import { Annotation } from './Annotation.js';
import { CodeableConcept } from './CodeableConcept.js';
import { DocumentReference } from './DocumentReference.js';
import { Extension } from './Extension.js';
import { FhirPrimitive } from './FhirPrimitive.js';
import { GenomicStudy_Analysis_Device } from './GenomicStudy_Analysis_Device.js';
import { GenomicStudy_Analysis_Input } from './GenomicStudy_Analysis_Input.js';
import { GenomicStudy_Analysis_Output } from './GenomicStudy_Analysis_Output.js';
import { GenomicStudy_Analysis_Performer } from './GenomicStudy_Analysis_Performer.js';
import { Identifier } from './Identifier.js';
import { Observation } from './Observation.js';
import { Procedure } from './Procedure.js';
import { Reference } from './Reference.js';
import { Resource } from './Resource.js';
import { Specimen } from './Specimen.js';
import { Task } from './Task.js';
export interface GenomicStudy_Analysis {
    /**
     * @description Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
     * @short Unique id for inter-element referencing
     */
    id?: string;
    /**
     * @description May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
     * @comment There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions.  The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
     * @short Additional content defined by implementations
     */
    extension?: Extension[];
    /**
     * @description May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained andor the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.
  
  Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
     * @comment There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions.  The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
     * @short Extensions that cannot be ignored even if unrecognized
     */
    modifierExtension?: Extension[];
    /**
     * @description Identifiers for the analysis event.
     * @short Identifiers for the analysis event
     */
    identifier?: Identifier[];
    /**
     * @description Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI).
     * @short Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)
     */
    methodType?: CodeableConcept[];
    /**
     * @description Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid change.
     * @short Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)
     */
    changeType?: CodeableConcept[];
    /**
     * @description The reference genome build that is used in this analysis.
     * @short Genome build that is used in this analysis
     */
    genomeBuild?: CodeableConcept;
    /**
     * @description The defined protocol that describes the analysis.
     * @short The defined protocol that describes the analysis
     */
    instantiatesCanonical?: FhirPrimitive<string>;
    /**
     * @description The URL pointing to an externally maintained protocol that describes the analysis.
     * @short The URL pointing to an externally maintained protocol that describes the analysis
     */
    instantiatesUri?: FhirPrimitive<string>;
    /**
     * @description Name of the analysis event (human friendly).
     * @short Name of the analysis event (human friendly)
     */
    title?: FhirPrimitive<string>;
    /**
     * @description The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.
     * @comment If the focus of the analysis is not known, the value of this field SHALL use the data absent extension.
     * @short What the genomic analysis is about, when it is not about the subject of record
     */
    focus?: Reference<Resource>[];
    /**
     * @description The specimen used in the analysis event.
     * @short The specimen used in the analysis event
     */
    specimen?: Reference<Specimen>[];
    /**
     * @description The date of the analysis event.
     * @short The date of the analysis event
     */
    date?: FhirPrimitive<string>;
    /**
     * @description Any notes capture with the analysis event.
     * @short Any notes capture with the analysis event
     */
    note?: Annotation[];
    /**
     * @description The protocol that was performed for the analysis event.
     * @short The protocol that was performed for the analysis event
     */
    protocolPerformed?: Reference<Procedure | Task>;
    /**
     * @description The genomic regions to be studied in the analysis (BED file).
     * @short The genomic regions to be studied in the analysis (BED file)
     */
    regionsStudied?: Reference<DocumentReference | Observation>[];
    /**
     * @description Genomic regions actually called in the analysis event (BED file).
     * @short Genomic regions actually called in the analysis event (BED file)
     */
    regionsCalled?: Reference<DocumentReference | Observation>[];
    /**
     * @backbone Nested BackboneElement: input [0..*]
     */
    input?: GenomicStudy_Analysis_Input[];
    /**
     * @backbone Nested BackboneElement: output [0..*]
     */
    output?: GenomicStudy_Analysis_Output[];
    /**
     * @backbone Nested BackboneElement: performer [0..*]
     */
    performer?: GenomicStudy_Analysis_Performer[];
    /**
     * @backbone Nested BackboneElement: device [0..*]
     */
    device?: GenomicStudy_Analysis_Device[];
}
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