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 =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 SequenceAnnotation *	getPartAnnotation (size_t pos, size_t len) const =0 throw (Exception)
virtual bool	isRemovable () const =0
virtual bool	isShared () const =0
virtual void	beforeSequenceChanged (const SymbolListEditionEvent &event)=0
virtual void	afterSequenceChanged (const SymbolListEditionEvent &event)=0
virtual void	beforeSequenceInserted (const SymbolListInsertionEvent &event)=0
virtual void	afterSequenceInserted (const SymbolListInsertionEvent &event)=0
virtual void	beforeSequenceDeleted (const SymbolListDeletionEvent &event)=0
virtual void	afterSequenceDeleted (const SymbolListDeletionEvent &event)=0
virtual void	beforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)=0
virtual void	afterSequenceSubstituted (const SymbolListSubstitutionEvent &event)=0

Detailed Description

Interface for sequence annotations.

Definition at line 57 of file SequenceWithAnnotation.h.

Member Function Documentation

afterSequenceChanged()

virtual void bpp::SymbolListListener::afterSequenceChanged ( const SymbolListEditionEvent &  event )

pure virtualinherited

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

afterSequenceDeleted()

virtual void bpp::SymbolListListener::afterSequenceDeleted ( const SymbolListDeletionEvent &  event )

pure virtualinherited

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

afterSequenceInserted()

virtual void bpp::SymbolListListener::afterSequenceInserted ( const SymbolListInsertionEvent &  event )

pure virtualinherited

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

afterSequenceSubstituted()

virtual void bpp::SymbolListListener::afterSequenceSubstituted ( const SymbolListSubstitutionEvent &  event )

pure virtualinherited

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

beforeSequenceChanged()

virtual void bpp::SymbolListListener::beforeSequenceChanged ( const SymbolListEditionEvent &  event )

pure virtualinherited

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

beforeSequenceDeleted()

virtual void bpp::SymbolListListener::beforeSequenceDeleted ( const SymbolListDeletionEvent &  event )

pure virtualinherited

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

beforeSequenceInserted()

virtual void bpp::SymbolListListener::beforeSequenceInserted ( const SymbolListInsertionEvent &  event )

pure virtualinherited

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

beforeSequenceSubstituted()

virtual void bpp::SymbolListListener::beforeSequenceSubstituted ( const SymbolListSubstitutionEvent &  event )

pure virtualinherited

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

clone()

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

pure virtual

Implements bpp::SymbolListListener.

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

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

getPartAnnotation()

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

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::getAnnotation(), 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.

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

isRemovable()

virtual bool bpp::SymbolListListener::isRemovable ( ) const

pure virtualinherited

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

Referenced by bpp::EdSymbolList::removeSymbolListListener().

isShared()

virtual bool bpp::SymbolListListener::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 complient 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 succesful.

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

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

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

• Bpp/Seq/SequenceWithAnnotation.h