bpp::Site Class Reference

The Site class. More...

#include <Bpp/Seq/Site.h>

Inheritance diagram for bpp::Site:

Collaboration diagram for bpp::Site:

Public Types
typedef int	SymbolType

Public Member Functions
	Site (std::shared_ptr< const Alphabet > &alphabet)
	Build a new void Site object with the specified alphabet. More...
	Site (std::shared_ptr< const Alphabet > &alphabet, int coordinate)
	Build a new void Site object with the specified alphabet and position. More...
	Site (const std::vector< std::string > &site, std::shared_ptr< const Alphabet > &alphabet)
	Build a new Site object with the specified alphabet. The content of the site is initialized from a vector of characters. More...
	Site (const std::vector< std::string > &site, std::shared_ptr< const Alphabet > &alphabet, int coordinate)
	Build a new Site object with the specified alphabet and position. The content of the site is initialized from a vector of characters. More...
	Site (const std::vector< int > &site, std::shared_ptr< const Alphabet > &alphabet)
	Build a new Site object with the specified alphabet. The content of the site is initialized from a vector of integers. More...
	Site (const std::vector< int > &site, std::shared_ptr< const Alphabet > alphabet, int coordinate)
	Build a new Site object with the specified alphabet and position. The content of the site is initialized from a vector of integers. More...
	Site (const Site &site)
	The copy constructor. More...
Site &	operator= (const Site &s)
	The assignment operator. More...
virtual	~Site ()
double	getStateValueAt (size_t sequencePosition, int state) const
	get value of a state at a position More...
virtual bool	operator== (const SiteInterface &site)
virtual bool	operator< (const SiteInterface &site)
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the list. More...
virtual const Alphabet &	alphabet () 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	operator() (size_t position, int state) const =0
	get value of a state at a position More...
int	getCoordinate () const override
	Get the coordinate associated to this site. More...
void	setCoordinate (int coordinate) override
	Set the position of this site. More...
void	setContent (const std::vector< int > &list) override
void	setContent (const std::vector< std::string > &list) override
	Set the whole content of the list. More...
std::string	toString () const override
	Convert the list as a string. More...
void	addElement (const std::string &c) override
	Add a character to the end of the list. More...
void	addElement (size_t pos, const std::string &c) override
	Add a character at a certain position in the list. More...
void	addElement (const T &c) override
void	addElement (const int &c) override
	Add a character to the end of the list. More...
void	addElement (size_t pos, const int &c) override
	Add a character at a certain position in the list. More...
void	setElement (size_t pos, const std::string &c) override
	Set the element at position 'pos' to character 'c'. More...
void	setElement (size_t pos, const T &c) override
void	setElement (size_t pos, const int &c) override
	Set the element at position 'pos' to character 'c'. More...
std::string	getChar (size_t pos) const override
	Get the element at position 'pos' as a character. More...
double	operator() (size_t siteIndex, int state) const override
	get value of a state at a position More...
virtual const std::vector< int > &	getContent () const override
const int &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...
const int &	getValue (size_t pos) const override
	checked access to a character in list. More...
const int &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...
int &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. More...
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	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	shuffle () override
	Randomly shuffle the content of the list, with linear complexity. More...
The Clonable interface
Site *	clone () const
Setting/getting the position of the site.
virtual int	getCoordinate () const =0
	Get the coordinate associated to this site. More...
virtual void	setCoordinate (int coordinate)=0
	Set the position of this site. 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 modify 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...
Acting on the content of the list.
virtual void	setContent (const std::vector< std::string > &list)=0
	Set the whole content of the list. More...
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
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 std::string &c)=0
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const std::string &c)=0
	Add a character at a certain position in the list. More...
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 std::string &c)=0
	Set the element at position 'pos' to character 'c'. More...
virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...
virtual std::string	getChar (size_t pos) const =0
	Get the element at position 'pos' as a character. 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...
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 modify 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...

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

Private Attributes
int	coordinate_
	The position associated with this site. More...
std::shared_ptr< const Alphabet >	alphabet_
	The Alphabet attribute must be initialized in constructor and then can never be changed. More...

Detailed Description

The Site class.

Define specific attributes and methods for sites manipulation. It is very similar to the Sequence object (a site is a vertical sequence!), and characters at each position are coded as integers. Sites have a 'position' attribute. This attribute stands for an indice in a an alignment, and may be used as a unique identifier, in the same manner that names identify sequence objects. But for now, we do not allow to construct a Site directly from a string. This should not be a constraint, since you never read sites directly from a file.

Definition at line 69 of file Site.h.

Member Typedef Documentation

SymbolType

typedef int bpp::IntSymbolListInterface::SymbolType

inherited

Definition at line 31 of file IntSymbolList.h.

Constructor & Destructor Documentation

Site() [1/7]

bpp::Site::Site ( std::shared_ptr< const Alphabet > &  alphabet )

inline

Build a new void Site object with the specified alphabet.

Parameters

alphabet

The alphabet to use.

Definition at line 80 of file Site.h.

Referenced by clone().

Site() [2/7]

bpp::Site::Site ( std::shared_ptr< const Alphabet > &  alphabet, int  coordinate  )

inline

Build a new void Site object with the specified alphabet and position.

Parameters

alphabet	The alphabet to use.
coordinate	The coordinate attribute of this site.

Definition at line 92 of file Site.h.

Site() [3/7]

bpp::Site::Site ( const std::vector< std::string > &  site, std::shared_ptr< const Alphabet > &  alphabet  )

inline

Build a new Site object with the specified alphabet. The content of the site is initialized from a vector of characters.

Parameters

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

Exceptions

BadCharException

If the content does not match the specified alphabet.

Definition at line 106 of file Site.h.

Site() [4/7]

bpp::Site::Site ( const std::vector< std::string > &  site, std::shared_ptr< const Alphabet > &  alphabet, int  coordinate  )

inline

Build a new Site object with the specified alphabet and position. The content of the site is initialized from a vector of characters.

Parameters

site	The content of the site.
alphabet	The alphabet to use.
coordinate	The coordinate attribute of this site.

Exceptions

BadCharException

If the content does not match the specified alphabet.

Definition at line 121 of file Site.h.

Site() [5/7]

bpp::Site::Site ( const std::vector< int > &  site, std::shared_ptr< const Alphabet > &  alphabet  )

inline

Build a new Site object with the specified alphabet. The content of the site is initialized from a vector of integers.

Parameters

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

Exceptions

BadIntException

If the content does not match the specified alphabet.

Definition at line 135 of file Site.h.

Site() [6/7]

bpp::Site::Site ( const std::vector< int > &  site, std::shared_ptr< const Alphabet >  alphabet, int  coordinate  )

inline

Build a new Site object with the specified alphabet and position. The content of the site is initialized from a vector of integers.

Parameters

site	The content of the site.
alphabet	The alphabet to use.
coordinate	The coordinate attribute of this site.

Exceptions

BadIntException

If the content does not match the specified alphabet.

Definition at line 150 of file Site.h.

Site() [7/7]

bpp::Site::Site ( const Site &  site )

inline

The copy constructor.

Definition at line 159 of file Site.h.

~Site()

virtual bpp::Site::~Site ( )

inlinevirtual

Definition at line 176 of file Site.h.

Member Function Documentation

addElement() [1/11]

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

inlineoverrideinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 152 of file SymbolList.h.

addElement() [2/11]

void bpp::IntSymbolList::addElement ( const std::string &  c )

inlineoverridevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 185 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

addElement() [3/11]

virtual void bpp::IntSymbolListInterface::addElement ( const std::string &  c )

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

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

addElement() [4/11]

void bpp::AbstractTemplateSymbolList< T >::addElement

inlineoverrideinherited

Definition at line 152 of file SymbolList.h.

Referenced by bpp::SequenceWithQuality::addElement().

addElement() [5/11]

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() [6/11]

virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement

inherited

Add a character to the end of the list.

Parameters

c	The character to add.

Referenced by bpp::SequenceWithQuality::addElement().

addElement() [7/11]

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

inlineoverrideinherited

Add a character at a certain position in the list.

Parameters

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

Definition at line 157 of file SymbolList.h.

addElement() [8/11]

void bpp::IntSymbolList::addElement ( size_t  pos, const std::string &  c  )

inlineoverridevirtualinherited

Add a character at a certain position in the list.

Parameters

pos	The position where to insert the element.
c	The character to add, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 192 of file IntSymbolList.h.

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

addElement() [9/11]

virtual void bpp::IntSymbolListInterface::addElement ( size_t  pos, const std::string &  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, given as a string.

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

addElement() [10/11]

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 >.

addElement() [11/11]

virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement

inherited

Add a character at a certain position in the list.

Parameters

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

alphabet() [1/2]

virtual const Alphabet& bpp::CruxSymbolListInterface::alphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns

A const reference to the alphabet.

See also

Alphabet class.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::concatenate(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::invertComplement(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), and bpp::AbstractTransliterator::translate().

alphabet() [2/2]

const Alphabet& bpp::AbstractTemplateSymbolList< int >::alphabet ( ) const

inlineoverridevirtualinherited

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.

clone()

Site* bpp::Site::clone ( ) const

inlinevirtual

Reimplemented from bpp::IntSymbolList.

Definition at line 184 of file Site.h.

References Site().

Referenced by bpp::SiteContainerTools::changeGapsToUnknownCharacters(), bpp::SiteContainerTools::changeUnresolvedCharactersToGaps(), bpp::CompressedVectorSiteContainer::CompressedVectorSiteContainer(), bpp::SiteContainerTools::getSitesWithoutStopCodon(), bpp::CompressedVectorSiteContainer::operator=(), bpp::SiteContainerTools::removeGapOnlySites(), bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites(), and bpp::SiteContainerTools::removeGapSites().

deleteElement() [1/2]

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

inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 138 of file SymbolList.h.

deleteElement() [2/2]

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

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), and bpp::SequenceTools::removeStops().

deleteElements() [1/2]

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

inlineoverridevirtualinherited

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< int >.

Definition at line 145 of file SymbolList.h.

deleteElements() [2/2]

virtual void bpp::CruxSymbolListInterface::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::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

getAlphabet() [1/2]

virtual std::shared_ptr<const Alphabet> bpp::CruxSymbolListInterface::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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::Sequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceWithQualityTools::complement(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::getComplement(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::jointEntropy(), bpp::SequenceWithAnnotation::merge(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::ProbabilisticSymbolList::operator=(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::SequenceWithQualityTools::reverseTranscript(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SequenceWithQualityTools::transcript(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::WordAlphabet::translate(), and bpp::SymbolListTools::variabilityShannon().

getAlphabet() [2/2]

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< int >::getAlphabet ( ) const

inlineoverridevirtualinherited

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.

getChar() [1/2]

virtual std::string bpp::IntSymbolListInterface::getChar ( 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::Sequence, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

getChar() [2/2]

string IntSymbolList::getChar ( size_t  pos ) const

overridevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::IntSymbolListInterface.

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

Definition at line 52 of file IntSymbolList.cpp.

Referenced by bpp::Sequence::getChar(), and bpp::SiteContainerTools::resolveDottedAlignment().

getContent() [1/2]

template<class T >

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

pure virtualinherited

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::Sequence::append(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::SequenceWithAnnotation::merge(), bpp::ProbabilisticSymbolList::operator=(), and bpp::Sequence::operator=().

getContent() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 131 of file SymbolList.h.

getCoordinate() [1/2]

virtual int bpp::CoreSiteInterface::getCoordinate ( ) const

pure virtualinherited

Get the coordinate associated to this site.

Returns

The coordinate of this site.

Implemented in bpp::AbstractCoreSite.

Referenced by bpp::SiteInterface::operator<(), bpp::AbstractCoreSite::operator=(), and bpp::SiteInterface::operator==().

getCoordinate() [2/2]

int bpp::AbstractCoreSite::getCoordinate ( ) const

inlineoverridevirtualinherited

Get the coordinate associated to this site.

Returns

The coordinate of this site.

Implements bpp::CoreSiteInterface.

Definition at line 144 of file CoreSite.h.

References bpp::AbstractCoreSite::coordinate_.

Referenced by bpp::SiteContainerTools::resolveDottedAlignment().

getElement() [1/2]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< 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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

getElement() [2/2]

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

inlineoverridevirtualinherited

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.

getStateValueAt()

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

inlinevirtual

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.

Reimplemented from bpp::IntSymbolList.

Definition at line 187 of file Site.h.

References bpp::AbstractTemplateSymbolList< int >::getAlphabet(), and bpp::AbstractTemplateSymbolList< int >::size().

Referenced by bpp::CompressedVectorSiteContainer::getStateValueAt(), and bpp::CompressedVectorSiteContainer::operator()().

getValue() [1/2]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< 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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by 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::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

getValue() [2/2]

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

inlineoverridevirtualinherited

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.

operator()() [1/2]

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()() [2/2]

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

inlineoverridevirtualinherited

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 218 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

operator<()

virtual bool bpp::SiteInterface::operator< ( const SiteInterface &  site )

inlinevirtualinherited

Definition at line 51 of file Site.h.

References bpp::CoreSiteInterface::getCoordinate().

operator=()

Site& bpp::Site::operator= ( const Site &  s )

inline

The assignment operator.

Definition at line 168 of file Site.h.

References bpp::AbstractCoreSite::operator=(), bpp::IntSymbolList::operator=(), and bpp::AbstractTemplateSymbolList< T >::operator=().

operator==()

virtual bool bpp::SiteInterface::operator== ( const SiteInterface &  site )

inlinevirtualinherited

Definition at line 31 of file Site.h.

References bpp::CoreSiteInterface::getCoordinate(), and bpp::CruxSymbolListInterface::size().

operator[]() [1/4]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< 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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

operator[]() [2/4]

const int & bpp::AbstractTemplateSymbolList< int >::operator[] ( size_t  pos ) const

inlineoverridevirtualinherited

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.

operator[]() [3/4]

int & bpp::AbstractTemplateSymbolList< int >::operator[] ( size_t  pos )

inlineoverridevirtualinherited

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.

operator[]() [4/4]

template<class T >

virtual T& bpp::TemplateCoreSymbolListInterface< 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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

setContent() [1/5]

void IntSymbolList::setContent ( const std::vector< int > &  list )

overridevirtualinherited

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

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

Definition at line 37 of file IntSymbolList.cpp.

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

setContent() [2/5]

void IntSymbolList::setContent ( const std::vector< std::string > &  list )

overridevirtualinherited

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::IntSymbolListInterface.

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

Definition at line 15 of file IntSymbolList.cpp.

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

setContent() [3/5]

virtual void bpp::IntSymbolListInterface::setContent ( const std::vector< std::string > &  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::SequenceInterface, bpp::SequenceWithAnnotation, bpp::Sequence, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

setContent() [4/5]

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() [5/5]

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 bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList(), bpp::IntSymbolList::IntSymbolList(), bpp::SequenceWithAnnotation::operator=(), bpp::Sequence::operator=(), bpp::Sequence::Sequence(), bpp::SequenceWithAnnotation::SequenceWithAnnotation(), bpp::Sequence::setContent(), and bpp::SequenceWithAnnotation::setContent().

setCoordinate() [1/2]

void bpp::AbstractCoreSite::setCoordinate ( int  coordinate )

inlineoverridevirtualinherited

Set the position of this site.

Parameters

coordinate

The new position of the site.

Implements bpp::CoreSiteInterface.

Definition at line 146 of file CoreSite.h.

References bpp::AbstractCoreSite::coordinate_.

Referenced by bpp::CompressedVectorSiteContainer::reindexSites(), and bpp::CompressedVectorSiteContainer::setSiteCoordinates().

setCoordinate() [2/2]

virtual void bpp::CoreSiteInterface::setCoordinate ( int  coordinate )

pure virtualinherited

Set the position of this site.

Parameters

coordinate

The new position of the site.

Implemented in bpp::AbstractCoreSite.

setElement() [1/6]

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

inlineoverrideinherited

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

Parameters

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

Definition at line 165 of file SymbolList.h.

setElement() [2/6]

void bpp::IntSymbolList::setElement ( size_t  pos, const std::string &  c  )

inlineoverridevirtualinherited

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

Parameters

pos	The position of the character to set.
c	The value of the element, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 201 of file IntSymbolList.h.

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

setElement() [3/6]

virtual void bpp::IntSymbolListInterface::setElement ( size_t  pos, const std::string &  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, given as a string.

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

Referenced by bpp::SequenceTools::complement(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), and bpp::SequenceTools::replaceStopsWithGaps().

setElement() [4/6]

void bpp::AbstractTemplateSymbolList< T >::setElement

inlineoverrideinherited

Definition at line 165 of file SymbolList.h.

setElement() [5/6]

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 >.

setElement() [6/6]

virtual void bpp::TemplateCoreSymbolListInterface< T >::setElement

inherited

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

Parameters

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

shuffle() [1/2]

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

inlineoverridevirtualinherited

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

Implements bpp::CruxSymbolListInterface.

Definition at line 191 of file SymbolList.h.

shuffle() [2/2]

virtual void bpp::CruxSymbolListInterface::shuffle ( )

pure virtualinherited

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

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

size() [1/2]

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

pure virtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::AbstractTemplateSymbolList< T >::AbstractTemplateSymbolList(), bpp::SequenceWithQuality::addElement(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getFrequencies(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getMajorAllele(), bpp::SymbolListTools::getMajorAlleleFrequency(), bpp::SymbolListTools::getMinorAllele(), bpp::SymbolListTools::getMinorAlleleFrequency(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SymbolListTools::getNumberOfDistinctCharacters(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasSingleton(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SymbolListTools::heterozygosity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isDoubleton(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::isParsimonyInformativeSite(), bpp::SymbolListTools::isTriplet(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), bpp::SymbolListTools::jointEntropy(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SiteInterface::operator==(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceWalker::SequenceWalker(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::SymbolListTools::variabilityFactorial(), and bpp::SymbolListTools::variabilityShannon().

size() [2/2]

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

inlineoverridevirtualinherited

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.

toString() [1/2]

virtual std::string bpp::CruxSymbolListInterface::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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, bpp::Sequence, bpp::ProbabilisticSymbolList, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

toString() [2/2]

std::string bpp::IntSymbolList::toString ( ) const

inlineoverridevirtualinherited

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.

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

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

Definition at line 179 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, bpp::StringSequenceTools::decodeSequence(), and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

Referenced by bpp::Sequence::toString().

Member Data Documentation

alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< int >::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 41 of file SymbolList.h.

content_

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

protectedinherited

The list content.

Definition at line 47 of file SymbolList.h.

coordinate_

int bpp::AbstractCoreSite::coordinate_

privateinherited

The position associated with this site.

Definition at line 85 of file CoreSite.h.

Referenced by bpp::AbstractCoreSite::getCoordinate(), bpp::AbstractCoreSite::operator=(), and bpp::AbstractCoreSite::setCoordinate().

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

• Bpp/Seq/Site.h