Sanger::CGP::Vagrent::Data::Annotation - Data object containing the description of an variation within a sequence
This holds annotation for a variation against a defined piece of sequence
my $annot = Sanger::CGP::Vagrent::Data::Annotation->new(%params);
Builds a new Sanger::CGP::Vagrent::Data::Annotation object
Sanger::CGP::Vagrent::Data::Annotation object initialized with parameter values
acc => Accession for the sequence record being annotated against accversion => version of the sequence record db => source DB the sequence record came from dbversion => version of the source DB seqlength => length of sequence in the sequence record context => sequence context of the annotation (defined by context constants) type => variation type the annotation describes (defined by type constants) subtype => variation type the annotation describes (defined by subtype constants) minpos => minimum coordinate in the sequence maxpos => maximum coordinate in the sequence minOffset => offset distance away from the minpos (typically used for splice site mutations) maxOffset => offset distance away from the maxpos (typically used for splice site mutations) wt => wild type sequence of variant mt => mutant sequence of variant description => HGVS style description string
my $min = $a->getMinPos;
Returns the lowest coordinate of the annotation on the sequence
Integer
my $minOff = $a->getMinOffset;
Returns the offset value from the minimim coordinate
Signed integer
my $min = $a->getMaxPos;
Returns the highest coordinate of the annotation on the sequence
Integer
my $maxOff = $a->getMaxOffset;
Returns the offset value from the maximum coordinate
Signed integer
my $wtSeq = $a->getWt;
Returns the wildtype sequence string
String
my $mtSeq = $a->getMt;
Returns the mutant sequence string
String
my $desc = $a->getDescription;
An HGVS style description string of the annotation
String
my $ctx = $a->getContext;
The context of the annotation, as defined by a context constant value
String
my $type = $a->getType;
The type of the annotation, as defined by a type constant value
String
my $subtype = $a->getSubtype;
The subtype of the annotation, as defined by a subtype constant value
String
my $accession = $a->getAccession;
The accession of the sequence record the annotation is built against
String
my $vers = $a->getSequenceVersion;
The version of the sequence record the annotation is built against
String
my $db = $a->getDatabase;
The database the sequence record originated from
String
my $dbVersion = $a->getDatabaseVersion;
The version of the database the sequence record originated from
String
my $seqLength = $a->getSequenceLength;
The full length of the sequence in the sequence record
Integer
$a->addClassification($class1,$class2);
Appends one or more classification terms to the annotation
An array of classification terms (Strings)
None
my @classes = $a->getClassifications;
Returns the stored classification terms
Array of Strings, or undef if none
if($a->hasClassification($checkClass)){ ..... }
Checks an annotation to see if it already contains the specified class
Boolean, 1 or 0
my $ctx = $anno->getmRNAAnnotationContext(); my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext();
Constant lookup, returns the mRNA Annotation Context value
String
my $ctx = $anno->getCDSAnnotationContext(); my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext();
Constant lookup, returns the CDS Annotation Context value
String
my $ctx = $anno->getProteinAnnotationContext(); my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getProteinAnnotationContext();
Constant lookup, returns the Protein Annotation Context value
String
my $type = $anno->getSubstitutionAnnotationType(); my $type = Sanger::CGP::Vagrent::Data::Annotation::getSubstitutionAnnotationType();
Constant lookup, returns the Substitution Annotation Type value
String
my $type = $anno->getDeletionAnnotationType(); my $type = Sanger::CGP::Vagrent::Data::Annotation::getDeletionAnnotationType();
Constant lookup, returns the Deletion Annotation Type value
String
my $type = $anno->getInsertionAnnotationType(); my $type = Sanger::CGP::Vagrent::Data::Annotation::getInsertionAnnotationType();
Constant lookup, returns the Insertion Annotation Type value
String
my $type = $anno->getComplexAnnotationType(); my $type = Sanger::CGP::Vagrent::Data::Annotation::getComplexAnnotationType();
Constant lookup, returns the Complex Annotation Type value
String
my $type = $anno->getFrameShiftAnnotationType(); my $type = Sanger::CGP::Vagrent::Data::Annotation::getFrameShiftAnnotationType();
Constant lookup, returns the Frameshift Annotation Type value
String
my $type = $anno->getUnknownAnnotationType(); my $type = Sanger::CGP::Vagrent::Data::Annotation::getUnknownAnnotationType();
Constant lookup, returns the Unknown Annotation Type value
String
my $subtype = $anno->getPositionKnownSubtype(); my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionKnownSubtype();
Constant lookup, returns the Position Known Subtype value
String
my $subtype = $anno->getPositionOffsetSubtype(); my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffsetSubtype();
Constant lookup, returns the Position Offset Subtype value
String
my $subtype = $anno->getPositionOffSequenceSubtype(); my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffSequenceSubtype();
Constant lookup, returns the Position Off-Sequence Subtype value
String