import * as t from 'io-ts' ; import { RTTI_id } from '../Scalar/RTTI_id' ; import { RTTI_Meta , IMeta } from './RTTI_Meta' ; import { RTTI_uri } from '../Scalar/RTTI_uri' ; import { RTTI_Element , IElement } from './RTTI_Element' ; import { RTTI_code } from '../Scalar/RTTI_code' ; import { RTTI_Narrative , INarrative } from './RTTI_Narrative' ; import { RTTI_ResourceList , IResourceList } from '../Union/RTTI_ResourceList' ; import { RTTI_Extension , IExtension } from './RTTI_Extension' ; import { RTTI_Identifier , IIdentifier } from './RTTI_Identifier' ; import { RTTI_integer } from '../Scalar/RTTI_integer' ; import { RTTI_Reference , IReference } from './RTTI_Reference' ; import { RTTI_Quantity , IQuantity } from './RTTI_Quantity' ; import { RTTI_MolecularSequence_ReferenceSeq , IMolecularSequence_ReferenceSeq } from './RTTI_MolecularSequence_ReferenceSeq' ; import { RTTI_MolecularSequence_Variant , IMolecularSequence_Variant } from './RTTI_MolecularSequence_Variant' ; import { RTTI_MolecularSequence_Quality , IMolecularSequence_Quality } from './RTTI_MolecularSequence_Quality' ; import { RTTI_MolecularSequence_Repository , IMolecularSequence_Repository } from './RTTI_MolecularSequence_Repository' ; import { RTTI_MolecularSequence_StructureVariant , IMolecularSequence_StructureVariant } from './RTTI_MolecularSequence_StructureVariant' ; export enum MolecularSequenceTypeKind { _aa = 'aa' , _dna = 'dna' , _rna = 'rna' } import { createEnumType } from '../../EnumType' ; import { IDomainResource } from './IDomainResource' ; export interface IMolecularSequence extends IDomainResource { /**
     * This is a MolecularSequence resource
     */ resourceType : 'MolecularSequence' ; /**
     * The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
     */ id ? : string ; /**
     * The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
     */ meta ? : IMeta ; /**
     * A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.
     */ implicitRules ? : string ; /**
     * Extensions for implicitRules
     */ _implicitRules ? : IElement ; /**
     * The base language in which the resource is written.
     */ language ? : string ; /**
     * Extensions for language
     */ _language ? : IElement ; /**
     * A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
     */ text ? : INarrative ; /**
     * These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.
     */ contained ? : IResourceList [ ] ; /**
     * May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, 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.
     */ extension ? : IExtension [ ] ; /**
                     * May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to 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).
                     */ modifierExtension ? : IExtension [ ] ; /**
     * A unique identifier for this particular sequence instance. This is a FHIR-defined id.
     */ identifier ? : IIdentifier [ ] ; /**
     * Amino Acid Sequence/ DNA Sequence / RNA Sequence.
     */ type ? : MolecularSequenceTypeKind ; /**
     * Extensions for type
     */ _type ? : IElement ; /**
     * 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 ; /**
     * Extensions for coordinateSystem
     */ _coordinateSystem ? : IElement ; /**
     * The patient whose sequencing results are described by this resource.
     */ patient ? : IReference ; /**
     * Specimen used for sequencing.
     */ specimen ? : IReference ; /**
     * The method for sequencing, for example, chip information.
     */ device ? : IReference ; /**
     * The organization or lab that should be responsible for this result.
     */ performer ? : IReference ; /**
     * The number of copies of the sequence of interest. (RNASeq).
     */ quantity ? : IQuantity ; /**
     * A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
     */ referenceSeq ? : IMolecularSequence_ReferenceSeq ; /**
     * The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.)  It can represent some complex mutation or segment variation with the assist of CIGAR string.
     */ variant ? : IMolecularSequence_Variant [ ] ; /**
     * 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 ; /**
     * Extensions for observedSeq
     */ _observedSeq ? : IElement ; /**
     * 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 ? : IMolecularSequence_Quality [ ] ; /**
     * Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
     */ readCoverage ? : number ; /**
     * Extensions for readCoverage
     */ _readCoverage ? : IElement ; /**
     * Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
     */ repository ? : IMolecularSequence_Repository [ ] ; /**
     * Pointer to next atomic sequence which at most contains one variant.
     */ pointer ? : IReference [ ] ; /**
     * Information about chromosome structure variation.
     */ structureVariant ? : IMolecularSequence_StructureVariant [ ] ; } export const RTTI_MolecularSequence = t . recursion ( 'IMolecularSequence' , ( ) => t . intersection ( [ t . type ( { resourceType : t . literal ( 'MolecularSequence' ) } ) , t . partial ( { id : RTTI_id , meta : RTTI_Meta , implicitRules : RTTI_uri , _implicitRules : RTTI_Element , language : RTTI_code , _language : RTTI_Element , text : RTTI_Narrative , contained : t . array ( RTTI_ResourceList ) , extension : t . array ( RTTI_Extension ) , modifierExtension : t . array ( RTTI_Extension ) , identifier : t . array ( RTTI_Identifier ) , type : createEnumType < MolecularSequenceTypeKind > ( MolecularSequenceTypeKind , 'MolecularSequenceTypeKind' ) , _type : RTTI_Element , coordinateSystem : RTTI_integer , _coordinateSystem : RTTI_Element , patient : RTTI_Reference , specimen : RTTI_Reference , device : RTTI_Reference , performer : RTTI_Reference , quantity : RTTI_Quantity , referenceSeq : RTTI_MolecularSequence_ReferenceSeq , variant : t . array ( RTTI_MolecularSequence_Variant ) , observedSeq : t . string , _observedSeq : RTTI_Element , quality : t . array ( RTTI_MolecularSequence_Quality ) , readCoverage : RTTI_integer , _readCoverage : RTTI_Element , repository : t . array ( RTTI_MolecularSequence_Repository ) , pointer : t . array ( RTTI_Reference ) , structureVariant : t . array ( RTTI_MolecularSequence_StructureVariant ) } ) ] ) ) ;