#include <Bpp/Seq/SequenceWithQuality.h>

Inheritance diagram for bpp::SequenceQuality:

Collaboration diagram for bpp::SequenceQuality:

Public Member Functions
void	init (const Sequence &seq)

const std::string &	getType () const

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

bool	isRemovable () const

bool	isShared () const

void	beforeSequenceChanged (const SymbolListEditionEvent &event)

void	afterSequenceChanged (const SymbolListEditionEvent &event)

void	beforeSequenceInserted (const SymbolListInsertionEvent &event)

void	afterSequenceInserted (const SymbolListInsertionEvent &event)

void	beforeSequenceDeleted (const SymbolListDeletionEvent &event)

void	afterSequenceDeleted (const SymbolListDeletionEvent &event)

void	beforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)

void	afterSequenceSubstituted (const SymbolListSubstitutionEvent &event)

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)
	Merge the input annotation with the current one. More...

SequenceQuality *	getPartAnnotation (size_t pos, size_t len) const throw (Exception)

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

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 65 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 92 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 106 of file SequenceWithQuality.h.

◆ ~SequenceQuality()

virtual bpp::SequenceQuality::~SequenceQuality ( )

inlinevirtual

Definition at line 120 of file SequenceWithQuality.h.

Member Function Documentation

◆ afterSequenceChanged()

void SequenceQuality::afterSequenceChanged ( const SymbolListEditionEvent & event )

virtual

Implements bpp::SymbolListListener.

Definition at line 55 of file SequenceWithQuality.cpp.

◆ afterSequenceDeleted()

void SequenceQuality::afterSequenceDeleted ( const SymbolListDeletionEvent & event )

virtual

Implements bpp::SymbolListListener.

Definition at line 72 of file SequenceWithQuality.cpp.

◆ afterSequenceInserted()

void SequenceQuality::afterSequenceInserted ( const SymbolListInsertionEvent & event )

virtual

Implements bpp::SymbolListListener.

Definition at line 63 of file SequenceWithQuality.cpp.

References bpp::SymbolListInsertionEvent::getLength().

◆ afterSequenceSubstituted()

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 159 of file SequenceWithQuality.h.

◆ beforeSequenceChanged()

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 152 of file SequenceWithQuality.h.

◆ beforeSequenceDeleted()

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 156 of file SequenceWithQuality.h.

◆ beforeSequenceInserted()

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 154 of file SequenceWithQuality.h.

◆ beforeSequenceSubstituted()

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 158 of file SequenceWithQuality.h.

◆ clone()

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

inlinevirtual

Implements bpp::SequenceAnnotation.

Definition at line 132 of file SequenceWithQuality.h.

References SequenceQuality().

◆ getPartAnnotation()

SequenceQuality* bpp::SequenceQuality::getPartAnnotation	(	size_t	pos,
		size_t	len
	)		const
throw	(	Exception
	)

inlinevirtual

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 199 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 175 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::SequenceWithQuality::getQualities(), and merge().

◆ getSize()

size_t bpp::SequenceQuality::getSize ( ) const

inline

Definition at line 161 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::SequenceWithQuality::append(), bpp::SequenceWithQuality::getQuality(), and bpp::SequenceWithQuality::setQualities().

◆ getType()

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

inlinevirtual

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

Implements bpp::SequenceAnnotation.

Definition at line 142 of file SequenceWithQuality.h.

References QUALITY_SCORE.

◆ init()

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

inlinevirtual

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 136 of file SequenceWithQuality.h.

References DEFAULT_QUALITY_VALUE, qualScores_, and bpp::SymbolList::size().

◆ isRemovable()

bool bpp::SequenceQuality::isRemovable ( ) const

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 150 of file SequenceWithQuality.h.

References removable_.

◆ isShared()

bool bpp::SequenceQuality::isShared ( ) const

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 151 of file SequenceWithQuality.h.

◆ isValidWith()

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

inlinevirtual

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 complient with the given sequence.

Implements bpp::SequenceAnnotation.

Definition at line 144 of file SequenceWithQuality.h.

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

◆ merge()

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

inlinevirtual

Merge the input annotation with the current one.

Parameters

anno	The annotation to fuse.

Returns: true if the fusion was possible and succesful.

Implements bpp::SequenceAnnotation.

Definition at line 189 of file SequenceWithQuality.h.

References getScores(), and qualScores_.

◆ operator[]() [1/2]

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

inline

Definition at line 163 of file SequenceWithQuality.h.

References qualScores_.

◆ operator[]() [2/2]

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

inline

Definition at line 164 of file SequenceWithQuality.h.

References qualScores_.

◆ setScore()

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

inline

Definition at line 177 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::SequenceWithQuality::addElement(), and bpp::SequenceWithQuality::setQuality().

◆ setScores() [1/2]

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

inline

Definition at line 166 of file SequenceWithQuality.h.

References qualScores_.

Referenced by bpp::SequenceWithQuality::append(), and bpp::SequenceWithQuality::setQualities().

◆ setScores() [2/2]

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

inline

Definition at line 183 of file SequenceWithQuality.h.

References qualScores_.

Member Data Documentation

◆ DEFAULT_QUALITY_VALUE

const int SequenceQuality::DEFAULT_QUALITY_VALUE = 20

static

Definition at line 74 of file SequenceWithQuality.h.

Referenced by init().

◆ QUALITY_SCORE

const string SequenceQuality::QUALITY_SCORE = "Quality score"

static

Definition at line 73 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 70 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 69 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()

◆ afterSequenceDeleted()

◆ afterSequenceInserted()

◆ afterSequenceSubstituted()

◆ beforeSequenceChanged()

◆ beforeSequenceDeleted()

◆ beforeSequenceInserted()

◆ beforeSequenceSubstituted()

◆ 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_