Sanger::CGP::Vagrent::Data::AnnotationGroup - Object holding data about the effect of a single variation on a transcript.
This holds information about a variation within a transcript along with a collection of Sanger::CGP::Vagrent::Data::Annotation objects detailing the descriptions of that variation in different sequence contexts.
my $annoGrp = Sanger::CGP::Vagrent::Data::AnnotationGroup->new(%params);
Builds a new Sanger::CGP::Vagrent::Data::AnnotationGroup object
Sanger::CGP::Vagrent::Data::AnnotationGroup object initialized with parameter values
accession => Accession for the transcript type => Gene type (defined by type constants in L<Sanger::CGP::Vagrent::Data::Transcript|Sanger::CGP::Vagrent::Data::Transcript>) label => text label for the transcript, typically the gene name ccds => CCDS reference number if the transcript has one
$annoGrp->addAnnotation($anno);
Validates and adds a Sanger::CGP::Vagrent::Data::Annotation object to the group. Only one annotation of each context can be added to a group
None
my $annoListRef = $annoGrp->getAllAnnotations;
Retrieves all annotations in the group
Array ref of Sanger::CGP::Vagrent::Data::Annotation objects, or undef
my $cdsAnno = $annoGrp->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext);
Retrieves annotation for the specified context
String - A context constant from Sanger::CGP::Vagrent::Data::Annotation
A Sanger::CGP::Vagrent::Data::Annotation object, or undef
my $label = $grp->getLabel;
The label for the transcript (Gene name or similar)
String or undef
my $ccds = $grp->getCCDS;
The CCDS reference number for the transcript
String or undef
my $acc = $grp->getAccession;
The accession number for the transcript
String or undef
my $type = $grp->getType;
Gene type (defined by type constants in Sanger::CGP::Vagrent::Data::Transcript)
String - A type constant from Sanger::CGP::Vagrent::Data::Transcript
$grp->addClassification($class1,$class2);
Appends one or more classification terms to the annotation group
An array of classification terms (Strings)
None
my @classes = $grp->getClassifications;
Returns the stored classification terms
Array of Strings, or undef if none
$g->addBookmark($bookmarker);
Adds a bookmark to the annotation group of a type defined by the supplied bookmarker
A Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker implementing object
None
if($grp->hasClassification($checkClass)){ ..... }
Checks an annotation to see if it already contains the specified class
Boolean, 1 or 0
$g->hasBookmark; $g->hasBookmark($bookmarker);
Returns true if the Annotation group has a bookmark, if a Bookmarker object is supplied it only returns true if that specific bookmark type is present
(Optional) A Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker implementing object
Boolean, 1 or 0