bpp::SequenceWithQuality Class Reference

A SequenceWithAnnotation class with quality scores attached. More...

#include <Bpp/Seq/SequenceWithQuality.h>

Inheritance diagram for bpp::SequenceWithQuality:

Collaboration diagram for bpp::SequenceWithQuality:

Public Types
typedef int	ElementType
typedef int	SymbolType

Public Member Functions
	SequenceWithQuality (const SequenceWithQuality &sequence)
SequenceWithQuality &	operator= (const SequenceWithQuality &sequence)
virtual void	addAnnotation (std::shared_ptr< SequenceAnnotation > anno)
	Add a new annotation to the sequence. More...
virtual bool	hasAnnotation (const std::string &type) const
virtual const SequenceAnnotation &	annotation (const std::string &type) const
virtual SequenceAnnotation &	annotation (const std::string &type)
virtual std::vector< std::string >	getAnnotationTypes () const
virtual void	merge (const SequenceWithAnnotation &swa)
	Merge a sequence with the current one. More...
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the list. More...
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the list. More...
virtual const Alphabet &	alphabet () const =0
	Get the alphabet associated to the list. More...
const Alphabet &	alphabet () const override
	Get the alphabet associated to the list. More...
virtual size_t	size () const =0
	Get the number of elements in the list. More...
size_t	size () const override
	Get the number of elements in the list. More...
virtual std::string	toString () const =0
	Convert the list as a string. More...
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	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	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...
virtual double	getStateValueAt (size_t position, int state) const =0
	get value of a state at a position More...
double	getStateValueAt (size_t siteIndex, int state) const override
	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...
double	operator() (size_t siteIndex, int state) const override
	get value of a state at a position More...
virtual const Comments &	getComments () const =0
	Get the comments. More...
const Comments &	getComments () const override
	Get the comments. More...
virtual void	setComments (const Comments &comments)=0
	Set the comments. More...
void	setComments (const Comments &comments) override
	Set the comments. More...
virtual void	clearComments ()=0
void	clearComments () override
virtual void	addElement (const std::string &c) override
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const std::string &c) override
	Add a character at a certain position in the list. More...
void	addElement (const int &v) override
	Add a character to the end of the list. More...
void	addElement (size_t pos, const int &v) override
	Add a character at a certain position in the list. More...
virtual void	addElement (const int &v) override
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const int &v) override
	Add a character at a certain position in the list. More...
virtual 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 &v) override
void	setElement (size_t pos, const int &v) override
	Set the element at position 'pos' to character 'c'. More...
virtual void	setElement (size_t pos, const int &v) override
	Set the element at position 'pos' to character 'c'. More...
virtual std::string	getChar (size_t pos) const override
	Get the element at position 'pos' as a character. 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...
void	addIntSymbolListListener (std::shared_ptr< IntSymbolListListener > listener)
Constructors
	SequenceWithQuality (std::shared_ptr< const Alphabet > &alpha)
	Build a new empty SequenceWithQuality. More...
	SequenceWithQuality (const std::string &name, const std::string &sequence, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::string. More...
	SequenceWithQuality (const std::string &name, const std::string &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::string. More...
	SequenceWithQuality (const std::string &name, const std::string &sequence, const std::vector< int > &quality, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::string. More...
	SequenceWithQuality (const std::string &name, const std::string &sequence, const std::vector< int > &quality, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::string. More...
	SequenceWithQuality (const std::string &name, const std::vector< int > &sequence, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::vector<int> More...
	SequenceWithQuality (const std::string &name, const std::vector< int > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::vector<int> More...
	SequenceWithQuality (const std::string &name, const std::vector< int > &sequence, const std::vector< int > &quality, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::vector<int> More...
	SequenceWithQuality (const std::string &name, const std::vector< int > &sequence, const std::vector< int > &quality, const Comments &comments, std::shared_ptr< const Alphabet > &alpha)
	Build a new SequenceWithQuality from a std::vector<int> More...
	SequenceWithQuality (const Sequence &s)
	Build a new SequenceWithQuality. More...
	SequenceWithQuality (const Sequence &s, const std::vector< int > &sc)
	Build a new SequenceWithQuality. More...
Destructor
virtual	~SequenceWithQuality ()
The Clonable interface
SequenceWithQuality *	clone () const override
Dealing with quality
void	setQuality (size_t pos, int quality)
	Set the quality score. More...
int	getQuality (size_t pos) const
	Get the quality score. More...
void	setQualities (const std::vector< int > &quality)
	Set the whole quality scores. More...
const std::vector< int > &	getQualities () const
	Get the whole quality scores. More...
virtual void	append (const std::vector< int > &content, const std::vector< int > &qualities)
	Append content with quality. More...
virtual void	append (const std::vector< std::string > &content, const std::vector< int > &qualities)
	Append content with quality. More...
virtual void	append (const std::string &content, const std::vector< int > &qualities)
	Append content with quality. More...
void	addElement (const std::string &c, int q)
void	addElement (size_t pos, const std::string &c, int q)
	Add a character to a certain position in the list with quality. More...
void	addElement (int v, int q)
	Add a character to the end of the list with quality. More...
void	addElement (size_t pos, int v, int q)
	Add a character to a certain position in the list with quality. More...
void	append (const SequenceInterface &seq) override
	Append the content of a sequence to the current one. More...
void	append (const std::vector< int > &content) override
void	append (const std::vector< std::string > &content) override
void	append (const std::string &content) override
virtual void	addElement (const T &c)=0
	Add a character to the end of the list with quality. More...
virtual void	addElement (size_t pos, const T &c)=0
	Add a character to the end of the list with quality. More...
virtual void	addElement (const std::string &c) override
virtual void	addElement (size_t pos, const std::string &c) override
Adjusting the size of the sequence.
virtual void	setContent (const std::string &sequence) override
	Set the whole content of the sequence. More...
void	setContent (const std::vector< std::string > &list) override
	Set the whole content of the list. More...
void	setContent (const std::vector< int > &list) override
void	setToSizeR (size_t newSize) override
	Set up the size of a sequence from the right side. More...
void	setToSizeL (size_t newSize) override
	Set up the size of a sequence from the left side. More...
void	append (const SequenceInterface &seq) override
	Append the content of a sequence to the current one. More...
void	append (const std::vector< int > &content) override
	Append the specified content to the sequence. More...
void	append (const std::vector< std::string > &content) override
	Append the specified content to the sequence. More...
void	append (const std::string &content) override
	Append the specified content to the sequence. 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...
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
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...
Setting/getting the name of the sequence.
const std::string &	getName () const override
	Get the name of this sequence. More...
void	setName (const std::string &name) override
	Set the name of this sequence. 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...
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	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 Member Functions
virtual void	beforeSequenceChanged (const IntSymbolListEditionEvent &event) override
virtual void	afterSequenceChanged (const IntSymbolListEditionEvent &event) override
virtual void	beforeSequenceInserted (const IntSymbolListInsertionEvent &event) override
virtual void	afterSequenceInserted (const IntSymbolListInsertionEvent &event) override
virtual void	beforeSequenceDeleted (const IntSymbolListDeletionEvent &event) override
virtual void	afterSequenceDeleted (const IntSymbolListDeletionEvent &event) override
virtual void	beforeSequenceSubstituted (const IntSymbolListSubstitutionEvent &event) override
virtual void	afterSequenceSubstituted (const IntSymbolListSubstitutionEvent &event) override
void	propagateEvents (bool yn) override
bool	propagateEvents () const override

Protected Attributes
Comments	comments_
std::vector< int >	content_
	The list content. More...
std::vector< std::shared_ptr< CoreSymbolListListener< int > > >	listeners_
	Contains the listeners. More...

Private Attributes
std::shared_ptr< SequenceQuality >	qualScores_
std::string	name_
	The sequence name. More...
std::shared_ptr< const Alphabet >	alphabet_
	The Alphabet attribute must be initialized in constructor and then can never be changed. More...
bool	propagateEvents_

Events handling
virtual size_t	getNumberOfListeners () const override
virtual const CoreSymbolListListener< int > &	listener (size_t i) const override
virtual CoreSymbolListListener< int > &	listener (size_t i) override
virtual std::shared_ptr< const CoreSymbolListListener< int > >	getListener (size_t i) const override
virtual std::shared_ptr< CoreSymbolListListener< int > >	getListener (size_t i) override
virtual void	addCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< int >> listener) override
virtual void	removeCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< int >> listener) override
void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< int > &event) override
void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< int > &event) override
void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< int > &event) override
void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< int > &event) override
void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< int > &event) override
void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< int > &event) override
void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< int > &event) override
void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< int > &event) override

Events handling
virtual void	addCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< T >> listener)=0
virtual void	removeCoreSymbolListListener (std::shared_ptr< CoreSymbolListListener< T >> listener)=0
virtual void	beforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	afterSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	beforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	afterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	beforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	afterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	beforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0
virtual void	afterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0
virtual void	fireBeforeSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	fireAfterSequenceChanged (const CoreSymbolListEditionEvent< T > &event)=0
virtual void	fireBeforeSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	fireAfterSequenceInserted (const CoreSymbolListInsertionEvent< T > &event)=0
virtual void	fireBeforeSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	fireAfterSequenceDeleted (const CoreSymbolListDeletionEvent< T > &event)=0
virtual void	fireBeforeSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0
virtual void	fireAfterSequenceSubstituted (const CoreSymbolListSubstitutionEvent< T > &event)=0

Detailed Description

A SequenceWithAnnotation class with quality scores attached.

This classes adds some useful functions to handle quality scores.

See also

SequenceQuality

Author

Sylvain Gaillard, Vincent Cahais, Julien Dutheil

Definition at line 181 of file SequenceWithQuality.h.

Member Typedef Documentation

ElementType

typedef int bpp::SequenceInterface::ElementType

inherited

Definition at line 36 of file Sequence.h.

SymbolType

typedef int bpp::IntSymbolListInterface::SymbolType

inherited

Definition at line 31 of file IntSymbolList.h.

Constructor & Destructor Documentation

SequenceWithQuality() [1/12]

bpp::SequenceWithQuality::SequenceWithQuality ( std::shared_ptr< const Alphabet > &  alpha )

inline

Build a new empty SequenceWithQuality.

Parameters

alpha

A pointer to an Alphabet

Exceptions

BadCharException

if a state is not allowed by the Alphabet

Definition at line 200 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

Referenced by clone().

SequenceWithQuality() [2/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::string &  sequence, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::string.

Build a new SequenceWithQuality and set the quality scores to the default value DEFAULT_QUALITY_VALUE.

Parameters

name	The name of the sequence
sequence	The string representing the sequence
alpha	A pointer to an Alphabet

Exceptions

BadCharException

if a state is not allowed by the Alphabet

Definition at line 221 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [3/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::string &  sequence, const Comments &  comments, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::string.

Build a new SequenceWithQuality and set the quality scores to the default value DEFAULT_QUALITY_VALUE.

Parameters

name	The name of the sequence
sequence	The string representing the sequence
comments	Comments to add to the sequence
alpha	A pointer to an Alphabet

Exceptions

BadCharException

if a state is not allowed by the Alphabet

Author

Vincent Cahais

Definition at line 247 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [4/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::string &  sequence, const std::vector< int > &  quality, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::string.

Build a new SequenceWithQuality and assign quality scores from a vector of int.

Parameters

name	The name of the sequence
sequence	The string representing the sequence
quality	The quality scores
alpha	A pointer to an alphabet

Exceptions

BadCharException	if a state is not allowed by the Alphabet
DimensionException	if the number of quality values is not equal to the number of sequence states

Definition at line 274 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [5/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::string &  sequence, const std::vector< int > &  quality, const Comments &  comments, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::string.

Build a new SequenceWithQuality and assign quality scores from a vector of int.

Parameters

name	The name of the sequence
sequence	The string representing the sequence
quality	The quality scores
comments	Comments to add to the sequence
alpha	A pointer to an alphabet

Exceptions

BadCharException	if a state is not allowed by the Alphabet
DimensionException	if the number of quality values is not equal to the number of sequence states

Author

Vincent Cahais

Definition at line 304 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [6/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::vector< int > &  sequence, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::vector<int>

Build a new SequenceWithQuality and set the quality scores to the default value DEFAULT_QUALITY_VALUE.

Parameters

name	The name of the sequence
sequence	The sequence in int
alpha	A pointer to an Alphabet

Exceptions

BadIntException

if a state is not allowed by the Alphabet

Definition at line 329 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [7/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::vector< int > &  sequence, const Comments &  comments, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::vector<int>

Build a new SequenceWithQuality and set the quality scores to the default value DEFAULT_QUALITY_VALUE.

Parameters

name	The name of the sequence
sequence	The sequence in int
comments	Comments to add to the sequence
alpha	A pointer to an Alphabet

Exceptions

BadIntException

if a state is not allowed by the Alphabet

Author

Vincent Cahais

Definition at line 355 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [8/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::vector< int > &  sequence, const std::vector< int > &  quality, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::vector<int>

Build a new SequenceWithQuality and assign quality scores from a vector of int.

Parameters

name	The name of the sequence
sequence	The sequence in int
quality	The quality scores
alpha	A pointer to an Alphabet

Exceptions

BadIntException	if a state is not allowed by the Alphabet
DimensionException	if the number of quality values is not equal to the number of sequence states

Definition at line 382 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [9/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const std::string &  name, const std::vector< int > &  sequence, const std::vector< int > &  quality, const Comments &  comments, std::shared_ptr< const Alphabet > &  alpha  )

inline

Build a new SequenceWithQuality from a std::vector<int>

Build a new SequenceWithQuality and assign quality scores from a vector of int.

Parameters

name	The name of the sequence
sequence	The sequence in int
quality	The quality scores
comments	Comments to add to the sequence
alpha	A pointer to an Alphabet

Exceptions

BadIntException	if a state is not allowed by the Alphabet
DimensionException	if the number of quality values is not equal to the number of sequence states

Author

Vincent Cahais

Definition at line 412 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [10/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const Sequence &  s )

inline

Build a new SequenceWithQuality.

Build a new SequenceWithQuality from a Sequence object and set the quality scores to the default value DEFAULT_QUALITY_VALUE.

Parameters

s	The Sequence object

Definition at line 433 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

SequenceWithQuality() [11/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const Sequence &  s, const std::vector< int > &  sc  )

inline

Build a new SequenceWithQuality.

Build a new SequenceWithQuality from a Sequence object and set the quality scores from a vector of int.

Parameters

s	The Sequence object
sc	The quality scores

Exceptions

DimensionException

if the number of quality values is not equal to the number of sequence states

Definition at line 452 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::addAnnotation(), and qualScores_.

~SequenceWithQuality()

virtual bpp::SequenceWithQuality::~SequenceWithQuality ( )

inlinevirtual

Definition at line 468 of file SequenceWithQuality.h.

SequenceWithQuality() [12/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const SequenceWithQuality &  sequence )

inline

Definition at line 471 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::annotation(), bpp::SequenceQuality::QUALITY_SCORE, and qualScores_.

Member Function Documentation

addAnnotation()

virtual void bpp::SequenceWithAnnotation::addAnnotation ( std::shared_ptr< SequenceAnnotation >  anno )

inlinevirtualinherited

Add a new annotation to the sequence.

Parameters

anno	The annotation object to be added. Unless the annotation is shared, the annotation object will be owned by the sequence object, and will be copied and deleted when needed.

Exceptions

Exception

If the annotation is not valid for this sequence.

See also

SequenceWithAnnotation::isValidWith

Definition at line 349 of file SequenceWithAnnotation.h.

References bpp::EventDrivenIntSymbolList::addIntSymbolListListener().

Referenced by SequenceWithQuality().

addCoreSymbolListListener() [1/2]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::addCoreSymbolListListener ( std::shared_ptr< CoreSymbolListListener< T >>  listener )

inlineoverridevirtualinherited

Definition at line 391 of file SymbolList.h.

addCoreSymbolListListener() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::addCoreSymbolListListener ( std::shared_ptr< CoreSymbolListListener< T >>  listener )

pure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

addElement() [1/18]

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() [2/18]

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

inlineoverridevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Definition at line 336 of file SymbolList.h.

addElement() [3/18]

void EventDrivenIntSymbolList::addElement ( const std::string &  c )

overridevirtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Reimplemented from bpp::IntSymbolList.

Definition at line 113 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::addElement().

addElement() [4/18]

void EventDrivenIntSymbolList::addElement

override

Definition at line 358 of file IntSymbolList.cpp.

addElement() [5/18]

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() [6/18]

void bpp::SequenceWithQuality::addElement ( const std::string &  c, int  q  )

inline

Definition at line 637 of file SequenceWithQuality.h.

References bpp::IntSymbolListInterface::addElement(), qualScores_, and bpp::CruxSymbolListInterface::size().

addElement() [7/18]

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() [8/18]

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

Add a character to the end of the list with quality.

Parameters

c	The element to add to the sequence
q	The quality of this element

Exceptions

BadCharException

if one of the character of the string is not in the Alphabet

addElement() [9/18]

void bpp::SequenceWithQuality::addElement ( int  v, int  q  )

inline

Add a character to the end of the list with quality.

Parameters

v	The element to add to the sequence
q	The quality of this element

Exceptions

BadIntException

if the value does not match the current Alphabet

Definition at line 672 of file SequenceWithQuality.h.

References bpp::IntSymbolList::addElement(), qualScores_, and bpp::CruxSymbolListInterface::size().

addElement() [10/18]

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() [11/18]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::addElement ( size_t  pos, const T &  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.

Definition at line 344 of file SymbolList.h.

addElement() [12/18]

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

overridevirtualinherited

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.

Reimplemented from bpp::IntSymbolList.

Definition at line 120 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::addElement().

addElement() [13/18]

void EventDrivenIntSymbolList::addElement

override

Definition at line 360 of file IntSymbolList.cpp.

addElement() [14/18]

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() [15/18]

void bpp::SequenceWithQuality::addElement ( size_t  pos, const std::string &  c, int  q  )

inline

Add a character to a certain position in the list with quality.

Parameters

pos	The position where the element will be inserted
c	The element to add to the sequence
q	The quality of this element

Exceptions

BadCharException	if one of the character of the string is not in the Alphabet
IndexOutOfBoundsException	if pos is greater than the sequence size

Definition at line 655 of file SequenceWithQuality.h.

References bpp::IntSymbolListInterface::addElement(), and qualScores_.

addElement() [16/18]

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() [17/18]

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

Add a character to the end of the list with quality.

Parameters

c	The element to add to the sequence
q	The quality of this element

Exceptions

BadCharException

if one of the character of the string is not in the Alphabet

addElement() [18/18]

void bpp::SequenceWithQuality::addElement ( size_t  pos, int  v, int  q  )

inline

Add a character to a certain position in the list with quality.

Parameters

pos	The position where the element will be inserted
v	The element to add to the sequence
q	The quality of this element

Exceptions

BadIntException	if the value does not match the current Alphabet
IndexOutOfBoundsException	if pos is greater than the sequence size

Definition at line 689 of file SequenceWithQuality.h.

References bpp::IntSymbolList::addElement(), and qualScores_.

addIntSymbolListListener()

void bpp::EventDrivenIntSymbolList::addIntSymbolListListener ( std::shared_ptr< IntSymbolListListener >  listener )

inlineinherited

Definition at line 368 of file IntSymbolList.h.

References bpp::AbstractTemplateEventDrivenSymbolList< int >::addCoreSymbolListListener(), and bpp::AbstractTemplateEventDrivenSymbolList< int >::listener().

Referenced by bpp::SequenceWithAnnotation::addAnnotation().

afterSequenceChanged() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::afterSequenceChanged ( const CoreSymbolListEditionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceChanged() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceChanged ( const IntSymbolListEditionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 375 of file IntSymbolList.h.

afterSequenceDeleted() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::afterSequenceDeleted ( const CoreSymbolListDeletionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceDeleted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceDeleted ( const IntSymbolListDeletionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 379 of file IntSymbolList.h.

afterSequenceInserted() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::afterSequenceInserted ( const CoreSymbolListInsertionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceInserted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceInserted ( const IntSymbolListInsertionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 377 of file IntSymbolList.h.

afterSequenceSubstituted() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::afterSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

afterSequenceSubstituted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::afterSequenceSubstituted ( const IntSymbolListSubstitutionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 381 of file IntSymbolList.h.

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.

annotation() [1/2]

virtual SequenceAnnotation& bpp::SequenceWithAnnotation::annotation ( const std::string &  type )

inlinevirtualinherited

Definition at line 386 of file SequenceWithAnnotation.h.

References bpp::AbstractTemplateEventDrivenSymbolList< int >::getNumberOfListeners(), bpp::SequenceAnnotation::getType(), and bpp::AbstractTemplateEventDrivenSymbolList< int >::listener().

annotation() [2/2]

virtual const SequenceAnnotation& bpp::SequenceWithAnnotation::annotation ( const std::string &  type ) const

inlinevirtualinherited

Definition at line 371 of file SequenceWithAnnotation.h.

References bpp::AbstractTemplateEventDrivenSymbolList< int >::getNumberOfListeners(), bpp::SequenceAnnotation::getType(), and bpp::AbstractTemplateEventDrivenSymbolList< int >::listener().

Referenced by bpp::SequenceWithAnnotation::merge(), operator=(), and SequenceWithQuality().

append() [1/11]

void SequenceWithAnnotation::append ( const SequenceInterface &  seq )

overridevirtualinherited

Append the content of a sequence to the current one.

Parameters

seq	The sequence to append. Only the raw content is appended, not additional fields such as annotations if any.

Exceptions

AlphabetMismatchException

In case the alphabet does not match the current one.

Implements bpp::SequenceInterface.

Definition at line 87 of file SequenceWithAnnotation.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), and bpp::CruxSymbolListInterface::size().

Referenced by append().

append() [2/11]

void SequenceWithAnnotation::append

override

Append the content of a sequence to the current one.

Parameters

seq	The sequence to append. Only the raw content is appended, not additional fields such as annotations if any.

Exceptions

AlphabetMismatchException

In case the alphabet does not match the current one.

Definition at line 330 of file SequenceWithAnnotation.cpp.

Referenced by append().

append() [3/11]

void SequenceWithAnnotation::append ( const std::string &  content )

overridevirtualinherited

Append the specified content to the sequence.

Parameters

content

The content to append to the sequence.

Exceptions

BadCharException

If the content does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 140 of file SequenceWithAnnotation.cpp.

References bpp::StringSequenceTools::codeSequence().

append() [4/11]

void SequenceWithAnnotation::append

override

Definition at line 336 of file SequenceWithAnnotation.cpp.

append() [5/11]

virtual void bpp::SequenceWithQuality::append ( const std::string &  content, const std::vector< int > &  qualities  )

inlinevirtual

Append content with quality.

Parameters

content	A string to append to the sequence
qualities	A vector of int to append to the qualities

Exceptions

BadCharException	if one of the character of the string is not in the Alphabet
DimensionException	if qualities does not have the same size as content

Definition at line 612 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append(), and qualScores_.

append() [6/11]

void SequenceWithAnnotation::append ( const std::vector< int > &  content )

overridevirtualinherited

Append the specified content to the sequence.

Parameters

content

The content to append to the sequence.

Exceptions

BadIntException

If the content does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 101 of file SequenceWithAnnotation.cpp.

append() [7/11]

void SequenceWithAnnotation::append

override

Definition at line 332 of file SequenceWithAnnotation.cpp.

append() [8/11]

virtual void bpp::SequenceWithQuality::append ( const std::vector< int > &  content, const std::vector< int > &  qualities  )

inlinevirtual

Append content with quality.

Parameters

content	A vector of int to append to the sequence
qualities	A vector of int to append to the qualities

Exceptions

BadIntException	if one of the content int is not in the Alphabet
DimensionException	if qualities does not have the same size as content

Definition at line 566 of file SequenceWithQuality.h.

References append(), and qualScores_.

Referenced by bpp::SequenceWithQualityTools::subseq().

append() [9/11]

void SequenceWithAnnotation::append ( const std::vector< std::string > &  content )

overridevirtualinherited

Append the specified content to the sequence.

Parameters

content

The content to append to the sequence.

Exceptions

BadCharException

If the content does not match the current alphabet.

Implements bpp::SequenceInterface.

Definition at line 120 of file SequenceWithAnnotation.cpp.

append() [10/11]

void SequenceWithAnnotation::append

override

Definition at line 334 of file SequenceWithAnnotation.cpp.

append() [11/11]

virtual void bpp::SequenceWithQuality::append ( const std::vector< std::string > &  content, const std::vector< int > &  qualities  )

inlinevirtual

Append content with quality.

Parameters

content	A vector of string to append to the sequence
qualities	A vector of int to append to the qualities

Exceptions

BadCharException	if one of the content string is not in the Alphabet
DimensionException	if qualities does not have the same size as content

Definition at line 589 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append(), and qualScores_.

beforeSequenceChanged() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::beforeSequenceChanged ( const CoreSymbolListEditionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceChanged() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceChanged ( const IntSymbolListEditionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 374 of file IntSymbolList.h.

beforeSequenceDeleted() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::beforeSequenceDeleted ( const CoreSymbolListDeletionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceDeleted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceDeleted ( const IntSymbolListDeletionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 378 of file IntSymbolList.h.

beforeSequenceInserted() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::beforeSequenceInserted ( const CoreSymbolListInsertionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceInserted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceInserted ( const IntSymbolListInsertionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 376 of file IntSymbolList.h.

beforeSequenceSubstituted() [1/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::beforeSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

beforeSequenceSubstituted() [2/2]

virtual void bpp::EventDrivenIntSymbolList::beforeSequenceSubstituted ( const IntSymbolListSubstitutionEvent &  event )

inlineoverrideprotectedvirtualinherited

Reimplemented from bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 380 of file IntSymbolList.h.

clearComments() [1/2]

void bpp::SimpleCommentable::clearComments ( )

inlineoverridevirtualinherited

Implements bpp::Commentable.

Definition at line 88 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

clearComments() [2/2]

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

clone()

SequenceWithQuality* bpp::SequenceWithQuality::clone ( ) const

inlineoverridevirtual

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 489 of file SequenceWithQuality.h.

References SequenceWithQuality().

Referenced by bpp::SequenceWithQualityTools::invert(), and bpp::SequenceWithQualityTools::removeGaps().

deleteElement() [1/3]

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() [2/3]

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

inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

Definition at line 319 of file SymbolList.h.

deleteElement() [3/3]

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() [1/3]

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() [2/3]

void bpp::AbstractTemplateEventDrivenSymbolList< 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.

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

Definition at line 328 of file SymbolList.h.

deleteElements() [3/3]

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.

fireAfterSequenceChanged() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireAfterSequenceChanged ( const CoreSymbolListEditionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 424 of file SymbolList.h.

fireAfterSequenceChanged() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireAfterSequenceChanged ( const CoreSymbolListEditionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireAfterSequenceDeleted() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireAfterSequenceDeleted ( const CoreSymbolListDeletionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 464 of file SymbolList.h.

fireAfterSequenceDeleted() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireAfterSequenceDeleted ( const CoreSymbolListDeletionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireAfterSequenceInserted() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireAfterSequenceInserted ( const CoreSymbolListInsertionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 444 of file SymbolList.h.

fireAfterSequenceInserted() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireAfterSequenceInserted ( const CoreSymbolListInsertionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireAfterSequenceSubstituted() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireAfterSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 484 of file SymbolList.h.

fireAfterSequenceSubstituted() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireAfterSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceChanged() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireBeforeSequenceChanged ( const CoreSymbolListEditionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 414 of file SymbolList.h.

fireBeforeSequenceChanged() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireBeforeSequenceChanged ( const CoreSymbolListEditionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceDeleted() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireBeforeSequenceDeleted ( const CoreSymbolListDeletionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 454 of file SymbolList.h.

fireBeforeSequenceDeleted() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireBeforeSequenceDeleted ( const CoreSymbolListDeletionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceInserted() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireBeforeSequenceInserted ( const CoreSymbolListInsertionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 434 of file SymbolList.h.

fireBeforeSequenceInserted() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireBeforeSequenceInserted ( const CoreSymbolListInsertionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

fireBeforeSequenceSubstituted() [1/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::fireBeforeSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > &  event )

inlineoverrideprotectedinherited

Definition at line 474 of file SymbolList.h.

fireBeforeSequenceSubstituted() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::fireBeforeSequenceSubstituted ( const CoreSymbolListSubstitutionEvent< T > &  event )

protectedpure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

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.

getAnnotationTypes()

vector< string > SequenceWithAnnotation::getAnnotationTypes ( ) const

virtualinherited

Returns

The list of annotation types contained in this sequence.

Definition at line 148 of file SequenceWithAnnotation.cpp.

References bpp::SequenceAnnotation::getType().

Referenced by bpp::SequenceWithAnnotation::merge().

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 EventDrivenIntSymbolList::getChar ( size_t  pos ) const

overridevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Reimplemented from bpp::IntSymbolList.

Definition at line 134 of file IntSymbolList.cpp.

getComments() [1/2]

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

pure virtualinherited

Get the comments.

Returns

The comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Mase::appendSequencesFromStream(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::AbstractCoreSequence::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

getComments() [2/2]

const Comments& bpp::SimpleCommentable::getComments ( ) const

inlineoverridevirtualinherited

Get the comments.

Returns

The comments.

Implements bpp::Commentable.

Definition at line 79 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::createEmptyContainer(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

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.

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.

getListener() [1/2]

virtual std::shared_ptr<const CoreSymbolListListener<int > > bpp::AbstractTemplateEventDrivenSymbolList< int >::getListener ( size_t  i ) const

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 374 of file SymbolList.h.

getListener() [2/2]

virtual std::shared_ptr<CoreSymbolListListener<int > > bpp::AbstractTemplateEventDrivenSymbolList< int >::getListener ( size_t  i )

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 386 of file SymbolList.h.

getName() [1/2]

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

pure virtualinherited

Get the name of this sequence.

Returns

This sequence name.

Implemented in bpp::AbstractCoreSequence.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractCoreSequence::operator=(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), and bpp::WordAlphabet::translate().

getName() [2/2]

const std::string& bpp::AbstractCoreSequence::getName ( ) const

inlineoverridevirtualinherited

Get the name of this sequence.

Returns

This sequence name.

Implements bpp::CoreSequenceInterface.

Definition at line 170 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::merge(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

getNumberOfListeners()

virtual size_t bpp::AbstractTemplateEventDrivenSymbolList< int >::getNumberOfListeners ( ) const

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 365 of file SymbolList.h.

getQualities()

const std::vector<int>& bpp::SequenceWithQuality::getQualities ( ) const

inline

Get the whole quality scores.

Returns

A reference to the quality vector

Definition at line 548 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::SequenceWithQualityTools::complement(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceWithQualityTools::reverseTranscript(), and bpp::SequenceWithQualityTools::transcript().

getQuality()

int bpp::SequenceWithQuality::getQuality ( size_t  pos ) const

inline

Get the quality score.

Parameters

pos	The position where the quality is read

Returns

The quality score

Exceptions

IndexOutOfBoundsException

if pos is greater than the sequence size

Definition at line 521 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::SequenceWithQualityTools::subseq().

getStateValueAt() [1/2]

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().

getStateValueAt() [2/2]

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

inlineoverridevirtualinherited

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.

Implements bpp::CruxSymbolListInterface.

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

Definition at line 210 of file IntSymbolList.h.

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

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.

hasAnnotation()

virtual bool bpp::SequenceWithAnnotation::hasAnnotation ( const std::string &  type ) const

inlinevirtualinherited

Definition at line 355 of file SequenceWithAnnotation.h.

References bpp::AbstractTemplateEventDrivenSymbolList< int >::getNumberOfListeners(), bpp::SequenceAnnotation::getType(), and bpp::AbstractTemplateEventDrivenSymbolList< int >::listener().

listener() [1/2]

virtual const CoreSymbolListListener<int >& bpp::AbstractTemplateEventDrivenSymbolList< int >::listener ( size_t  i ) const

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 367 of file SymbolList.h.

listener() [2/2]

virtual CoreSymbolListListener<int >& bpp::AbstractTemplateEventDrivenSymbolList< int >::listener ( size_t  i )

inlineoverridevirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 379 of file SymbolList.h.

merge()

void SequenceWithAnnotation::merge ( const SequenceWithAnnotation &  swa )

virtualinherited

Merge a sequence with the current one.

Sequences must have the same name and alphabets. Only first sequence's commentaries are kept. Annotations that could not be merged will not be added in the concatenated sequence. See the documentation of each annotation class for more details.

Parameters

swa	The sequence to merge with.

Exceptions

AlphabetMismatchException	If the two alphabets do not match.
Exception	If the sequence names do not match.

Definition at line 166 of file SequenceWithAnnotation.cpp.

References bpp::SequenceWithAnnotation::annotation(), bpp::SequenceAnnotation::clone(), bpp::CruxSymbolListInterface::getAlphabet(), bpp::SequenceWithAnnotation::getAnnotationTypes(), bpp::TemplateCoreSymbolListInterface< T >::getContent(), and bpp::AbstractCoreSequence::getName().

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=()

SequenceWithQuality& bpp::SequenceWithQuality::operator= ( const SequenceWithQuality &  sequence )

inline

Definition at line 478 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::annotation(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceQuality::QUALITY_SCORE, and qualScores_.

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.

propagateEvents() [1/2]

bool bpp::AbstractTemplateEventDrivenSymbolList< int >::propagateEvents ( ) const

inlineoverrideprotectedvirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 497 of file SymbolList.h.

propagateEvents() [2/2]

void bpp::AbstractTemplateEventDrivenSymbolList< int >::propagateEvents ( bool  yn )

inlineoverrideprotectedvirtualinherited

Implements bpp::TemplateEventDrivenCoreSymbolListInterface< T >.

Definition at line 496 of file SymbolList.h.

removeCoreSymbolListListener() [1/2]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::removeCoreSymbolListListener ( std::shared_ptr< CoreSymbolListListener< T >>  listener )

inlineoverridevirtualinherited

Definition at line 396 of file SymbolList.h.

removeCoreSymbolListListener() [2/2]

template<class T >

virtual void bpp::TemplateEventDrivenCoreSymbolListInterface< T >::removeCoreSymbolListListener ( std::shared_ptr< CoreSymbolListListener< T >>  listener )

pure virtualinherited

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >.

setComments() [1/2]

void bpp::SimpleCommentable::setComments ( const Comments &  comments )

inlineoverridevirtualinherited

Set the comments.

Parameters

comments

The new comments.

Implements bpp::Commentable.

Definition at line 86 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), and bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer().

setComments() [2/2]

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

pure virtualinherited

Set the comments.

Parameters

comments

The new comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Pasta::appendAlignmentFromStream(), bpp::Clustal::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), and bpp::Mase::appendSequencesFromStream().

setContent() [1/5]

void SequenceWithAnnotation::setContent ( const std::string &  sequence )

overridevirtualinherited

Set the whole content of the sequence.

Parameters

sequence

The new content of the sequence.

See also

The Sequence constructor for information about the way sequences are internally stored.

Implements bpp::SequenceInterface.

Definition at line 20 of file SequenceWithAnnotation.cpp.

References bpp::StringSequenceTools::codeSequence(), and bpp::TextTools::removeWhiteSpaces().

setContent() [2/5]

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

inlineoverridevirtualinherited

Reimplemented from bpp::EventDrivenIntSymbolList.

Definition at line 315 of file SequenceWithAnnotation.h.

References bpp::IntSymbolListInterface::setContent().

setContent() [3/5]

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

inlineoverridevirtualinherited

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.

Reimplemented from bpp::EventDrivenIntSymbolList.

Definition at line 310 of file SequenceWithAnnotation.h.

References bpp::IntSymbolListInterface::setContent().

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().

setElement() [1/7]

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() [2/7]

virtual void bpp::AbstractTemplateEventDrivenSymbolList< int >::setElement ( size_t  pos, const T &  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.

Definition at line 352 of file SymbolList.h.

setElement() [3/7]

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

overridevirtualinherited

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.

Reimplemented from bpp::IntSymbolList.

Definition at line 127 of file IntSymbolList.cpp.

References bpp::AbstractTemplateEventDrivenSymbolList< T >::setElement().

setElement() [4/7]

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() [5/7]

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() [6/7]

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.

setElement() [7/7]

void bpp::AbstractTemplateSymbolList< T >::setElement

inlineoverrideinherited

Definition at line 165 of file SymbolList.h.

setName() [1/2]

void bpp::AbstractCoreSequence::setName ( const std::string &  name )

inlineoverridevirtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::CoreSequenceInterface.

Definition at line 172 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::Pasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPhd::nextSequence(), and bpp::SequenceWithAnnotation::operator=().

setName() [2/2]

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

pure virtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::AbstractCoreSequence.

setQualities()

void bpp::SequenceWithQuality::setQualities ( const std::vector< int > &  quality )

inline

Set the whole quality scores.

Parameters

quality

The vector of quality scores

Exceptions

DimensionException

if the quality vector does not feet the sequence size

Definition at line 536 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::PhredPhd::nextSequence().

setQuality()

void bpp::SequenceWithQuality::setQuality ( size_t  pos, int  quality  )

inline

Set the quality score.

Parameters

pos	The position where the quality must be set
quality	The quality value

Exceptions

IndexOutOfBoundsException

if pos is greater than the sequence size

Definition at line 506 of file SequenceWithQuality.h.

References qualScores_.

setToSizeL()

void SequenceWithAnnotation::setToSizeL ( size_t  newSize )

overridevirtualinherited

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.

Implements bpp::CoreSequenceInterface.

Definition at line 60 of file SequenceWithAnnotation.cpp.

setToSizeR()

void SequenceWithAnnotation::setToSizeR ( size_t  newSize )

overridevirtualinherited

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.

Implements bpp::CoreSequenceInterface.

Definition at line 33 of file SequenceWithAnnotation.cpp.

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(), 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]

string EventDrivenIntSymbolList::toString ( ) const

overridevirtualinherited

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::IntSymbolList.

Definition at line 105 of file IntSymbolList.cpp.

References bpp::StringSequenceTools::decodeSequence().

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.

comments_

Comments bpp::SimpleCommentable::comments_

protectedinherited

Definition at line 50 of file Commentable.h.

Referenced by bpp::SimpleCommentable::clearComments(), bpp::SimpleCommentable::getComments(), bpp::SimpleCommentable::operator=(), and bpp::SimpleCommentable::setComments().

content_

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

protectedinherited

The list content.

Definition at line 47 of file SymbolList.h.

listeners_

std::vector<std::shared_ptr<CoreSymbolListListener<int > > > bpp::AbstractTemplateEventDrivenSymbolList< int >::listeners_

protectedinherited

Contains the listeners.

Definition at line 218 of file SymbolList.h.

name_

std::string bpp::AbstractCoreSequence::name_

privateinherited

The sequence name.

Definition at line 103 of file CoreSequence.h.

Referenced by bpp::AbstractCoreSequence::getName(), bpp::AbstractCoreSequence::operator=(), and bpp::AbstractCoreSequence::setName().

propagateEvents_

bool bpp::AbstractTemplateEventDrivenSymbolList< int >::propagateEvents_

privateinherited

Definition at line 212 of file SymbolList.h.

qualScores_

std::shared_ptr<SequenceQuality> bpp::SequenceWithQuality::qualScores_

private

Definition at line 185 of file SequenceWithQuality.h.

Referenced by addElement(), append(), getQualities(), getQuality(), operator=(), SequenceWithQuality(), setQualities(), and setQuality().

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

• Bpp/Seq/SequenceWithQuality.h