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

#include <Bpp/Seq/SequenceWithQuality.h>

Inheritance diagram for bpp::SequenceWithQuality:

Collaboration diagram for bpp::SequenceWithQuality:

Public Member Functions
	SequenceWithQuality (const SequenceWithQuality &sequence)

SequenceWithQuality &	operator= (const SequenceWithQuality &sequence)

virtual void	addAnnotation (SequenceAnnotation *anno) throw (Exception)
	Add a new annotation to the sequence. More...

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

virtual const SequenceAnnotation &	getAnnotation (const std::string &type) const

virtual SequenceAnnotation &	getAnnotation (const std::string &type)

virtual std::vector< std::string >	getAnnotationTypes () const

virtual void	merge (const SequenceWithAnnotation &swa) throw (AlphabetMismatchException, Exception)
	Merge a sequence with the current one. More...

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

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

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

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

virtual const std::vector< int > &	getContent () const
	Get the whole content of the list as a vector of int. More...

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

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

virtual void	setElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'. More...

virtual void	setElement (size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'. More...

virtual void	deleteElement (size_t pos) throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'. More...

virtual void	deleteElements (size_t pos, size_t len) throw (IndexOutOfBoundsException)
	Delete the elements at position 'pos'. More...

virtual std::string	getChar (size_t pos) const throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character. More...

virtual int	getValue (size_t pos) const throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as an int. More...

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

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

virtual void	shuffle ()
	Randomly shuffle the content of the list, with linear complexity. More...

Constructors
	SequenceWithQuality (const Alphabet *alpha)
	Build a new empty SequenceWithQuality. More...

	SequenceWithQuality (const std::string &name, const std::string &sequence, const Alphabet *alpha) throw (BadCharException)
	Build a new SequenceWithQuality from a std::string. More...

	SequenceWithQuality (const std::string &name, const std::string &sequence, const Comments &comments, const Alphabet *alpha) throw (BadCharException)
	Build a new SequenceWithQuality from a std::string. More...

	SequenceWithQuality (const std::string &name, const std::string &sequence, const std::vector< int > &quality, const Alphabet *alpha) throw (BadCharException, DimensionException)
	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, const Alphabet *alpha) throw (BadCharException, DimensionException)
	Build a new SequenceWithQuality from a std::string. More...

	SequenceWithQuality (const std::string &name, const std::vector< int > &sequence, const Alphabet *alpha) throw (BadIntException)
	Build a new SequenceWithQuality from a std::vector<int> More...

	SequenceWithQuality (const std::string &name, const std::vector< int > &sequence, const Comments &comments, const Alphabet *alpha) throw (BadIntException)
	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 Alphabet *alpha) throw (BadIntException, DimensionException)
	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, const Alphabet *alpha) throw (BadIntException, DimensionException)
	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) throw (DimensionException)
	Build a new SequenceWithQuality. More...

Destructor
virtual	~SequenceWithQuality ()

The Clonable interface
SequenceWithQuality *	clone () const

Dealing with quality
void	setQuality (size_t pos, int quality) throw (IndexOutOfBoundsException)
	Set the quality score. More...

int	getQuality (size_t pos) const throw (IndexOutOfBoundsException)
	Get the quality score. More...

void	setQualities (const std::vector< int > &quality) throw (DimensionException)
	Set the whole quality scores. More...

const std::vector< int > &	getQualities () const
	Get the whole quality scores. More...

void	append (const std::vector< int > &content) throw (BadIntException)
	Append the specified content to the sequence. More...

void	append (const std::vector< int > &content, const std::vector< int > &qualities) throw (BadIntException, DimensionException)
	Append content with quality. More...

void	append (const std::vector< std::string > &content) throw (BadCharException)
	Append the specified content to the sequence. More...

void	append (const std::vector< std::string > &content, const std::vector< int > &qualities) throw (BadCharException, DimensionException)
	Append content with quality. More...

void	append (const std::string &content) throw (BadCharException)
	Append the specified content to the sequence. More...

void	append (const std::string &content, const std::vector< int > &qualities) throw (BadCharException, DimensionException)
	Append content with quality. More...

void	addElement (const std::string &c) throw (BadCharException)
	Add a character to the end of the list. More...

void	addElement (const std::string &c, int q) throw (BadCharException)
	Add a character to the end of the list with quality. More...

void	addElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Add a character at a certain position in the list. More...

void	addElement (size_t pos, const std::string &c, int q) throw (BadCharException, IndexOutOfBoundsException)
	Add a character to a certain position in the list with quality. More...

void	addElement (int v) throw (BadIntException)
	Add a character to the end of the list. More...

void	addElement (int v, int q) throw (BadIntException)
	Add a character to the end of the list with quality. More...

void	addElement (size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
	Add a character at a certain position in the list. More...

void	addElement (size_t pos, int v, int q) throw (BadCharException, IndexOutOfBoundsException)
	Add a character to a certain position in the list with quality. More...

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

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

Setting/getting the comments associated to the sequence.
const Comments &	getComments () const
	Get the comments associated to this sequence. More...

void	setComments (const Comments &comments)
	Set the comments associated to this sequence. More...

Adjusting the size of the sequence.
virtual void	setContent (const std::string &sequence) throw (BadCharException)
	Set the whole content of the sequence. More...

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

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

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

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

Acting on the content of the list.
virtual const std::vector< int > &	getContent () const =0
	Get the whole content of the list as a vector of int. More...

Edition methods.
virtual void	setElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'. More...

virtual void	setElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'. More...

virtual void	deleteElement (size_t pos)=0 throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'. More...

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

virtual std::string	getChar (size_t pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character. More...

virtual int	getValue (size_t pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as an int. More...

Provide direct access to the list content.
Warning These operators allow you to modifiy the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual const int &	operator[] (size_t i) const =0
	Operator [] overloaded for quick access to a character in list. More...

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

virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

Protected Member Functions
void	propagateEvents (bool yn)

bool	propagateEvents () const

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

std::vector< SymbolListListener * >	listeners_
	Contains the listeners. More...

Private Attributes
SequenceQuality *	qualScores_

Events handling
virtual size_t	getNumberOfListeners () const

virtual const SymbolListListener &	getListener (size_t i) const

virtual SymbolListListener &	getListener (size_t i)

virtual void	addSymbolListListener (SymbolListListener *listener)

virtual void	removeSymbolListListener (SymbolListListener *listener)

virtual void	beforeSequenceChanged (const SymbolListEditionEvent &event)

virtual void	afterSequenceChanged (const SymbolListEditionEvent &event)

virtual void	beforeSequenceInserted (const SymbolListInsertionEvent &event)

virtual void	afterSequenceInserted (const SymbolListInsertionEvent &event)

virtual void	beforeSequenceDeleted (const SymbolListDeletionEvent &event)

virtual void	afterSequenceDeleted (const SymbolListDeletionEvent &event)

virtual void	beforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)

virtual void	afterSequenceSubstituted (const SymbolListSubstitutionEvent &event)

void	fireBeforeSequenceChanged (const SymbolListEditionEvent &event)

void	fireAfterSequenceChanged (const SymbolListEditionEvent &event)

void	fireBeforeSequenceInserted (const SymbolListInsertionEvent &event)

void	fireAfterSequenceInserted (const SymbolListInsertionEvent &event)

void	fireBeforeSequenceDeleted (const SymbolListDeletionEvent &event)

void	fireAfterSequenceDeleted (const SymbolListDeletionEvent &event)

void	fireBeforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)

void	fireAfterSequenceSubstituted (const SymbolListSubstitutionEvent &event)

Detailed Description

A SequenceWithAnnotation class with quality scores attached.

This classes adds some usefull functions to handle quality scores.

See also: SequenceQuality

Author: Sylvain Gaillard, Vincent Cahais, Julien Dutheil

Definition at line 218 of file SequenceWithQuality.h.

Constructor & Destructor Documentation

◆ SequenceWithQuality() [1/12]

bpp::SequenceWithQuality::SequenceWithQuality ( const Alphabet * alpha )

inline

Build a new empty SequenceWithQuality.

Parameters

alpha A pointer to an Alphabet

Exceptions

BadCharException if a state is not alowed by the Alphabet

Definition at line 238 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,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

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 alowed by the Alphabet

Definition at line 259 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,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

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 alowed by the Alphabet

Author: Vincent Cahais

Definition at line 285 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,
		const Alphabet *	alpha
	)
throw	(	BadCharException,
		DimensionException
	)

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 alowed by the Alphabet
DimensionException	if the number of quality values is not equal to the number of sequence states

Definition at line 312 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,
		const Alphabet *	alpha
	)
throw	(	BadCharException,
		DimensionException
	)

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 alowed 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 342 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,
		const Alphabet *	alpha
	)
throw	(	BadIntException
	)

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 alowed by the Alphabet

Definition at line 367 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,
		const Alphabet *	alpha
	)
throw	(	BadIntException
	)

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 alowed by the Alphabet

Author: Vincent Cahais

Definition at line 393 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,
		const Alphabet *	alpha
	)
throw	(	BadIntException,
		DimensionException
	)

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 alowed by the Alphabet
DimensionException	if the number of quality values is not equal to the number of sequence states

Definition at line 420 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,
		const Alphabet *	alpha
	)
throw	(	BadIntException,
		DimensionException
	)

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 alowed 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 450 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 471 of file SequenceWithQuality.h.

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

◆ SequenceWithQuality() [11/12]

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

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 489 of file SequenceWithQuality.h.

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

◆ ~SequenceWithQuality()

virtual bpp::SequenceWithQuality::~SequenceWithQuality ( )

inlinevirtual

Definition at line 505 of file SequenceWithQuality.h.

◆ SequenceWithQuality() [12/12]

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

inline

Definition at line 508 of file SequenceWithQuality.h.

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

Member Function Documentation

◆ addAnnotation()

virtual void bpp::SequenceWithAnnotation::addAnnotation	(	SequenceAnnotation *	anno	)
throw	(	Exception
	)

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 380 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::addSymbolListListener().

Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation(), and SequenceWithQuality().

◆ addElement() [1/8]

void bpp::SequenceWithQuality::addElement	(	const std::string &	c	)
throw	(	BadCharException
	)

inlinevirtual

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Reimplemented from bpp::EdSymbolList.

Definition at line 684 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement().

◆ addElement() [2/8]

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

inline

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

Definition at line 700 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement(), qualScores_, bpp::SequenceQuality::setScore(), and bpp::EdSymbolList::size().

◆ addElement() [3/8]

void bpp::SequenceWithQuality::addElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

inlinevirtual

Add a character at a certain position in the list.

Parameters

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

Reimplemented from bpp::EdSymbolList.

Definition at line 708 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement().

◆ addElement() [4/8]

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

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 726 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement(), qualScores_, and bpp::SequenceQuality::setScore().

◆ addElement() [5/8]

void bpp::SequenceWithQuality::addElement	(	int	v	)
throw	(	BadIntException
	)

inlinevirtual

Add a character to the end of the list.

Parameters

v	The character to add, given as an int.

Reimplemented from bpp::EdSymbolList.

Definition at line 734 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement().

◆ addElement() [6/8]

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

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 748 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement(), qualScores_, bpp::SequenceQuality::setScore(), and bpp::EdSymbolList::size().

◆ addElement() [7/8]

void bpp::SequenceWithQuality::addElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

inlinevirtual

Add a character at a certain position in the list.

Parameters

pos	The postion where to insert the element.
v	The character to add, given as an int.

Reimplemented from bpp::EdSymbolList.

Definition at line 755 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement().

◆ addElement() [8/8]

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

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 772 of file SequenceWithQuality.h.

References bpp::EdSymbolList::addElement(), qualScores_, and bpp::SequenceQuality::setScore().

◆ addSymbolListListener()

virtual void bpp::EdSymbolList::addSymbolListListener ( SymbolListListener * listener )

inlinevirtualinherited

Definition at line 657 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

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

◆ afterSequenceChanged()

virtual void bpp::EdSymbolList::afterSequenceChanged ( const SymbolListEditionEvent & event )

inlineprotectedvirtualinherited

Definition at line 670 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireAfterSequenceChanged().

◆ afterSequenceDeleted()

virtual void bpp::EdSymbolList::afterSequenceDeleted ( const SymbolListDeletionEvent & event )

inlineprotectedvirtualinherited

Definition at line 674 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireAfterSequenceDeleted().

◆ afterSequenceInserted()

virtual void bpp::EdSymbolList::afterSequenceInserted ( const SymbolListInsertionEvent & event )

inlineprotectedvirtualinherited

Definition at line 672 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireAfterSequenceInserted().

◆ afterSequenceSubstituted()

virtual void bpp::EdSymbolList::afterSequenceSubstituted ( const SymbolListSubstitutionEvent & event )

inlineprotectedvirtualinherited

Definition at line 676 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireAfterSequenceSubstituted().

◆ append() [1/6]

void bpp::SequenceWithQuality::append	(	const std::vector< int > &	content	)
throw	(	BadIntException
	)

inlinevirtual

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.

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 593 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append().

Referenced by append().

◆ append() [2/6]

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

inline

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 610 of file SequenceWithQuality.h.

References append(), bpp::SequenceQuality::getSize(), qualScores_, and bpp::SequenceQuality::setScores().

◆ append() [3/6]

void bpp::SequenceWithQuality::append	(	const std::vector< std::string > &	content	)
throw	(	BadCharException
	)

inlinevirtual

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.

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 623 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append().

◆ append() [4/6]

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

inline

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 640 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append(), bpp::SequenceQuality::getSize(), qualScores_, and bpp::SequenceQuality::setScores().

◆ append() [5/6]

void bpp::SequenceWithQuality::append	(	const std::string &	content	)
throw	(	BadCharException
	)

inlinevirtual

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.

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 653 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append().

◆ append() [6/6]

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

inline

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 670 of file SequenceWithQuality.h.

References bpp::SequenceWithAnnotation::append(), bpp::EdSymbolList::getAlphabet(), bpp::SequenceQuality::getSize(), bpp::Alphabet::getStateCodingSize(), qualScores_, and bpp::SequenceQuality::setScores().

◆ beforeSequenceChanged()

virtual void bpp::EdSymbolList::beforeSequenceChanged ( const SymbolListEditionEvent & event )

inlineprotectedvirtualinherited

Definition at line 669 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireBeforeSequenceChanged().

◆ beforeSequenceDeleted()

virtual void bpp::EdSymbolList::beforeSequenceDeleted ( const SymbolListDeletionEvent & event )

inlineprotectedvirtualinherited

Definition at line 673 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireBeforeSequenceDeleted().

◆ beforeSequenceInserted()

virtual void bpp::EdSymbolList::beforeSequenceInserted ( const SymbolListInsertionEvent & event )

inlineprotectedvirtualinherited

Definition at line 671 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireBeforeSequenceInserted().

◆ beforeSequenceSubstituted()

virtual void bpp::EdSymbolList::beforeSequenceSubstituted ( const SymbolListSubstitutionEvent & event )

inlineprotectedvirtualinherited

Definition at line 675 of file SymbolList.h.

Referenced by bpp::EdSymbolList::fireBeforeSequenceSubstituted().

◆ clone()

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

inlinevirtual

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 530 of file SequenceWithQuality.h.

References SequenceWithQuality().

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

◆ deleteElement() [1/2]

virtual void bpp::SymbolList::deleteElement	(	size_t	pos	)
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Delete the element at position 'pos'.

Parameters

pos	The position of the element to delete.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

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

◆ deleteElement() [2/2]

void EdSymbolList::deleteElement	(	size_t	pos	)
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Delete the element at position 'pos'.

Parameters

pos	The position of the element to delete.

Implements bpp::SymbolList.

Definition at line 369 of file SymbolList.cpp.

◆ deleteElements() [1/2]

virtual void bpp::SymbolList::deleteElements	(	size_t	pos,
		size_t	len
	)
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Delete the elements at position 'pos'.

Parameters

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

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ deleteElements() [2/2]

void EdSymbolList::deleteElements	(	size_t	pos,
		size_t	len
	)
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Delete the elements at position 'pos'.

Parameters

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

Implements bpp::SymbolList.

Definition at line 381 of file SymbolList.cpp.

◆ fireAfterSequenceChanged()

void bpp::EdSymbolList::fireAfterSequenceChanged ( const SymbolListEditionEvent & event )

inlineprotectedinherited

Definition at line 685 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceChanged(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

◆ fireAfterSequenceDeleted()

void bpp::EdSymbolList::fireAfterSequenceDeleted ( const SymbolListDeletionEvent & event )

inlineprotectedinherited

Definition at line 713 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceDeleted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

◆ fireAfterSequenceInserted()

void bpp::EdSymbolList::fireAfterSequenceInserted ( const SymbolListInsertionEvent & event )

inlineprotectedinherited

Definition at line 699 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceInserted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

◆ fireAfterSequenceSubstituted()

void bpp::EdSymbolList::fireAfterSequenceSubstituted ( const SymbolListSubstitutionEvent & event )

inlineprotectedinherited

Definition at line 727 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceSubstituted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

◆ fireBeforeSequenceChanged()

void bpp::EdSymbolList::fireBeforeSequenceChanged ( const SymbolListEditionEvent & event )

inlineprotectedinherited

Definition at line 678 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceChanged(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

◆ fireBeforeSequenceDeleted()

void bpp::EdSymbolList::fireBeforeSequenceDeleted ( const SymbolListDeletionEvent & event )

inlineprotectedinherited

Definition at line 706 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceDeleted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

◆ fireBeforeSequenceInserted()

void bpp::EdSymbolList::fireBeforeSequenceInserted ( const SymbolListInsertionEvent & event )

inlineprotectedinherited

Definition at line 692 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceInserted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

◆ fireBeforeSequenceSubstituted()

void bpp::EdSymbolList::fireBeforeSequenceSubstituted ( const SymbolListSubstitutionEvent & event )

inlineprotectedinherited

Definition at line 720 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceSubstituted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

◆ getAlphabet() [1/2]

virtual const Alphabet* bpp::SymbolList::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::EdSymbolList, and bpp::BasicSymbolList.

◆ getAlphabet() [2/2]

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

inlinevirtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::SymbolList.

Definition at line 599 of file SymbolList.h.

References bpp::EdSymbolList::alphabet_.

Referenced by append(), bpp::EdSymbolList::operator=(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

◆ getAnnotation() [1/2]

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

inlinevirtualinherited

Definition at line 397 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

Referenced by operator=(), and SequenceWithQuality().

◆ getAnnotation() [2/2]

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

inlinevirtualinherited

Definition at line 407 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

◆ getAnnotationTypes()

vector< string > SequenceWithAnnotation::getAnnotationTypes ( ) const

virtualinherited

Returns: The list of annotation types contained in this sequence.

Definition at line 244 of file SequenceWithAnnotation.cpp.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

◆ getChar() [1/2]

virtual std::string bpp::SymbolList::getChar	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

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

◆ getChar() [2/2]

string EdSymbolList::getChar	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

virtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::SymbolList.

Definition at line 354 of file SymbolList.cpp.

◆ getComments()

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

inlinevirtualinherited

Get the comments associated to this sequence.

Returns: The comments of the sequence.

Implements bpp::Sequence.

Definition at line 290 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::comments_.

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

◆ getContent() [1/2]

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

pure virtualinherited

Get the whole content of the list as a vector of int.

Returns: A reference to the content of the list.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SequenceWithQualityTools::complement(), bpp::AbstractSequenceContainer::getContent(), bpp::SymbolListTools::getCounts(), bpp::BasicSymbolList::operator=(), bpp::EdSymbolList::operator=(), bpp::SequenceWithQualityTools::reverseTranscript(), and bpp::SequenceWithQualityTools::transcript().

◆ getContent() [2/2]

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

inlinevirtualinherited

Get the whole content of the list as a vector of int.

Returns: A reference to the content of the list.

Implements bpp::SymbolList.

Definition at line 603 of file SymbolList.h.

References bpp::EdSymbolList::content_.

Referenced by bpp::SequenceWithQualityTools::invert(), and bpp::EdSymbolList::operator=().

◆ getListener() [1/2]

virtual const SymbolListListener& bpp::EdSymbolList::getListener ( size_t i ) const

inlinevirtualinherited

Definition at line 647 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

Referenced by bpp::SequenceWithAnnotation::getAnnotation(), bpp::SequenceWithAnnotation::getAnnotationTypes(), and bpp::SequenceWithAnnotation::hasAnnotation().

◆ getListener() [2/2]

virtual SymbolListListener& bpp::EdSymbolList::getListener ( size_t i )

inlinevirtualinherited

Definition at line 652 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

◆ getName()

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

inlinevirtualinherited

Get the name of this sequence.

Returns: This sequence name.

Implements bpp::Sequence.

Definition at line 268 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::name_.

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

◆ getNumberOfListeners()

virtual size_t bpp::EdSymbolList::getNumberOfListeners ( ) const

inlinevirtualinherited

Definition at line 645 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

Referenced by bpp::SequenceWithAnnotation::getAnnotation(), bpp::SequenceWithAnnotation::getAnnotationTypes(), and bpp::SequenceWithAnnotation::hasAnnotation().

◆ 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 589 of file SequenceWithQuality.h.

References bpp::SequenceQuality::getScores(), and qualScores_.

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

◆ getQuality()

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

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 564 of file SequenceWithQuality.h.

References bpp::SequenceQuality::getSize(), and qualScores_.

◆ getValue() [1/2]

virtual int bpp::SymbolList::getValue	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Get the element at position 'pos' as an int.

Parameters

pos	The position of the character to retrieve.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

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

◆ getValue() [2/2]

int EdSymbolList::getValue	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Get the element at position 'pos' as an int.

Parameters

pos	The position of the character to retrieve.

Implements bpp::SymbolList.

Definition at line 434 of file SymbolList.cpp.

◆ hasAnnotation()

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

inlinevirtualinherited

Definition at line 386 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

◆ merge()

void SequenceWithAnnotation::merge	(	const SequenceWithAnnotation &	swa	)
throw	(	AlphabetMismatchException,
		Exception
	)

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 257 of file SequenceWithAnnotation.cpp.

References bpp::SequenceAnnotation::clone(), bpp::SequenceAnnotation::init(), and bpp::SequenceAnnotation::merge().

◆ operator=()

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

inline

Definition at line 514 of file SequenceWithQuality.h.

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

◆ operator[]() [1/4]

virtual const int& bpp::SymbolList::operator[] ( size_t i ) const

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ operator[]() [2/4]

virtual int& bpp::SymbolList::operator[] ( size_t i )

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ operator[]() [3/4]

virtual const int& bpp::EdSymbolList::operator[] ( size_t i ) const

inlinevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implements bpp::SymbolList.

Definition at line 631 of file SymbolList.h.

References bpp::EdSymbolList::content_.

◆ operator[]() [4/4]

virtual int& bpp::EdSymbolList::operator[] ( size_t i )

inlinevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implements bpp::SymbolList.

Definition at line 633 of file SymbolList.h.

References bpp::EdSymbolList::content_.

◆ propagateEvents() [1/2]

void bpp::EdSymbolList::propagateEvents ( bool yn )

inlineprotectedinherited

Definition at line 736 of file SymbolList.h.

References bpp::EdSymbolList::propagateEvents_.

◆ propagateEvents() [2/2]

bool bpp::EdSymbolList::propagateEvents ( ) const

inlineprotectedinherited

Definition at line 737 of file SymbolList.h.

References bpp::EdSymbolList::propagateEvents_.

◆ removeSymbolListListener()

virtual void bpp::EdSymbolList::removeSymbolListListener ( SymbolListListener * listener )

inlinevirtualinherited

Definition at line 661 of file SymbolList.h.

References bpp::SymbolListListener::isRemovable(), and bpp::EdSymbolList::listeners_.

◆ setComments()

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

inlinevirtualinherited

Set the comments associated to this sequence.

Parameters

comments The new comments of the sequence.

Implements bpp::Sequence.

Definition at line 297 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::comments_.

◆ setContent() [1/3]

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

virtualinherited

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 internaly stored.

Implements bpp::Sequence.

Definition at line 143 of file SequenceWithAnnotation.cpp.

References bpp::StringSequenceTools::codeSequence().

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

◆ setContent() [2/3]

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

inlinevirtualinherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internaly stored.

Implements bpp::Sequence.

Definition at line 315 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::setContent().

◆ setContent() [3/3]

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

inlinevirtualinherited

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internaly stored.

Implements bpp::Sequence.

Definition at line 319 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::setContent().

◆ setElement() [1/4]

virtual void bpp::SymbolList::setElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

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::EdSymbolList, and bpp::BasicSymbolList.

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

◆ setElement() [2/4]

virtual void bpp::SymbolList::setElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

pure virtualinherited

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

Parameters

pos	The position of the character to set.
v	The value of the element, given as an int.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ setElement() [3/4]

void EdSymbolList::setElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

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.

Implements bpp::SymbolList.

Definition at line 342 of file SymbolList.cpp.

◆ setElement() [4/4]

void EdSymbolList::setElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

virtualinherited

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

Parameters

pos	The position of the character to set.
v	The value of the element, given as an int.

Implements bpp::SymbolList.

Definition at line 420 of file SymbolList.cpp.

◆ setName()

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

inlinevirtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::Sequence.

Definition at line 275 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::name_.

◆ setQualities()

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

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 578 of file SequenceWithQuality.h.

References bpp::SequenceQuality::getSize(), qualScores_, and bpp::SequenceQuality::setScores().

Referenced by bpp::PhredPhd::nextSequence(), and bpp::SequenceWithQualityTools::removeGaps().

◆ setQuality()

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

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 547 of file SequenceWithQuality.h.

References qualScores_, and bpp::SequenceQuality::setScore().

◆ setToSizeL()

void SequenceWithAnnotation::setToSizeL ( size_t newSize )

virtualinherited

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

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

Parameters

newSize The new size of the sequence.

Implements bpp::Sequence.

Definition at line 180 of file SequenceWithAnnotation.cpp.

References bpp::EdSymbolList::content_, bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

◆ setToSizeR()

void SequenceWithAnnotation::setToSizeR ( size_t newSize )

virtualinherited

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

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

Parameters

newSize The new size of the sequence.

Implements bpp::Sequence.

Definition at line 155 of file SequenceWithAnnotation.cpp.

References bpp::EdSymbolList::content_, bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

◆ shuffle() [1/2]

virtual void bpp::SymbolList::shuffle ( )

pure virtualinherited

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

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ shuffle() [2/2]

virtual void bpp::EdSymbolList::shuffle ( )

inlinevirtualinherited

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

Implements bpp::SymbolList.

Definition at line 635 of file SymbolList.h.

References bpp::EdSymbolList::content_.

◆ size() [1/2]

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

pure virtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ size() [2/2]

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

inlinevirtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::SymbolList.

Definition at line 601 of file SymbolList.h.

References bpp::EdSymbolList::content_.

Referenced by addElement(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), and bpp::SequenceWithQualityTools::removeGaps().

◆ toString() [1/2]

virtual std::string bpp::SymbolList::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::EdSymbolList, and bpp::BasicSymbolList.

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

◆ toString() [2/2]

string EdSymbolList::toString ( ) const

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.

Implements bpp::SymbolList.

Definition at line 314 of file SymbolList.cpp.

References bpp::EdSymbolList::alphabet_, bpp::EdSymbolList::content_, and bpp::StringSequenceTools::decodeSequence().

Member Data Documentation

◆ content_

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

protectedinherited

The list content.

Definition at line 518 of file SymbolList.h.

Referenced by bpp::EdSymbolList::getContent(), bpp::EdSymbolList::operator=(), bpp::EdSymbolList::operator[](), bpp::SequenceWithAnnotation::setToSizeL(), bpp::SequenceWithAnnotation::setToSizeR(), bpp::EdSymbolList::shuffle(), bpp::EdSymbolList::size(), and bpp::EdSymbolList::toString().

◆ listeners_

std::vector<SymbolListListener*> bpp::EdSymbolList::listeners_

protectedinherited

Contains the listeners.

Definition at line 523 of file SymbolList.h.

◆ qualScores_

SequenceQuality* bpp::SequenceWithQuality::qualScores_

private

Definition at line 222 of file SequenceWithQuality.h.

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

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

Bpp/Seq/SequenceWithQuality.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Events handling

Detailed Description

Constructor & Destructor Documentation

◆ SequenceWithQuality() [1/12]

◆ SequenceWithQuality() [2/12]

◆ SequenceWithQuality() [3/12]

◆ SequenceWithQuality() [4/12]

◆ SequenceWithQuality() [5/12]

◆ SequenceWithQuality() [6/12]

◆ SequenceWithQuality() [7/12]

◆ SequenceWithQuality() [8/12]

◆ SequenceWithQuality() [9/12]

◆ SequenceWithQuality() [10/12]

◆ SequenceWithQuality() [11/12]

◆ ~SequenceWithQuality()

◆ SequenceWithQuality() [12/12]

Member Function Documentation

◆ addAnnotation()

◆ addElement() [1/8]

◆ addElement() [2/8]

◆ addElement() [3/8]

◆ addElement() [4/8]

◆ addElement() [5/8]

◆ addElement() [6/8]

◆ addElement() [7/8]

◆ addElement() [8/8]

◆ addSymbolListListener()

◆ afterSequenceChanged()

◆ afterSequenceDeleted()

◆ afterSequenceInserted()

◆ afterSequenceSubstituted()

◆ append() [1/6]

◆ append() [2/6]

◆ append() [3/6]

◆ append() [4/6]

◆ append() [5/6]

◆ append() [6/6]

◆ beforeSequenceChanged()

◆ beforeSequenceDeleted()

◆ beforeSequenceInserted()

◆ beforeSequenceSubstituted()

◆ clone()

◆ deleteElement() [1/2]

◆ deleteElement() [2/2]

◆ deleteElements() [1/2]

◆ deleteElements() [2/2]

◆ fireAfterSequenceChanged()

◆ fireAfterSequenceDeleted()

◆ fireAfterSequenceInserted()

◆ fireAfterSequenceSubstituted()

◆ fireBeforeSequenceChanged()

◆ fireBeforeSequenceDeleted()

◆ fireBeforeSequenceInserted()

◆ fireBeforeSequenceSubstituted()

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getAnnotation() [1/2]

◆ getAnnotation() [2/2]

◆ getAnnotationTypes()

◆ getChar() [1/2]

◆ getChar() [2/2]

◆ getComments()

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getListener() [1/2]

◆ getListener() [2/2]

◆ getName()

◆ getNumberOfListeners()

◆ getQualities()

◆ getQuality()

◆ getValue() [1/2]

◆ getValue() [2/2]

◆ hasAnnotation()

◆ merge()

◆ operator=()

◆ operator[]() [1/4]