProbabilisticSymbolList.h.

References content_.

◆ getValue()

const std::vector<double>& bpp::ProbabilisticSymbolList::getValue ( size_t pos ) const

inlineoverridevirtual

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 192 of file ProbabilisticSymbolList.h.

References getElement().

◆ operator()()

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

inlineoverridevirtual

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 214 of file ProbabilisticSymbolList.h.

References content_, getAlphabet(), and bpp::Table< class >::getColumn().

◆ operator=() [1/2]

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

The assignment operator.

Definition at line 67 of file ProbabilisticSymbolList.cpp.

References alphabet_, and content_.

◆ operator=() [2/2]

ProbabilisticSymbolList & ProbabilisticSymbolList::operator= ( const ProbabilisticSymbolListInterface & list )

The generic assignment operator.

Definition at line 60 of file ProbabilisticSymbolList.cpp.

References alphabet_, bpp::CruxSymbolListInterface::getAlphabet(), bpp::TemplateCoreSymbolListInterface< T >::getContent(), and bpp::ProbabilisticSymbolListInterface::setContent().

Referenced by bpp::ProbabilisticSequence::operator=(), and bpp::ProbabilisticSite::operator=().

◆ operator[]() [1/2]

const std::vector<double>& bpp::ProbabilisticSymbolList::operator[] ( size_t pos ) const

inlineoverridevirtual

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 197 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::getColumn().

◆ operator[]() [2/2]

std::vector<double>& bpp::ProbabilisticSymbolList::operator[] ( size_t pos )

inlineoverridevirtual

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 202 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::getColumn().

◆ setContent() [1/4]

void ProbabilisticSymbolList::setContent ( const DTable & list )

overridevirtual

Implements bpp::ProbabilisticSymbolListInterface.

Definition at line 76 of file ProbabilisticSymbolList.cpp.

References alphabet_, content_, bpp::Table< class >::getNumberOfRows(), bpp::Table< class >::getRowNames(), bpp::Table< class >::hasRowNames(), bpp::Table< class >::setRowNames(), size(), and bpp::TextTools::toString().

◆ setContent() [2/4]

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

override

Definition at line 132 of file ProbabilisticSymbolList.cpp.

References alphabet_, content_, bpp::Table< class >::setRowNames(), and size().

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

◆ 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 operator=(), and ProbabilisticSymbolList().

◆ setElement() [1/2]

void ProbabilisticSymbolList::setElement	(	size_t	pos,
		const std::vector< double > &	element
	)

override

Definition at line 188 of file ProbabilisticSymbolList.cpp.

References content_, bpp::Table< class >::getNumberOfRows(), and bpp::Table< class >::setColumn().

◆ setElement() [2/2]

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 >.

◆ shuffle()

void bpp::ProbabilisticSymbolList::shuffle ( )

inlineoverridevirtual

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

Implements bpp::CruxSymbolListInterface.

Definition at line 219 of file ProbabilisticSymbolList.h.

◆ size()

size_t bpp::ProbabilisticSymbolList::size ( ) const

inlineoverridevirtual

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::CruxSymbolListInterface.

Definition at line 146 of file ProbabilisticSymbolList.h.

References content_, and bpp::Table< class >::getNumberOfColumns().

Referenced by bpp::SequenceContainerTools::getFrequencies(), bpp::ProbabilisticSite::getStateValueAt(), bpp::ProbabilisticSequence::getStateValueAt(), ProbabilisticSymbolList(), and setContent().

◆ toString()

string ProbabilisticSymbolList::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.

Implements bpp::CruxSymbolListInterface.

Definition at line 108 of file ProbabilisticSymbolList.cpp.

References content_, bpp::Table< class >::getNumberOfColumns(), bpp::Table< class >::getNumberOfRows(), and bpp::Table< class >::getRowName().

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::ProbabilisticSymbolList::alphabet_

private

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

To apply another alphabet to the list requires creating another list.

Definition at line 71 of file ProbabilisticSymbolList.h.

Referenced by alphabet(), getAlphabet(), operator=(), ProbabilisticSymbolList(), and setContent().

◆ content_

DTable bpp::ProbabilisticSymbolList::content_

protected

The list content.

Definition at line 77 of file ProbabilisticSymbolList.h.

Referenced by addElement(), deleteElement(), deleteElements(), getContent(), getElement(), getStateValueAt(), getTable(), operator()(), operator=(), operator[](), ProbabilisticSymbolList(), setContent(), setElement(), size(), and toString().

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

Bpp/Seq/ProbabilisticSymbolList.h
Bpp/Seq/ProbabilisticSymbolList.cpp

Public Types

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

◆ DTable

◆ SymbolType

Constructor & Destructor Documentation

◆ ProbabilisticSymbolList() [1/6]

◆ ProbabilisticSymbolList() [2/6]

◆ ProbabilisticSymbolList() [3/6]

◆ ProbabilisticSymbolList() [4/6]

◆ ProbabilisticSymbolList() [5/6]

◆ ProbabilisticSymbolList() [6/6]

◆ ~ProbabilisticSymbolList()

Member Function Documentation

◆ addElement() [1/4]

◆ addElement() [2/4]

◆ addElement() [3/4]

◆ addElement() [4/4]

◆ alphabet()

◆ clone()

◆ deleteElement()

◆ deleteElements()

◆ getAlphabet()

◆ getContent()

◆ getElement()

◆ getStateValueAt()

◆ getTable()

◆ getValue()

◆ operator()()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setContent() [1/4]

◆ setContent() [2/4]

◆ setContent() [3/4]

◆ setContent() [4/4]

◆ setElement() [1/2]

◆ setElement() [2/2]

◆ shuffle()

◆ size()

◆ toString()

Member Data Documentation

◆ alphabet_

◆ content_