Sanger::CGP::Vagrent::Annotators::AbstractAnnotator - Abstract base class for the annotation generators
This is an abstract template class for the mutation annotators, it provides a lot of shared behind the scenes functionality. All subclasses must implement the _getAnnotation method.
my $source = Sanger::CGP::Vagrent::Annotators::AbstractAnnotatorSubClass->new(%params);
Builds a new Sanger::CGP::Vagrent::Annotators::AbstractAnnotator inheriting object
Sanger::CGP::Vagrent::Annotators::AbstractAnnotator object initialized with parameter values
Hash of parameter values
transcriptSource => A Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource inheriting object bookmarker => (Optional) An array reference of, or single, Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker inheriting object only_bookmarked => (Optional) Boolean, only return annotations that get bookmarked
my @annoGrps = $annotator->getAnnotation($variation);
Annotates the supplied Variation object and returns a list of AnnotationGroups objects. If Bookmarkers have been set, the AnnotationGroups will have been marked before being returned. If 'only_bookmarked' was set to true, only AnnotationGroups that match Bookmarkers will be returned.
An array of Sanger::CGP::Vagrent::Data::AnnotationGroup objects
A Sanger::CGP::Vagrent::Data::AbstractVariation implementing object
$annotator->addMessage("Interesting event found");
Adds a text message to the message list. All messages are reset every time getAnnotation
is called
Nothing
String
my @mess = $annotator->getMessages();
Retrieves a list of message strings about the most recent annotation attempt
Array of String
my $type = $annotator->_getAnnotation($variation);
Abstract internal function, must be implemented in subclass. Returns a list of AnnotationGroups
An array of Sanger::CGP::Vagrent::Data::AnnotationGroup objects
A Sanger::CGP::Vagrent::Data::AbstractVariation implementing object
my $type = $annotator->_getDefaultCDSAnnotationType();
Abstract internal function, must be implemented in subclass. Returns default CDS annotation (Annotation type constant) type for the Annotator
String - Annotation type constant
my $varSeq = $annotator->_getMutatedCdsSequence();
Abstract internal function, must be implemented in subclass. Returns the full variant form of the CDS sequence
String, DNA sequence
String - Full wildtype CDS DNA sequence Integer - Minimum position of the variant on the wildtype CDS sequence Integer - Maximum position of the variant on the wildtype CDS sequence String - Mutant DNA sequence for the variant
my $wtseq = $annotator->_getWildTypeStringForCDSAnno($var,$tran,$mrnaAnno);
Abstract internal function, must be implemented in subclass. Generates the CDS wildtype string from the mRNA annotation
String, DNA sequence
A Sanger::CGP::Vagrent::Data::AbstractVariation implementing object A Sanger::CGP::Vagrent::Data::Transcript object A Sanger::CGP::Vagrent::Data::Annotation object
my $varseq = $annotator->_getMutantStringForCDSAnno($var,$tran,$mrnaAnno);
Abstract internal function, must be implemented in subclass. Generates the CDS variant string from the mRNA annotation
String, DNA sequence
A Sanger::CGP::Vagrent::Data::AbstractVariation implementing object A Sanger::CGP::Vagrent::Data::Transcript object A Sanger::CGP::Vagrent::Data::Annotation object
my $desc = $annotator->_getCDSDescriptionString($tran,$cdsMin,$cdsMax,$cdsMinOffset,$cdsMaxOffset,$wt,$mt);
Abstract internal function, must be implemented in subclass. Takes the plotted CDS variation data and returns the HGVS syntax describing the change
String, HGVS description
A Sanger::CGP::Vagrent::Data::Transcript object Integer - CDS minimum position Integer - CDS maximum position Integer - Offset from the CDS minimum position (signed) Integer - Offset from the CDS maximum position (signed) String - Wildtype cDNA sequence of variant String - Variant cDNA sequence of variant
my $type = $annotator->_getDefaultProteinAnnotationType();
Abstract internal function, must be implemented in subclass. Returns default Protein annotation (Annotation type constant) type for the Annotator
String - Annotation type constant
my $max = $annotator->_getCdsMinPosForProteinCalculation($cDNAAnnot);
Abstract internal function, must be implemented in subclass. Returns the minimum cDNA location of the variant that can be used for protein annotation
Integer - cDNA position
A Annotation representing the cDNA annotation
my $max = $annotator->_getCdsMaxPosForProteinCalculation($cDNAAnnot);
Abstract internal function, must be implemented in subclass. Returns the maximum cDNA location of the variant that can be used for protein annotation
Integer - cDNA position
A Annotation representing the cDNA annotation
if($annotator->_isStartGained($var,$tran,$mRNAmin,$mRNAmax,$wt,$mt)){ ....... }
Abstract internal function, must be implemented in subclass. Returns returns true if there is a start codon created or moved in the 5' UTR
Boolean
A Sanger::CGP::Vagrent::Data::AbstractVariation implementing object A Sanger::CGP::Vagrent::Data::Transcript object Integer - Minimum mRNA coordinate of the variant Integer - Maximum mRNA coordinate of the variant String - Wildtype variant sequence String - Mutant variant sequence