#include <Bpp/Seq/SequenceWithAnnotationTools.h>

Inheritance diagram for bpp::SequenceMask:

Collaboration diagram for bpp::SequenceMask:

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 bool	operator[] (size_t i) const

void	setMask (const std::vector< bool > &mask)

const std::vector< bool > &	getMask () const

void	setMask (size_t pos, bool mask)

void	setMask (size_t pos, const std::vector< bool > &mask)

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

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

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

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

Destructor
virtual	~SequenceMask ()

The Clonable interface
SequenceMask *	clone () const

Static Public Attributes
static const std::string	MASK = "Boolean mask"

Private Attributes
bool	removable_

std::vector< bool >	mask_

Detailed Description

Definition at line 49 of file SequenceWithAnnotationTools.h.

Constructor & Destructor Documentation

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

inline

Build a new SequenceMask object.

Build a new SequenceMask object and set the mask to false.

Parameters

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

Definition at line 74 of file SequenceWithAnnotationTools.h.

Referenced by clone(), and getPartAnnotation().

bpp::SequenceMask::SequenceMask	(	const std::vector< bool > &	mask,
		bool	removable = `true`
	)

inline

Build a new SequenceMask object.

Build a new SequenceMask object and set the mask as a vector of bool.

Parameters

mask	The boolean mask
removable	Tell if this listener can be removed by the user.

Definition at line 88 of file SequenceWithAnnotationTools.h.

virtual bpp::SequenceMask::~SequenceMask ( )

inlinevirtual

Definition at line 99 of file SequenceWithAnnotationTools.h.

Member Function Documentation

void SequenceMask::afterSequenceChanged ( const SymbolListEditionEvent & event )

virtual

Implements bpp::SymbolListListener.

Definition at line 50 of file SequenceWithAnnotationTools.cpp.

void SequenceMask::afterSequenceDeleted ( const SymbolListDeletionEvent & event )

virtual

Implements bpp::SymbolListListener.

Definition at line 65 of file SequenceWithAnnotationTools.cpp.

void SequenceMask::afterSequenceInserted ( const SymbolListInsertionEvent & event )

virtual

Implements bpp::SymbolListListener.

Definition at line 58 of file SequenceWithAnnotationTools.cpp.

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 138 of file SequenceWithAnnotationTools.h.

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 131 of file SequenceWithAnnotationTools.h.

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 135 of file SequenceWithAnnotationTools.h.

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 133 of file SequenceWithAnnotationTools.h.

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

inlinevirtual

Implements bpp::SymbolListListener.

Definition at line 137 of file SequenceWithAnnotationTools.h.

SequenceMask* bpp::SequenceMask::clone ( ) const

inlinevirtual

Implements bpp::SequenceAnnotation.

Definition at line 111 of file SequenceWithAnnotationTools.h.

References SequenceMask().

const std::vector<bool>& bpp::SequenceMask::getMask ( ) const

inline

Returns: The mask as a vector.

Definition at line 153 of file SequenceWithAnnotationTools.h.

References mask_.

Referenced by merge().

SequenceAnnotation* bpp::SequenceMask::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