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NAME

Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker - Abstract base class for the AnnotationGroup bookmarkers

DESCRIPTION

This is an abstract base class for the AnnotationGroup bookmarkers, it provides some simple shared functionality. All subclasses must implement the _getAnnotation object method, and optionally the _init object method.

METHODS

Constructor

new

Usage :
 my $marker = Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarkerSubClass->new();
Function :

Builds a new Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker inheriting object

Returns :

Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker object initialized with parameter values

Params :

Hash of parameter values, the actual keys/values required depend on the sub class.

Functions

getAnnotation

Usage :
 my $markedGroup = $bookmarker->getAnnotation(@annotationGroups);
Function :

Returns the AnnotationGroup that matches the bookmark

Returns :

A Sanger::CGP::Vagrent::Data::AnnotationGroup object

Params :

An array of Sanger::CGP::Vagrent::Data::AnnotationGroup objects

markAnnotation

Usage :
 $bookmarker->markAnnotation(@annotationGroups);
Function :

Calls getAnnotation, but marks annotation group rather than returning it

Returns :

None

Params :

An array of Sanger::CGP::Vagrent::Data::AnnotationGroup objects

Abstract

_getAnnotation

Usage :
 my $markedGroup = $self->_getAnnotation(@annotationGroups);
Function :

Abstract internal function, must be overridden by a subclass. This method should contain the actual bookmarking logic

Returns :

A Sanger::CGP::Vagrent::Data::AnnotationGroup object

Params :

An array of Sanger::CGP::Vagrent::Data::AnnotationGroup objects

_init

Usage :
 $self->_init(@params);
Function :

Abstract internal function, optionally can be overridden by a subclass. This method is used to handle constructor parameters, its called by new.

Returns :

None

Params :

The array of constructor paramaters to be parsed.

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