#include <Bpp/Seq/SequenceWithAnnotationTools.h>

Inheritance diagram for bpp::SequenceMask:

Collaboration diagram for bpp::SequenceMask:

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 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) 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
	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 override

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

Private Attributes
bool	removable_

std::vector< bool >	mask_

Detailed Description

Definition at line 16 of file SequenceWithAnnotationTools.h.

Constructor & Destructor Documentation

◆ SequenceMask() [1/2]

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 40 of file SequenceWithAnnotationTools.h.

Referenced by clone(), and getPartAnnotation().

◆ SequenceMask() [2/2]

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 54 of file SequenceWithAnnotationTools.h.

◆ ~SequenceMask()

virtual bpp::SequenceMask::~SequenceMask ( )

inlinevirtual

Definition at line 65 of file SequenceWithAnnotationTools.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 SequenceMask::afterSequenceChanged ( const IntSymbolListEditionEvent & event )

override

Definition at line 15 of file SequenceWithAnnotationTools.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 SequenceMask::afterSequenceDeleted ( const IntSymbolListDeletionEvent & event )

override

Definition at line 31 of file SequenceWithAnnotationTools.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 SequenceMask::afterSequenceInserted ( const IntSymbolListInsertionEvent & event )

override

Definition at line 23 of file SequenceWithAnnotationTools.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::SequenceMask::afterSequenceSubstituted ( const IntSymbolListSubstitutionEvent & event )

inlineoverride

Definition at line 99 of file SequenceWithAnnotationTools.h.

◆ beforeSequenceChanged() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceChanged() [2/2]

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

inlineoverride

Definition at line 92 of file SequenceWithAnnotationTools.h.

◆ beforeSequenceDeleted() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceDeleted() [2/2]

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

inlineoverride

Definition at line 96 of file SequenceWithAnnotationTools.h.

◆ beforeSequenceInserted() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceInserted() [2/2]

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

inlineoverride

Definition at line 94 of file SequenceWithAnnotationTools.h.

◆ beforeSequenceSubstituted() [1/2]

template<class T >

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

pure virtualinherited

◆ beforeSequenceSubstituted() [2/2]

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

inlineoverride

Definition at line 98 of file SequenceWithAnnotationTools.h.

◆ clone()

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

inlineoverridevirtual

Implements bpp::SequenceAnnotation.

Definition at line 72 of file SequenceWithAnnotationTools.h.

References SequenceMask().

◆ getMask()

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

inline

Returns: The mask as a vector.

Definition at line 115 of file SequenceWithAnnotationTools.h.

References mask_.

Referenced by merge().

◆ getPartAnnotation()

std::unique_ptr<SequenceAnnotation> bpp::SequenceMask::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