A basic ProbabilisticSymbolList object. More...

#include <Bpp/Seq/ProbabilisticSymbolList.h>

Inheritance diagram for bpp::BasicProbabilisticSymbolList:

Collaboration diagram for bpp::BasicProbabilisticSymbolList:

Public Types
typedef Table< double >	DataTable

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

	BasicProbabilisticSymbolList (const DataTable &list, const Alphabet *alpha)
	Build a new BasicProbabilisticSymbolList object with the specified alphabet. More...

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

	BasicProbabilisticSymbolList (const CruxSymbolList &list)

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

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

BasicProbabilisticSymbolList &	operator= (const BasicProbabilisticSymbolList &list)
	The assignement operator. More...

virtual	~BasicProbabilisticSymbolList ()

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...

void	setContent (const std::vector< std::vector< double > > &list)
	Set the whole content of the list. More...

void	setContent (const DataTable &list)

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

void	addElement (const std::vector< double > &element)
	Add a character to the end of the list. More...

void	addElement (size_t pos, const std::vector< double > &element)
	Add a character at a certain position in the list. More...

void	setElement (size_t pos, const std::vector< double > &element)
	Set the element at position 'pos' to character 'c'. More...

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

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

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

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

const DataTable &	getTable () const

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

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

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

double	getStateValueAt (size_t siteIndex, int state) const

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

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

The Clonable interface
BasicProbabilisticSymbolList *	clone () const

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

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

Detailed Description

A basic 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 106 of file ProbabilisticSymbolList.h.

Member Typedef Documentation

◆ DataTable

typedef Table<double> bpp::BasicProbabilisticSymbolList::DataTable

Definition at line 110 of file ProbabilisticSymbolList.h.

Constructor & Destructor Documentation

◆ BasicProbabilisticSymbolList() [1/5]

BasicProbabilisticSymbolList::BasicProbabilisticSymbolList ( const Alphabet * alpha )

Build a new void BasicProbabilisticSymbolList object with the specified alphabet.

Parameters

alpha the alphabet to use.

Definition at line 51 of file ProbabilisticSymbolList.cpp.

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

Referenced by clone().

◆ BasicProbabilisticSymbolList() [2/5]

BasicProbabilisticSymbolList::BasicProbabilisticSymbolList	(	const DataTable &	list,
		const Alphabet *	alpha
	)

Build a new BasicProbabilisticSymbolList object with the specified alphabet.

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 57 of file ProbabilisticSymbolList.cpp.

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

◆ BasicProbabilisticSymbolList() [3/5]

BasicProbabilisticSymbolList::BasicProbabilisticSymbolList ( const ProbabilisticSymbolList & list )

The generic copy constructor.

Definition at line 66 of file ProbabilisticSymbolList.cpp.

◆ BasicProbabilisticSymbolList() [4/5]

BasicProbabilisticSymbolList::BasicProbabilisticSymbolList ( const CruxSymbolList & list )

Definition at line 74 of file ProbabilisticSymbolList.cpp.

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

◆ BasicProbabilisticSymbolList() [5/5]

BasicProbabilisticSymbolList::BasicProbabilisticSymbolList ( const BasicProbabilisticSymbolList & list )

The copy constructor.

Definition at line 70 of file ProbabilisticSymbolList.cpp.

◆ ~BasicProbabilisticSymbolList()

virtual bpp::BasicProbabilisticSymbolList::~BasicProbabilisticSymbolList ( )

inlinevirtual

Definition at line 180 of file ProbabilisticSymbolList.h.

Member Function Documentation

◆ addElement() [1/2]

void BasicProbabilisticSymbolList::addElement ( const std::vector< double > & c )

virtual

Add a character to the end of the list.

Parameters

c	The character to add.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 175 of file ProbabilisticSymbolList.cpp.

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

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet().

◆ addElement() [2/2]

void BasicProbabilisticSymbolList::addElement	(	size_t	pos,
		const std::vector< double > &	c
	)

virtual

Add a character at a certain position in the list.

Parameters

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

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 199 of file ProbabilisticSymbolList.cpp.

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

◆ clone()

BasicProbabilisticSymbolList* bpp::BasicProbabilisticSymbolList::clone ( ) const

inlinevirtual

Implements bpp::ProbabilisticSymbolList.

Definition at line 173 of file ProbabilisticSymbolList.h.

References BasicProbabilisticSymbolList().

◆ deleteElement()

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

inlinevirtual

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolList.

Definition at line 213 of file ProbabilisticSymbolList.h.

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

◆ deleteElements()

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

inlinevirtual

Remove the elements at position 'pos'.

Parameters

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

Implements bpp::CruxSymbolList.

Definition at line 215 of file ProbabilisticSymbolList.h.

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

◆ getAlphabet()

const Alphabet* bpp::BasicProbabilisticSymbolList::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::CruxSymbolList.

Definition at line 183 of file ProbabilisticSymbolList.h.

References alphabet_.

Referenced by BasicProbabilisticSymbolList(), getStateValueAt(), and operator()().

◆ getContent()

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

inlinevirtual

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 220 of file ProbabilisticSymbolList.h.

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

Referenced by bpp::BasicProbabilisticSequence::getContent().

◆ getElement()

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

inlinevirtual

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 208 of file ProbabilisticSymbolList.h.

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

Referenced by getValue().

◆ getStateValueAt()

double bpp::BasicProbabilisticSymbolList::getStateValueAt	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtual

Reimplemented from bpp::CruxSymbolList.

Definition at line 239 of file ProbabilisticSymbolList.h.

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

◆ getTable()

const DataTable& bpp::BasicProbabilisticSymbolList::getTable ( ) const

inlinevirtual

Implements bpp::ProbabilisticSymbolList.

Definition at line 222 of file ProbabilisticSymbolList.h.

References content_.

Referenced by bpp::BasicProbabilisticSequence::getTable().

◆ getValue()

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

inlinevirtual

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< std::vector< double > >.

Definition at line 224 of file ProbabilisticSymbolList.h.

References getElement().

◆ operator()()

double bpp::BasicProbabilisticSymbolList::operator()	(	size_t	siteIndex,
		int	state
	)		const

inlinevirtual

Reimplemented from bpp::CruxSymbolList.

Definition at line 246 of file ProbabilisticSymbolList.h.

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

◆ operator=() [1/2]

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

The assignement operator.

Definition at line 96 of file ProbabilisticSymbolList.cpp.

References alphabet_, and content_.

◆ operator=() [2/2]

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

The generic assignment operator.

Definition at line 89 of file ProbabilisticSymbolList.cpp.

References alphabet_, bpp::CruxSymbolList::getAlphabet(), bpp::CoreSymbolList< T >::getContent(), and setContent().

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

◆ operator[]() [1/2]

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

inlinevirtual

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< std::vector< double > >.

Definition at line 234 of file ProbabilisticSymbolList.h.

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

◆ operator[]() [2/2]

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

inlinevirtual

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< std::vector< double > >.

Definition at line 229 of file ProbabilisticSymbolList.h.

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

◆ setContent() [1/2]

void BasicProbabilisticSymbolList::setContent ( const DataTable & list )

Definition at line 105 of file ProbabilisticSymbolList.cpp.

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

◆ setContent() [2/2]

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

virtual

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.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 161 of file ProbabilisticSymbolList.cpp.

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

Referenced by BasicProbabilisticSymbolList(), operator=(), and bpp::BasicProbabilisticSequence::setContent().

◆ setElement()

void BasicProbabilisticSymbolList::setElement	(	size_t	pos,
		const std::vector< double > &	c
	)

virtual

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

Parameters

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

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 216 of file ProbabilisticSymbolList.cpp.

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

◆ shuffle()

void bpp::BasicProbabilisticSymbolList::shuffle ( )

inlinevirtual

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

Implements bpp::CruxSymbolList.

Definition at line 251 of file ProbabilisticSymbolList.h.

◆ size()

size_t bpp::BasicProbabilisticSymbolList::size ( ) const

inlinevirtual

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::CruxSymbolList.

Definition at line 185 of file ProbabilisticSymbolList.h.

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

Referenced by BasicProbabilisticSymbolList(), and setContent().

◆ toString()

string BasicProbabilisticSymbolList::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.

Implements bpp::CruxSymbolList.

Definition at line 136 of file ProbabilisticSymbolList.cpp.

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

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::BasicProbabilisticSymbolList::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 119 of file ProbabilisticSymbolList.h.

Referenced by BasicProbabilisticSymbolList(), getAlphabet(), operator=(), and setContent().

◆ content_

DataTable bpp::BasicProbabilisticSymbolList::content_

protected

The list content.

Definition at line 125 of file ProbabilisticSymbolList.h.

Referenced by addElement(), BasicProbabilisticSymbolList(), deleteElement(), deleteElements(), getContent(), getElement(), getStateValueAt(), getTable(), operator()(), operator=(), operator[](), 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

◆ DataTable

Constructor & Destructor Documentation

◆ BasicProbabilisticSymbolList() [1/5]

◆ BasicProbabilisticSymbolList() [2/5]

◆ BasicProbabilisticSymbolList() [3/5]

◆ BasicProbabilisticSymbolList() [4/5]

◆ BasicProbabilisticSymbolList() [5/5]

◆ ~BasicProbabilisticSymbolList()

Member Function Documentation

◆ addElement() [1/2]

◆ addElement() [2/2]

◆ clone()

◆ deleteElement()

◆ deleteElements()

◆ getAlphabet()

◆ getContent()

◆ getElement()

◆ getStateValueAt()

◆ getTable()

◆ getValue()

◆ operator()()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setContent() [1/2]

◆ setContent() [2/2]

◆ setElement()

◆ shuffle()

◆ size()

◆ toString()

Member Data Documentation

◆ alphabet_

◆ content_