The CoreSequenceSymbolList interface. More...

#include <Bpp/Seq/CoreSequenceSymbolList.h>

Inheritance diagram for bpp::CoreSequenceSymbolList< T >:

Collaboration diagram for bpp::CoreSequenceSymbolList< T >:

Public Member Functions
virtual	~CoreSequenceSymbolList ()

virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the list. More...

virtual size_t	size () const =0
	Get the number of elements in the list. More...

virtual std::string	toString () const =0
	Convert the list as a string. 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
CoreSequenceSymbolList *	clone () const =0

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

virtual const std::vector< T > &	getContent () const =0

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...

virtual const T &	getElement (size_t pos) const =0
	Get the element at position 'pos' as a character. More...

Provide direct access to the list content.
Warning These operators allow you to modifiy the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual const T &	getValue (size_t pos) const =0
	checked access to a character in list. More...

virtual const T &	operator[] (size_t pos) const =0
	Operator [] overloaded for quick access to a character in list. More...

virtual T &	operator[] (size_t pos)=0
	Operator [] overloaded for quick access to a character in list. More...

Edition methods.
virtual void	deleteElement (size_t pos)=0
	Remove the element at position 'pos'. More...

virtual void	deleteElements (size_t pos, size_t len)=0
	Remove the elements at position 'pos'. More...

Provide direct access to the list content.
Warning These operators allow you to modifiy the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

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...

Detailed Description

template<class T>
class bpp::CoreSequenceSymbolList< T >

The CoreSequenceSymbolList interface.

Definition at line 62 of file CoreSequenceSymbolList.h.

Constructor & Destructor Documentation

◆ ~CoreSequenceSymbolList()

template<class T >

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

inlinevirtual

Definition at line 76 of file CoreSequenceSymbolList.h.

Member Function Documentation

◆ addElement() [1/2]

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() [2/2]

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.

◆ 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 >

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

pure virtual

Implements bpp::CoreSequence.

Implemented in bpp::Sequence, bpp::ProbabilisticSequence, bpp::AbstractSequenceSymbolList< T >, bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

◆ deleteElement()

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

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

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

Referenced by bpp::AlignedSequenceContainer::deleteSite(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), bpp::VectorSiteContainer::removeSequence(), bpp::AlignedSequenceContainer::removeSite(), and bpp::SequenceTools::removeStops().

◆ deleteElements()

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

pure virtualinherited

Remove the elements at position 'pos'.

Parameters

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

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

Referenced by bpp::AlignedSequenceContainer::deleteSites().

◆ getAlphabet()

virtual const Alphabet* bpp::CruxSymbolList::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

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

◆ 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::CoreSymbolList< T >::getContent ( ) const

pure virtualinherited

Implemented in bpp::ProbabilisticSequence, bpp::SymbolList< T >, bpp::SymbolList< int >, bpp::BasicProbabilisticSymbolList, and bpp::BasicProbabilisticSequence.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::BasicProbabilisticSymbolList::operator=(), bpp::BasicSequence::operator=(), and bpp::SequenceWithAnnotation::operator=().

◆ getElement()

template<class T >

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

pure virtualinherited

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

Parameters

pos	The position of the character to retrieve.

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

◆ 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::CoreSymbolList< T >::getValue ( size_t pos ) const

pure virtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns: The T value of character at position pos.

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

Referenced by bpp::VectorSiteContainer::addSequence(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::findFirstOf(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

◆ 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 const T& bpp::CoreSymbolList< T >::operator[] ( size_t pos ) const

pure virtualinherited

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.

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

◆ operator[]() [2/2]

template<class T >

virtual T& bpp::CoreSymbolList< T >::operator[] ( size_t pos )

pure virtualinherited

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.

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

◆ 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::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()

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().

◆ 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()

virtual void bpp::CruxSymbolList::shuffle ( )

pure virtualinherited

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

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

◆ size()

virtual size_t bpp::CruxSymbolList::size ( ) const

pure virtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

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

◆ toString()

virtual std::string bpp::CruxSymbolList::toString ( ) const

pure virtualinherited

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.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, bpp::BasicSequence, bpp::BasicProbabilisticSymbolList, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::toString(), bpp::AbstractSequenceContainer::toString(), bpp::VectorProbabilisticSequenceContainer::toString(), bpp::Clustal::writeAlignment(), and bpp::Stockholm::writeAlignment().

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

Bpp/Seq/CoreSequenceSymbolList.h

Public Member Functions

Detailed Description

template<class T> class bpp::CoreSequenceSymbolList< T >

Constructor & Destructor Documentation

◆ ~CoreSequenceSymbolList()

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()

template<class T>
class bpp::CoreSequenceSymbolList< T >