bpp::SequenceAnnotation Class Reference

Interface for sequence annotations. More...

#include <Bpp/Seq/SequenceWithAnnotation.h>

Inheritance diagram for bpp::SequenceAnnotation:

Collaboration diagram for bpp::SequenceAnnotation:

Public Member Functions
virtual SequenceAnnotation *	clone () const override=0
virtual void	init (const Sequence &seq)=0
virtual const std::string &	getType () const =0
virtual bool	isValidWith (const SequenceWithAnnotation &sequence, bool throwException=true) const =0
	Test is the annotation is valid for a given sequence. More...
virtual bool	merge (const SequenceAnnotation &anno)=0
	Merge the input annotation with the current one. More...
virtual std::unique_ptr< SequenceAnnotation >	getPartAnnotation (size_t pos, size_t len) const =0
virtual bool	isRemovable () const =0
virtual bool	isShared () const =0
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

Detailed Description

Interface for sequence annotations.

Definition at line 24 of file SequenceWithAnnotation.h.

Member Function Documentation

afterSequenceChanged()

template<class T >

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

pure virtualinherited

afterSequenceDeleted()

template<class T >

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

pure virtualinherited

afterSequenceInserted()

template<class T >

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

pure virtualinherited

afterSequenceSubstituted()

template<class T >

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

pure virtualinherited

beforeSequenceChanged()

template<class T >

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

pure virtualinherited

beforeSequenceDeleted()

template<class T >

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

pure virtualinherited

beforeSequenceInserted()

template<class T >

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

pure virtualinherited

beforeSequenceSubstituted()

template<class T >

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

pure virtualinherited

clone()

virtual SequenceAnnotation* bpp::SequenceAnnotation::clone ( ) const

overridepure virtual

Implements bpp::CoreSymbolListListener< T >.

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

Referenced by bpp::SequenceWithAnnotation::merge().

getPartAnnotation()

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

pure 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

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

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

getType()

virtual const std::string& bpp::SequenceAnnotation::getType ( ) const

pure virtual

Returns

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

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

Referenced by bpp::SequenceWithAnnotation::annotation(), bpp::SequenceWithAnnotation::getAnnotationTypes(), and bpp::SequenceWithAnnotation::hasAnnotation().

init()

virtual void bpp::SequenceAnnotation::init ( const Sequence &  seq )

pure virtual

Creates a default annotation according to a given sequence.

Parameters

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

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

isRemovable()

template<class T >

virtual bool bpp::CoreSymbolListListener< T >::isRemovable ( ) const

pure virtualinherited

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

isShared()

template<class T >

virtual bool bpp::CoreSymbolListListener< T >::isShared ( ) const

pure virtualinherited

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

isValidWith()

virtual bool bpp::SequenceAnnotation::isValidWith ( const SequenceWithAnnotation &  sequence, bool  throwException = true  ) const

pure virtual

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.

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

merge()

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

pure virtual

Merge the input annotation with the current one.

Parameters

anno	The annotation to fuse.

Returns

true if the fusion was possible and successful.

Implemented in bpp::SequenceQuality, and bpp::SequenceMask.

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

• Bpp/Seq/SequenceWithAnnotation.h