#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.
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.
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.
	SequenceQuality (const std::vector< int > &quality, bool removable=true)
	Build a new SequenceQuality object.
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 64 of file SequenceWithQuality.h.

Constructor & Destructor Documentation

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 91 of file SequenceWithQuality.h.

Referenced by clone(), and getPartAnnotation().

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 105 of file SequenceWithQuality.h.

virtual bpp::SequenceQuality::~SequenceQuality ( ) [inline, virtual]

Definition at line 119 of file SequenceWithQuality.h.

Member Function Documentation

void SequenceQuality::afterSequenceChanged ( const SymbolListEditionEvent & event ) [virtual]

Implements bpp::SymbolListListener.

Definition at line 55 of file SequenceWithQuality.cpp.

void SequenceQuality::afterSequenceDeleted ( const SymbolListDeletionEvent & event ) [virtual]

Implements bpp::SymbolListListener.

Definition at line 70 of file SequenceWithQuality.cpp.

void SequenceQuality::afterSequenceInserted ( const SymbolListInsertionEvent & event ) [virtual]

Implements bpp::SymbolListListener.

Definition at line 63 of file SequenceWithQuality.cpp.

void bpp::SequenceQuality::afterSequenceSubstituted ( const SymbolListSubstitutionEvent & event ) [inline, virtual]

Implements bpp::SymbolListListener.

Definition at line 158 of file SequenceWithQuality.h.

void bpp::SequenceQuality::beforeSequenceChanged ( const SymbolListEditionEvent & event ) [inline, virtual]

Implements bpp::SymbolListListener.

Definition at line 151 of file SequenceWithQuality.h.

void bpp::SequenceQuality::beforeSequenceDeleted ( const SymbolListDeletionEvent & event ) [inline, virtual]

Implements bpp::SymbolListListener.

Definition at line 155 of file SequenceWithQuality.h.

void bpp::SequenceQuality::beforeSequenceInserted ( const SymbolListInsertionEvent & event ) [inline, virtual]

Implements bpp::SymbolListListener.

Definition at line 153 of file SequenceWithQuality.h.

void bpp::SequenceQuality::beforeSequenceSubstituted ( const SymbolListSubstitutionEvent & event ) [inline, virtual]

Implements bpp::SymbolListListener.

Definition at line 157 of file SequenceWithQuality.h.

SequenceQuality* bpp::SequenceQuality::clone ( ) const [inline, virtual]

Implements bpp::SequenceAnnotation.

Definition at line 131 of file SequenceWithQuality.h.

References SequenceQuality().

SequenceQuality* bpp::SequenceQuality::getPartAnnotation	(	size_t	pos,
		size_t	len
	)		const throw (Exception) `[inline, virtual]`

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: