Class AnnotationStoreElement
Represents an annotation of a genomic feature.

Defined in <seqan/store.h>
Signature template <typename TPos[, typename TSpec]> struct AnnotationStoreElement;

Template Parameters

TPos The position type to use.
TSpec The specializing type.

Member Function Overview

Member Typedef Overview

Member Variable Overview

Detailed Description

Value type of the annotationStore stirng. The id of an annotation (aka annotationId) is not stored explicitly as it is implicitly given byt he position in the annotationStore.

Member Functions Detail

AnnotationStoreElement::AnnotationStoreElement();

Constructor.

The default constructor sets all members to INVALID_ID and beginPos and endPos to INVALID_POS.

Data Races

Thread safety unknown!

Member Typedef Detail

typedef (...) TAnnotationStoreElement::TId;

Type of annotationId and contigId.

TId is the result of Id<AnnotationStoreElement<> >::Type, see Id.

typedef (...) TAnnotationStoreElement::TPos;

Type of the beginPos and endPos.

typedef (...) TAnnotationStoreElement::TValues;

StringSet type of the values member.

Member Variables Detail

TPos AnnotationStoreElement::beginPos

Begin position of the annotation in gap space.

If endPos < beginPos then the annotation feature is located on the reverse strand where beginPos and endPos are the corresponding positions on the forward strand.

TId AnnotationStoreElement::contigId

Refers to the contig in contigStore that the annotation is part of.

TPos AnnotationStoreElement::endPos

End position of the annotation in gap space.

If endPos < beginPos then the annotation feature is located on the reverse strand where beginPos and endPos are the corresponding positions on the forward strand.

TId AnnotationStoreElement::INVALID_ID

Constant to represent an invalid id.

TId AnnotationStoreElement::INVALID_POS

Constant to represent an invalid position.

TId AnnotationStoreElement::lastChildId

The id of the parent annotation.

TId AnnotationStoreElement::nextSiblingId

The id of the right sibling annotation.

TId AnnotationStoreElement::parentId

The id of the parent annotation.

TId AnnotationStoreElement::typeId

Refers to an entry in the annotationTypeStore.

There are some type ids predefined for commonly used types, e.g. $ANNO_GENE$. See FragmentStore::PredefinedAnnotationTypes.

TValues AnnotationStoreElement::values

StringSet that stores additional values addressed by keyId.

The GFF and FTF file formats allow to define user-specific key-value pairs. The set of all keys addressed by keyId are stored in annotationKeyStore.