bpp::AbstractTemplateSymbolList< T > Class Template Reference

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

#include <Bpp/Seq/SymbolList.h>

Inheritance diagram for bpp::AbstractTemplateSymbolList< T >:

Collaboration diagram for bpp::AbstractTemplateSymbolList< T >:

Public Member Functions
	AbstractTemplateSymbolList (std::shared_ptr< const Alphabet > alpha)
	Build a new void SymbolList object with the specified alphabet. More...
	AbstractTemplateSymbolList (const std::vector< T > &list, std::shared_ptr< const Alphabet > alpha)
	Build a new SymbolList object with the specified alphabet. The content of the site is initialized from a vector of T objects. More...
	AbstractTemplateSymbolList (const AbstractTemplateSymbolList< T > &list)
	The generic copy constructor. More...
	AbstractTemplateSymbolList (const TemplateCoreSymbolListInterface< T > &list)
	The copy constructor. More...
AbstractTemplateSymbolList< T > &	operator= (const TemplateCoreSymbolListInterface< T > &list)
	The generic assignment operator. More...
AbstractTemplateSymbolList< T > &	operator= (const AbstractTemplateSymbolList< T > &list)
	The assignment operator. More...
virtual	~AbstractTemplateSymbolList ()
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the list. More...
const Alphabet &	alphabet () const override
	Get the alphabet associated to the list. More...
size_t	size () const override
	Get the number of elements in the list. More...
virtual void	setContent (const std::vector< T > &list) override
	Set the whole content of the list. More...
virtual const std::vector< T > &	getContent () const override
virtual std::string	toString () const override
	Convert the list as a string. 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	addElement (const T &c) override
	Add a character to the end of the list. More...
void	addElement (size_t pos, const T &c) override
	Add a character at a certain position in the list. More...
void	setElement (size_t pos, const T &c) override
	Set the element at position 'pos' to character 'c'. More...
const T &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...
const T &	getValue (size_t pos) const override
	checked access to a character in list. More...
const T &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...
T &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. More...
void	shuffle () override
	Randomly shuffle the content of the list, with linear complexity. More...
virtual double	getStateValueAt (size_t position, int state) const =0
	get value of a state at a position More...
virtual double	operator() (size_t position, int state) const =0
	get value of a state at a position More...
The Clonable interface
TemplateCoreSymbolListInterface *	clone () const override=0

Protected Attributes
std::vector< T >	content_
	The list content. More...

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

Detailed Description

template<class T>
class bpp::AbstractTemplateSymbolList< T >

A partial implementation of a SymbolList object.

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

See also

Alphabet

Definition at line 32 of file SymbolList.h.

Constructor & Destructor Documentation

AbstractTemplateSymbolList() [1/4]

template<class T >

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

inline

Build a new void SymbolList object with the specified alphabet.

Parameters

alpha

The alphabet to use.

Definition at line 55 of file SymbolList.h.

AbstractTemplateSymbolList() [2/4]

template<class T >

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

inline

Build a new SymbolList object with the specified alphabet. The content of the site is initialized from a vector of T objects.

Parameters

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

Definition at line 65 of file SymbolList.h.

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

AbstractTemplateSymbolList() [3/4]

template<class T >

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

inline

The generic copy constructor.

Definition at line 74 of file SymbolList.h.

AbstractTemplateSymbolList() [4/4]

template<class T >

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

inline

The copy constructor.

Definition at line 82 of file SymbolList.h.

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

~AbstractTemplateSymbolList()

template<class T >

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

inlinevirtual

Definition at line 117 of file SymbolList.h.

Member Function Documentation

addElement() [1/2]

template<class T >

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

inlineoverridevirtual

Add a character to the end of the list.

Parameters

c	The character to add.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

Definition at line 152 of file SymbolList.h.

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

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

addElement() [2/2]

template<class T >

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

inlineoverridevirtual

Add a character at a certain position in the list.

Parameters

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

Implements bpp::TemplateCoreSymbolListInterface< T >.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

Definition at line 157 of file SymbolList.h.

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

alphabet()

template<class T >

const Alphabet& bpp::AbstractTemplateSymbolList< T >::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 122 of file SymbolList.h.

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

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

clone()

template<class T >

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

overridepure virtualinherited

Implements bpp::CruxSymbolListInterface.

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

deleteElement()

template<class T >

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

inlineoverridevirtual

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 138 of file SymbolList.h.

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

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

deleteElements()

template<class T >

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

inlineoverridevirtual

Remove the elements at position 'pos'.

Parameters

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

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, and bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 145 of file SymbolList.h.

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

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

getAlphabet()

template<class T >

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< T >::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 120 of file SymbolList.h.

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

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

getContent()

template<class T >

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

inlineoverridevirtual

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 131 of file SymbolList.h.

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

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

getElement()

template<class T >

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

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 173 of file SymbolList.h.

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

getStateValueAt()

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

pure virtualinherited

get value of a state at a position

Parameters

position	position in the list
state	state in the alphabet

Returns

The state value at the given position.

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

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

getValue()

template<class T >

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

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 180 of file SymbolList.h.

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

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

operator()()

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

pure virtualinherited

get value of a state at a position

Short-cut for getStateValueAt.

Parameters

position	position in the list
state	state in the alphabet

Returns

The state value at the given position.

Implemented in bpp::ProbabilisticSymbolList, and bpp::IntSymbolList.

operator=() [1/2]

template<class T >

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

inline

The assignment operator.

Definition at line 109 of file SymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::alphabet_, and bpp::AbstractTemplateSymbolList< T >::content_.

operator=() [2/2]

template<class T >

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

inline

The generic assignment operator.

Definition at line 95 of file SymbolList.h.

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

Referenced by bpp::IntSymbolList::operator=(), bpp::EventDrivenIntSymbolList::operator=(), bpp::Site::operator=(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::operator=().

operator[]() [1/2]

template<class T >

const T& bpp::AbstractTemplateSymbolList< T >::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 187 of file SymbolList.h.

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

operator[]() [2/2]

template<class T >

T& bpp::AbstractTemplateSymbolList< T >::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 189 of file SymbolList.h.

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

setContent()

template<class T >

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

inlineoverridevirtual

Set the whole content of the list.

Parameters

list	The new content of the list.

See also

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

Implements bpp::TemplateCoreSymbolListInterface< T >.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::SequenceWithAnnotation, bpp::Sequence, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

Definition at line 126 of file SymbolList.h.

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

Referenced by bpp::AbstractTemplateSymbolList< T >::AbstractTemplateSymbolList(), bpp::IntSymbolList::setContent(), and bpp::AbstractTemplateEventDrivenSymbolList< T >::setContent().

setElement()

template<class T >

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

inlineoverridevirtual

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

Parameters

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

Implements bpp::TemplateCoreSymbolListInterface< T >.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

Definition at line 165 of file SymbolList.h.

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

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

shuffle()

template<class T >

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

inlineoverridevirtual

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

Implements bpp::CruxSymbolListInterface.

Definition at line 191 of file SymbolList.h.

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

size()

template<class T >

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

inlineoverridevirtual

Get the number of elements in the list.

Returns

The number of sites in the list.

Implements bpp::CruxSymbolListInterface.

Definition at line 124 of file SymbolList.h.

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

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

toString()

template<class T >

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

inlineoverridevirtual

Convert the list as a string.

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

Returns

The whole list as a string.

Implements bpp::CruxSymbolListInterface.

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

Definition at line 133 of file SymbolList.h.

Member Data Documentation

alphabet_

template<class T >

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

private

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

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

Definition at line 41 of file SymbolList.h.

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

content_

template<class T >

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

protected

The list content.

Definition at line 47 of file SymbolList.h.

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

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

• Bpp/Seq/SymbolList.h