#include <Bpp/Seq/SequenceWithQuality.h>

Inheritance diagram for bpp::SequenceQuality:

Collaboration diagram for bpp::SequenceQuality:

Public Member Functions
void	init (const Sequence &seq) override

const std::string &	getType () const override

bool	isValidWith (const SequenceWithAnnotation &sequence, bool throwException=true) const override
	Test is the annotation is valid for a given sequence. More...

bool	isRemovable () const override

bool	isShared () const override

void	beforeSequenceChanged (const IntSymbolListEditionEvent &event) override

void	afterSequenceChanged (const IntSymbolListEditionEvent &event) override

void	beforeSequenceInserted (const IntSymbolListInsertionEvent &event) override

void	afterSequenceInserted (const IntSymbolListInsertionEvent &event) override

void	beforeSequenceDeleted (const IntSymbolListDeletionEvent &event) override

void	afterSequenceDeleted (const IntSymbolListDeletionEvent &event) override

void	beforeSequenceSubstituted (const IntSymbolListSubstitutionEvent &event) override

void	afterSequenceSubstituted (const IntSymbolListSubstitutionEvent &event) override

size_t	getSize () const

const int &	operator[] (size_t i) const

int &	operator[] (size_t i)

void	setScores (const std::vector< int > &scores)

const std::vector< int > &	getScores () const

void	setScore (size_t pos, int score)

void	setScores (size_t pos, const std::vector< int > &scores)

bool	merge (const SequenceAnnotation &anno) override
	Merge the input annotation with the current one. More...

std::unique_ptr< SequenceAnnotation >	getPartAnnotation (size_t pos, size_t len) const override

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

Constructors
	SequenceQuality (size_t size=0, bool removable=true)
	Build a new SequenceQuality object. More...

	SequenceQuality (const std::vector< int > &quality, bool removable=true)
	Build a new SequenceQuality object. More...

Destructor
virtual	~SequenceQuality ()

The Clonable interface
SequenceQuality *	clone () const override

Static Public Attributes
static const std::string	QUALITY_SCORE = "Quality score"

static const int	DEFAULT_QUALITY_VALUE = 20

Private Attributes
bool	removable_

std::vector< int >	qualScores_

Detailed Description

The SequenceQuality class.

This is a sequence with quality score associated to each element. The score is a signed int value that can represent the phred or the Solexa quality score for nucleic sequence.

Author: Sylvain Gaillard, Vincent Cahais, Julien Dutheil

Definition at line 30 of file SequenceWithQuality.h.

Constructor & Destructor Documentation

◆ SequenceQuality() [1/2]

bpp::SequenceQuality::SequenceQuality	(	size_t	size = `0`,
		bool	removable = `true`
	)

inline

Build a new SequenceQuality object.

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

Parameters

size	The size of the sequence.
removable	Tell if this listener can be removed by the user.

Definition at line 56 of file SequenceWithQuality.h.

Referenced by clone(), and getPartAnnotation().

◆ SequenceQuality() [2/2]

bpp::SequenceQuality::SequenceQuality	(	const std::vector< int > &	quality,
		bool	removable = `true`
	)

inline

Build a new SequenceQuality object.

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

Parameters

quality	The quality scores
removable	Tell if this listener can be removed by the user.

Definition at line 70 of file SequenceWithQuality.h.

◆ ~SequenceQuality()

virtual bpp::SequenceQuality::~SequenceQuality ( )

inlinevirtual

Definition at line 81 of file SequenceWithQuality.h.

Member Function Documentation

◆ afterSequenceChanged() [1/2]

template<class T >

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

pure virtualinherited

◆ afterSequenceChanged() [2/2]

void SequenceQuality::afterSequenceChanged ( const IntSymbolListEditionEvent & event )

override

Definition at line 21 of file SequenceWithQuality.cpp.

References bpp::CoreSymbolListEditionEvent< T >::getCoreSymbolList().

◆ afterSequenceDeleted() [1/2]

template<class T >

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

pure virtualinherited

◆ afterSequenceDeleted() [2/2]

void SequenceQuality::afterSequenceDeleted ( const IntSymbolListDeletionEvent & event )

override

Definition at line 38 of file SequenceWithQuality.cpp.

References bpp::CoreSymbolListDeletionEvent< T >::getLength(), and bpp::CoreSymbolListDeletionEvent< T >::getPosition().

◆ afterSequenceInserted() [1/2]

template<class T >

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

pure virtualinherited

◆ afterSequenceInserted() [2/2]

void SequenceQuality::afterSequenceInserted ( const IntSymbolListInsertionEvent & event )

override

Definition at line 29 of file SequenceWithQuality.cpp.

References bpp::CoreSymbolListInsertionEvent< T >::getLength(), and bpp::CoreSymbolListInsertionEvent< T >::getPosition().

◆ afterSequenceSubstituted() [1/2]

template<class T >

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

pure virtualinherited

◆ afterSequenceSubstituted() [2/2]

void bpp::SequenceQuality::afterSequenceSubstituted ( const IntSymbolListSubstitutionEvent & event )

inlineoverride

Definition at line 115 of file SequenceWithQuality.h.

◆ beforeSequenceChanged() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceChanged() [2/2]

void bpp::SequenceQuality::beforeSequenceChanged ( const IntSymbolListEditionEvent & event )

inlineoverride

Definition at line 108 of file SequenceWithQuality.h.

◆ beforeSequenceDeleted() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceDeleted() [2/2]

void bpp::SequenceQuality::beforeSequenceDeleted ( const IntSymbolListDeletionEvent & event )

inlineoverride

Definition at line 112 of file SequenceWithQuality.h.

◆ beforeSequenceInserted() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceInserted() [2/2]

void bpp::SequenceQuality::beforeSequenceInserted ( const IntSymbolListInsertionEvent & event )

inlineoverride

Definition at line 110 of file SequenceWithQuality.h.

◆ beforeSequenceSubstituted() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceSubstituted() [2/2]

void bpp::SequenceQuality::beforeSequenceSubstituted ( const IntSymbolListSubstitutionEvent & event )

inlineoverride

Definition at line 114 of file SequenceWithQuality.h.

◆ clone()

SequenceQuality* bpp::SequenceQuality::clone ( ) const

inlineoverridevirtual

Implements bpp::SequenceAnnotation.

Definition at line 88 of file SequenceWithQuality.h.

References SequenceQuality().

◆ getPartAnnotation()

std::unique_ptr<SequenceAnnotation> bpp::SequenceQuality::getPartAnnotation	(	size_t	pos,
		size_t	len
	)		const

inlineoverridevirtual

Returns: A new annotation corresponding to a part of the sequence. The implementation of this highly depends on the annotation type, and might not be supported.

Parameters

pos	Starting point of the region.
len	The length of the region, in number of positions.

Implements bpp::SequenceAnnotation.

Definition at line 162 of file SequenceWithQuality.h.

References qualScores_, removable_, and SequenceQuality().

◆ getScores()

const std::vector<int>& bpp::SequenceQuality::getScores ( ) const

inline

Returns: All scores as a vector.

Definition at line 132 of file SequenceWithQuality.h.

References qualScores_.

Referenced by merge().

◆ getSize()

size_t bpp::SequenceQuality::getSize ( ) const

inline

Definition at line 117 of file SequenceWithQuality.h.

References qualScores_.

◆ getType()

const std::string& bpp::SequenceQuality::getType ( ) const

inlineoverridevirtual

Returns: The type of the annotation. This is used for querying annotations.

Implements bpp::SequenceAnnotation.

Definition at line 98 of file SequenceWithQuality.h.

References QUALITY_SCORE.

◆ init()

void bpp::SequenceQuality::init ( const Sequence & seq )

inlineoverridevirtual

Creates a default annotation according to a given sequence.

Parameters

seq	The template sequence (typically the one with which the annotation will be attached).

Implements bpp::SequenceAnnotation.

Definition at line 92 of file SequenceWithQuality.h.

References DEFAULT_QUALITY_VALUE, qualScores_, and bpp::AbstractTemplateSymbolList< T >::size().

◆ isRemovable()

bool bpp::SequenceQuality::isRemovable ( ) const

inlineoverridevirtual

Implements bpp::CoreSymbolListListener< T >.

Definition at line 106 of file SequenceWithQuality.h.

References removable_.

◆ isShared()

bool bpp::SequenceQuality::isShared ( ) const

inlineoverridevirtual

Implements bpp::CoreSymbolListListener< T >.

Definition at line 107 of file SequenceWithQuality.h.

◆ isValidWith()

bool bpp::SequenceQuality::isValidWith	(	const SequenceWithAnnotation &	sequence,
		bool	throwException = `true`
	)		const

inlineoverridevirtual

Test is the annotation is valid for a given sequence.

Parameters

sequence	The sequence to be validated against.
throwException	If set to yes, throw an exception if the sequence is not valid.

Returns: true if this annotation is compliant with the given sequence.

Implements bpp::SequenceAnnotation.

Definition at line 100 of file SequenceWithQuality.h.

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

◆ merge()

bool bpp::SequenceQuality::merge ( const SequenceAnnotation & anno )

inlineoverridevirtual

Merge the input annotation with the current one.

Parameters

anno	The annotation to fuse.

Returns: true if the fusion was possible and successful.

Implements bpp::SequenceAnnotation.

Definition at line 148 of file SequenceWithQuality.h.

References bpp::VectorTools::append(), getScores(), and qualScores_.

◆ operator[]() [1/2]

int& bpp::SequenceQuality::operator[] ( size_t i )

inline

Definition at line 120 of file SequenceWithQuality.h.

References qualScores_.

◆ operator[]() [2/2]

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

inline

Definition at line 119 of file SequenceWithQuality.h.

References qualScores_.

◆ setScore()

void bpp::SequenceQuality::setScore	(	size_t	pos,
		int	score
	)

inline

Definition at line 134 of file SequenceWithQuality.h.

References qualScores_, and bpp::TextTools::toString().

◆ setScores() [1/2]

void bpp::SequenceQuality::setScores ( const std::vector< int > & scores )

inline

Definition at line 122 of file SequenceWithQuality.h.

References qualScores_.

◆ setScores() [2/2]

void bpp::SequenceQuality::setScores	(	size_t	pos,
		const std::vector< int > &	scores
	)

inline

Definition at line 141 of file SequenceWithQuality.h.

References qualScores_, and bpp::TextTools::toString().

Member Data Documentation

◆ DEFAULT_QUALITY_VALUE

const int SequenceQuality::DEFAULT_QUALITY_VALUE = 20

static

Definition at line 39 of file SequenceWithQuality.h.

Referenced by init().

◆ QUALITY_SCORE

const string SequenceQuality::QUALITY_SCORE = "Quality score"

static

Definition at line 38 of file SequenceWithQuality.h.

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

◆ qualScores_

std::vector<int> bpp::SequenceQuality::qualScores_

private

Definition at line 35 of file SequenceWithQuality.h.

Referenced by getPartAnnotation(), getScores(), getSize(), init(), isValidWith(), merge(), operator[](), setScore(), and setScores().

◆ removable_

bool bpp::SequenceQuality::removable_

private

Definition at line 34 of file SequenceWithQuality.h.

Referenced by getPartAnnotation(), and isRemovable().

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

Bpp/Seq/SequenceWithQuality.h
Bpp/Seq/SequenceWithQuality.cpp

Public Member Functions

Static Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SequenceQuality() [1/2]

◆ SequenceQuality() [2/2]

◆ ~SequenceQuality()

Member Function Documentation

◆ afterSequenceChanged() [1/2]

◆ afterSequenceChanged() [2/2]

◆ afterSequenceDeleted() [1/2]

◆ afterSequenceDeleted() [2/2]

◆ afterSequenceInserted() [1/2]

◆ afterSequenceInserted() [2/2]

◆ afterSequenceSubstituted() [1/2]

◆ afterSequenceSubstituted() [2/2]

◆ beforeSequenceChanged() [1/2]

◆ beforeSequenceChanged() [2/2]

◆ beforeSequenceDeleted() [1/2]

◆ beforeSequenceDeleted() [2/2]

◆ beforeSequenceInserted() [1/2]

◆ beforeSequenceInserted() [2/2]

◆ beforeSequenceSubstituted() [1/2]

◆ beforeSequenceSubstituted() [2/2]

◆ clone()

◆ getPartAnnotation()

◆ getScores()

◆ getSize()

◆ getType()

◆ init()

◆ isRemovable()

◆ isShared()

◆ isValidWith()

◆ merge()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ setScore()

◆ setScores() [1/2]

◆ setScores() [2/2]

Member Data Documentation

◆ DEFAULT_QUALITY_VALUE

◆ QUALITY_SCORE

◆ qualScores_

◆ removable_