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NAME

Sanger::CGP::Vagrent::Data::Annotation - Data object containing the description of an variation within a sequence

DESCRIPTION

This holds annotation for a variation against a defined piece of sequence

METHODS

Constructor

new

Usage :
 my $annot = Sanger::CGP::Vagrent::Data::Annotation->new(%params);
Function :

Builds a new Sanger::CGP::Vagrent::Data::Annotation object

Returns :

Sanger::CGP::Vagrent::Data::Annotation object initialized with parameter values

Params :
 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

Attributes

getMinPos

Usage :
 my $min = $a->getMinPos;
Function :

Returns the lowest coordinate of the annotation on the sequence

Returns :

Integer

getMinOffset

Usage :
 my $minOff = $a->getMinOffset;
Function :

Returns the offset value from the minimim coordinate

Returns :

Signed integer

getMaxPos

Usage :
 my $min = $a->getMaxPos;
Function :

Returns the highest coordinate of the annotation on the sequence

Returns :

Integer

getMaxOffset

Usage :
 my $maxOff = $a->getMaxOffset;
Function :

Returns the offset value from the maximum coordinate

Returns :

Signed integer

getWt

Usage :
 my $wtSeq = $a->getWt;
Function :

Returns the wildtype sequence string

Returns :

String

getMt

Usage :
 my $mtSeq = $a->getMt;
Function :

Returns the mutant sequence string

Returns :

String

getDescription

Usage :
 my $desc = $a->getDescription;
Function

An HGVS style description string of the annotation

Returns

String

getContext

Usage :
 my $ctx = $a->getContext;
Function

The context of the annotation, as defined by a context constant value

Returns

String

getType

Usage :
 my $type = $a->getType;
Function

The type of the annotation, as defined by a type constant value

Returns

String

getSubtype

Usage :
 my $subtype = $a->getSubtype;
Function

The subtype of the annotation, as defined by a subtype constant value

Returns

String

getAccession

Usage :
 my $accession = $a->getAccession;
Function

The accession of the sequence record the annotation is built against

Returns

String

getSequenceVersion

Usage :
 my $vers = $a->getSequenceVersion;
Function

The version of the sequence record the annotation is built against

Returns

String

getDatabase

Usage :
 my $db = $a->getDatabase;
Function

The database the sequence record originated from

Returns

String

getDatabaseVersion

Usage :
 my $dbVersion = $a->getDatabaseVersion;
Function

The version of the database the sequence record originated from

Returns

String

getSequenceLength

Usage :
 my $seqLength = $a->getSequenceLength;
Function

The full length of the sequence in the sequence record

Returns

Integer

addClassification

Usage :
 $a->addClassification($class1,$class2);
Function

Appends one or more classification terms to the annotation

Params

An array of classification terms (Strings)

Returns

None

getClassifications

Usage :
 my @classes = $a->getClassifications;
Function

Returns the stored classification terms

Returns

Array of Strings, or undef if none

Functions

hasClassification

Usage :
 if($a->hasClassification($checkClass)){
  .....
 }
Function

Checks an annotation to see if it already contains the specified class

Returns

Boolean, 1 or 0

Constants

getmRNAAnnotationContext

Usage :
 my $ctx = $anno->getmRNAAnnotationContext();
 my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext();
Function :

Constant lookup, returns the mRNA Annotation Context value

Returns :

String

getCDSAnnotationContext

Usage :
 my $ctx = $anno->getCDSAnnotationContext();
 my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext();
Function :

Constant lookup, returns the CDS Annotation Context value

Returns :

String

getProteinAnnotationContext

Usage :
 my $ctx = $anno->getProteinAnnotationContext();
 my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getProteinAnnotationContext();
Function :

Constant lookup, returns the Protein Annotation Context value

Returns :

String

getSubstitutionAnnotationType

Usage :
 my $type = $anno->getSubstitutionAnnotationType();
 my $type = Sanger::CGP::Vagrent::Data::Annotation::getSubstitutionAnnotationType();
Function :

Constant lookup, returns the Substitution Annotation Type value

Returns :

String

getDeletionAnnotationType

Usage :
 my $type = $anno->getDeletionAnnotationType();
 my $type = Sanger::CGP::Vagrent::Data::Annotation::getDeletionAnnotationType();
Function :

Constant lookup, returns the Deletion Annotation Type value

Returns :

String

getInsertionAnnotationType

Usage :
 my $type = $anno->getInsertionAnnotationType();
 my $type = Sanger::CGP::Vagrent::Data::Annotation::getInsertionAnnotationType();
Function :

Constant lookup, returns the Insertion Annotation Type value

Returns :

String

getComplexAnnotationType

Usage :
 my $type = $anno->getComplexAnnotationType();
 my $type = Sanger::CGP::Vagrent::Data::Annotation::getComplexAnnotationType();
Function :

Constant lookup, returns the Complex Annotation Type value

Returns :

String

getFrameShiftAnnotationType

Usage :
 my $type = $anno->getFrameShiftAnnotationType();
 my $type = Sanger::CGP::Vagrent::Data::Annotation::getFrameShiftAnnotationType();
Function :

Constant lookup, returns the Frameshift Annotation Type value

Returns :

String

getUnknownAnnotationType

Usage :
 my $type = $anno->getUnknownAnnotationType();
 my $type = Sanger::CGP::Vagrent::Data::Annotation::getUnknownAnnotationType();
Function :

Constant lookup, returns the Unknown Annotation Type value

Returns :

String

getPositionKnownSubtype

Usage :
 my $subtype = $anno->getPositionKnownSubtype();
 my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionKnownSubtype();
Function :

Constant lookup, returns the Position Known Subtype value

Returns :

String

getPositionOffsetSubtype

Usage :
 my $subtype = $anno->getPositionOffsetSubtype();
 my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffsetSubtype();
Function :

Constant lookup, returns the Position Offset Subtype value

Returns :

String

getPositionOffSequenceSubtype

Usage :
 my $subtype = $anno->getPositionOffSequenceSubtype();
 my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffSequenceSubtype();
Function :

Constant lookup, returns the Position Off-Sequence Subtype value

Returns :

String

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