import { IMolecularSequenceQuality, IMolecularSequenceReferenceSeq, IMolecularSequenceRepository, IMolecularSequenceStructureVariant, IMolecularSequenceVariant } from '../backbones';
import { IDomainResource, IElement } from '../base';
import { IIdentifier, IQuantity, IReference } from '../datatypes';
import { SequenceTypeType } from '../types';
/**
 * @name IMolecularSequence
 * @description Raw data describing a biological sequence.
 * @see <a href="https://hl7.org/fhir/R4/molecularsequence.html">MolecularSequence</a>
 * @version R4
 * @extends {IDomainResource}
 * @author Claudia Alarcón Lazo
 */
export interface IMolecularSequence extends IDomainResource {
    /**
     * @description A unique identifier for this particular sequence instance. This is a FHIR-defined id.
     */
    identifier?: IIdentifier[];
    /**
     * @description Amino Acid Sequence/ DNA Sequence / RNA Sequence.
     * @description aa | dna | rna
     * @see <a href="https://hl7.org/fhir/R4/valueset-sequence-type.html">SequenceType</a>
     */
    type?: SequenceTypeType;
    /**
     * @description Extensions for type
     */
    _type?: IElement;
    /**
     * @description Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).
     */
    coordinateSystem: number;
    /**
     * @description Extensions for coordinateSystem
     */
    _coordinateSystem?: IElement;
    /**
     * @description The patient whose sequencing results are described by this resource.
     */
    patient?: IReference;
    /**
     * @description Specimen used for sequencing.
     */
    specimen?: IReference;
    /**
     * @description The method for sequencing, for example, chip information.
     */
    device?: IReference;
    /**
     * @description The organization or lab that should be responsible for this result.
     */
    performer?: IReference;
    /**
     * @description The number of copies of the sequence of interest. (RNASeq).
     */
    quantity?: IQuantity;
    /**
     * @description A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
     */
    referenceSeq?: IMolecularSequenceReferenceSeq;
    /**
     * @description A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
     */
    variant?: IMolecularSequenceVariant[];
    /**
     * @description Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
     */
    observedSeq?: string;
    /**
     * @description Extensions for observedSeq
     */
    _observedSeq?: IElement;
    /**
     * @description An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
     */
    quality?: IMolecularSequenceQuality[];
    /**
     * @description Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
     */
    readCoverage?: number;
    /**
     * @description Extensions for readCoverage
     */
    _readCoverage?: IElement;
    /**
     * @description Configurations of the external repository. The repository shall store target\u0027s observedSeq or records related with target\u0027s observedSeq.
     */
    repository?: IMolecularSequenceRepository[];
    /**
     * @description Pointer to next atomic sequence which at most contains one variant.
     */
    pointer?: IReference[];
    /**
     * @description Information about chromosome structure variation.
     */
    structureVariant?: IMolecularSequenceStructureVariant[];
}