The AbstractSequenceSymbolList virtual class : SymbolList<T> is built, there. More...

#include <Bpp/Seq/CoreSequenceSymbolList.h>

Inheritance diagram for bpp::AbstractSequenceSymbolList< T >:

Collaboration diagram for bpp::AbstractSequenceSymbolList< T >:

Public Member Functions
virtual	~AbstractSequenceSymbolList ()

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

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

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

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...

void	addElement (const T &v)
	Add a character to the end of the list. More...

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

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

virtual const T &	getElement (size_t pos) const
	Get the element at position 'pos' as a character. More...

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

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

virtual T &	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	operator() (size_t siteIndex, int state) const

virtual const Comments &	getComments () const =0
	Get the comments. More...

virtual void	setComments (const Comments &comments)=0
	Set the comments. More...

virtual void	clearComments ()=0
	Clear the comments. More...

The Clonable interface
AbstractSequenceSymbolList *	clone () const =0

Setting/getting the name of the sequence.
virtual const std::string &	getName () const =0
	Get the name of this sequence. More...

virtual void	setName (const std::string &name)=0
	Set the name of this sequence. More...

Adjusting the size of the sequence.
virtual void	setToSizeR (size_t newSize)=0
	Set up the size of a sequence from the right side. More...

virtual void	setToSizeL (size_t newSize)=0
	Set up the size of a sequence from the left side. More...

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

Private Attributes
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::AbstractSequenceSymbolList< T >

The AbstractSequenceSymbolList virtual class : SymbolList<T> is built, there.

Definition at line 93 of file CoreSequenceSymbolList.h.

Constructor & Destructor Documentation

◆ ~AbstractSequenceSymbolList()

template<class T >

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

inlinevirtual

Definition at line 107 of file CoreSequenceSymbolList.h.

Member Function Documentation

◆ addElement() [1/2]

template<class T >

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

inlinevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Implements bpp::CoreSymbolList< T >.

Reimplemented in bpp::EdSymbolList< T >.

Definition at line 199 of file SymbolList.h.

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

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

◆ addElement() [2/2]

template<class T >

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

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.

Implements bpp::CoreSymbolList< T >.

Reimplemented in bpp::EdSymbolList< T >.

Definition at line 204 of file SymbolList.h.

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

◆ clearComments()

virtual void bpp::CoreSequence::clearComments ( )

pure virtualinherited

Clear the comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

◆ clone()

template<class T >

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

pure virtual

Implements bpp::CoreSequenceSymbolList< T >.

◆ deleteElement()

template<class T >

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

inlinevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolList.

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

Definition at line 185 of file SymbolList.h.

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

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

◆ deleteElements()

template<class T >

void bpp::SymbolList< T >::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.

Implements bpp::CruxSymbolList.

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

Definition at line 192 of file SymbolList.h.

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

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

◆ getAlphabet()

template<class T >

const Alphabet* bpp::SymbolList< T >::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.

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

Referenced by bpp::SequenceWithQualityTools::complement(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithAnnotation::merge(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceWithQualityTools::reverseTranscript(), bpp::SequenceWithQualityTools::subseq(), and bpp::SequenceWithQualityTools::transcript().

◆ getComments()

virtual const Comments& bpp::CoreSequence::getComments ( ) const

pure virtualinherited

Get the comments.

Returns: The comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::getComments(), bpp::AbstractSequenceContainer::getComments(), bpp::VectorProbabilisticSequenceContainer::getComments(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getContent()

template<class T >

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

inlinevirtualinherited

Implements bpp::CoreSymbolList< T >.

Definition at line 178 of file SymbolList.h.

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

◆ getElement()

template<class T >

virtual const T& bpp::SymbolList< T >::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.

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

◆ getName()

virtual const std::string& bpp::CoreSequence::getName ( ) const

pure virtualinherited

Get the name of this sequence.

Returns: This sequence name.

Implemented in bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::VectorSequenceContainer::deleteSequenceByName(), bpp::AbstractProbabilisticSequenceContainer::getName(), bpp::AbstractSequenceContainer::getName(), bpp::VectorProbabilisticSequenceContainer::getName(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::VectorSequenceContainer::getSequenceByName(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::VectorSequenceContainer::removeSequenceByName(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

◆ getStateValueAt()

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().

◆ getValue()

template<class T >

virtual const T& bpp::SymbolList< T >::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.

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

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

◆ operator()()

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[]() [1/2]

template<class T >

virtual T& bpp::SymbolList< T >::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.

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

◆ operator[]() [2/2]

template<class T >

virtual const T& bpp::SymbolList< T >::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.

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

◆ setComments()

virtual void bpp::CoreSequence::setComments ( const Comments & comments )

pure virtualinherited

Set the comments.

Parameters

comments The new comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setComments(), bpp::VectorSequenceContainer::setComments(), and bpp::SequenceTools::subseq().

◆ setContent()

template<class T >

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

inlinevirtualinherited

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< T >.

Reimplemented in bpp::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SequenceWithAnnotation, bpp::BasicSequence, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

Definition at line 173 of file SymbolList.h.

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

Referenced by bpp::BasicIntSymbolList::setContent(), bpp::EdSymbolList< T >::setContent(), and bpp::SymbolList< T >::SymbolList().

◆ setElement()

template<class T >

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

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.

Implements bpp::CoreSymbolList< T >.

Reimplemented in bpp::EdSymbolList< T >.

Definition at line 212 of file SymbolList.h.

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

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

◆ setName()

virtual void bpp::CoreSequence::setName ( const std::string & name )

pure virtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::SequenceTools::getPutativeHaplotypes(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::PhredPhd::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setSequenceNames(), bpp::VectorSequenceContainer::setSequenceNames(), and bpp::SequenceTools::subseq().

◆ setToSizeL()

virtual void bpp::CoreSequence::setToSizeL ( size_t newSize )

pure virtualinherited

Set up the size of a sequence from the left side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize The new size of the sequence.

Implemented in bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

◆ setToSizeR()

virtual void bpp::CoreSequence::setToSizeR ( size_t newSize )

pure virtualinherited

Set up the size of a sequence from the right side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize The new size of the sequence.

Implemented in bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

Referenced by bpp::SequenceTools::concatenate().

◆ shuffle()

template<class T >

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

inlinevirtualinherited

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

Implements bpp::CruxSymbolList.

Definition at line 238 of file SymbolList.h.

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

◆ size()

template<class T >

size_t bpp::SymbolList< T >::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.

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

Referenced by bpp::SymbolList< T >::addElement(), bpp::SymbolList< T >::deleteElement(), bpp::SymbolList< T >::deleteElements(), bpp::SymbolList< T >::getElement(), bpp::SymbolList< T >::getValue(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SymbolList< T >::setElement(), and bpp::SequenceWithQualityTools::subseq().

◆ toString()

template<class T >

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

inlinevirtualinherited

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.

Reimplemented in bpp::BasicSequence, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

Definition at line 180 of file SymbolList.h.

Member Data Documentation

◆ alphabet_

template<class T >

const Alphabet* bpp::SymbolList< T >::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.

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

◆ content_

template<class T >

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

protectedinherited

The list content.

Definition at line 85 of file SymbolList.h.

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

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

Bpp/Seq/CoreSequenceSymbolList.h

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

template<class T> class bpp::AbstractSequenceSymbolList< T >

Constructor & Destructor Documentation

◆ ~AbstractSequenceSymbolList()

Member Function Documentation

◆ addElement() [1/2]

◆ addElement() [2/2]

◆ clearComments()

◆ clone()

◆ deleteElement()

◆ deleteElements()

◆ getAlphabet()

◆ getComments()

◆ getContent()

◆ getElement()

◆ getName()

◆ getStateValueAt()

◆ getValue()

◆ operator()()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setComments()

◆ setContent()

◆ setElement()

◆ setName()

◆ setToSizeL()

◆ setToSizeR()

◆ shuffle()

◆ size()

◆ toString()

Member Data Documentation

◆ alphabet_

◆ content_

template<class T>
class bpp::AbstractSequenceSymbolList< T >