Class MolecularSequence

MolecularSequence Class

Remarks

Raw data describing a biological sequence.

FHIR Specification

Short: Information about a biological sequence
Definition: Raw data describing a biological sequence.
FHIR Version: 4.0.1

See

FHIR MolecularSequence

Hierarchy (View Summary)

DomainResource
- MolecularSequence

Implements

IDomainResource

Index

Constructors

constructor

new MolecularSequence(
coordinateSystem?: null | number | IntegerType,
): MolecularSequence
Parameters
- coordinateSystem: null | number | IntegerType = null
Returns MolecularSequence
Overrides DomainResource.constructor
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:112

Properties

`Private` `Optional`identifier

identifier?: Identifier[]

MolecularSequence.identifier Element

Remarks

FHIR Specification

Short: Unique ID for this particular sequence. This is a FHIR-defined id
Definition: A unique identifier for this particular sequence instance. This is a FHIR-defined id.
Requirements: Allows sequences to be distinguished and referenced.
FHIR Type: Identifier
Cardinality: 0..*
isModifier: false
isSummary: true

`Private` `Readonly`sequenceTypeEnum

sequenceTypeEnum: SequenceTypeEnum

FHIR CodeSystem: SequenceType

See

SequenceTypeEnum

`Private` `Optional`type_

type_?: EnumCodeType

MolecularSequence.type Element

Remarks

FHIR Specification

Short: aa | dna | rna
Definition: Amino Acid Sequence/ DNA Sequence / RNA Sequence.
FHIR Type: code
Cardinality: 0..1
isModifier: false
isSummary: true

See

CodeSystem Enumeration: SequenceTypeEnum

`Private`coordinateSystem

coordinateSystem: null | IntegerType

MolecularSequence.coordinateSystem Element

Remarks

FHIR Specification

Short: Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Definition: 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).
FHIR Type: integer
Cardinality: 1..1
isModifier: false
isSummary: true

`Private` `Optional`patient

patient?: Reference

MolecularSequence.patient Element

Remarks

FHIR Specification

Short: Who and/or what this is about
Definition: The patient whose sequencing results are described by this resource.
FHIR Type: Reference
- TargetProfiles: [ 'http://hl7.org/fhir/StructureDefinition/Patient', ]
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`specimen

specimen?: Reference

MolecularSequence.specimen Element

Remarks

FHIR Specification

Short: Specimen used for sequencing
Definition: Specimen used for sequencing.
FHIR Type: Reference
- TargetProfiles: [ 'http://hl7.org/fhir/StructureDefinition/Specimen', ]
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`device

device?: Reference

MolecularSequence.device Element

Remarks

FHIR Specification

Short: The method for sequencing
Definition: The method for sequencing, for example, chip information.
FHIR Type: Reference
- TargetProfiles: [ 'http://hl7.org/fhir/StructureDefinition/Device', ]
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`performer

performer?: Reference

MolecularSequence.performer Element

Remarks

FHIR Specification

Short: Who should be responsible for test result
Definition: The organization or lab that should be responsible for this result.
FHIR Type: Reference
- TargetProfiles: [ 'http://hl7.org/fhir/StructureDefinition/Organization', ]
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`quantity

quantity?: Quantity

MolecularSequence.quantity Element

Remarks

FHIR Specification

Short: The number of copies of the sequence of interest. (RNASeq)
Definition: The number of copies of the sequence of interest. (RNASeq).
FHIR Type: Quantity
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`referenceSeq

referenceSeq?: MolecularSequenceReferenceSeqComponent

MolecularSequence.referenceSeq Element

Remarks

FHIR Specification

Short: A sequence used as reference
Definition: A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
FHIR Type: BackboneElement
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`variant

variant?: MolecularSequenceVariantComponent[]

MolecularSequence.variant Element

Remarks

FHIR Specification

Short: Variant in sequence
Definition: The definition of variant here originates from Sequence ontology (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.
FHIR Type: BackboneElement
Cardinality: 0..*
isModifier: false
isSummary: true

`Private` `Optional`observedSeq

observedSeq?: StringType

MolecularSequence.observedSeq Element

Remarks

FHIR Specification

Short: Sequence that was observed
Definition: 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.
FHIR Type: string
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`quality

quality?: MolecularSequenceQualityComponent[]

MolecularSequence.quality Element

Remarks

FHIR Specification

Short: An set of value as quality of sequence
Definition: An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score (SO:0001686).
FHIR Type: BackboneElement
Cardinality: 0..*
isModifier: false
isSummary: true

`Private` `Optional`readCoverage

readCoverage?: IntegerType

MolecularSequence.readCoverage Element

Remarks

FHIR Specification

Short: Average number of reads representing a given nucleotide in the reconstructed sequence
Definition: Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
FHIR Type: integer
Cardinality: 0..1
isModifier: false
isSummary: true

`Private` `Optional`repository

repository?: MolecularSequenceRepositoryComponent[]

MolecularSequence.repository Element

Remarks

FHIR Specification

Short: External repository which contains detailed report related with observedSeq in this resource
Definition: Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
FHIR Type: BackboneElement
Cardinality: 0..*
isModifier: false
isSummary: true

`Private` `Optional`pointer

pointer?: Reference[]

MolecularSequence.pointer Element

Remarks

FHIR Specification

Short: Pointer to next atomic sequence
Definition: Pointer to next atomic sequence which at most contains one variant.
FHIR Type: Reference
- TargetProfiles: [ 'http://hl7.org/fhir/StructureDefinition/MolecularSequence', ]
Cardinality: 0..*
isModifier: false
isSummary: true

`Private` `Optional`structureVariant

structureVariant?: MolecularSequenceStructureVariantComponent[]

MolecularSequence.structureVariant Element

Remarks

FHIR Specification

Short: Structural variant
Definition: Information about chromosome structure variation.
FHIR Type: BackboneElement
Cardinality: 0..*
isModifier: false
isSummary: true

Methods

`Static`parse

parse(sourceJson: Value, optSourceField?: string): undefined | MolecularSequence
Parse the provided MolecularSequence JSON to instantiate the MolecularSequence data model.
Parameters
- sourceJson: Value
  JSON representing FHIR MolecularSequence
- OptionaloptSourceField: string
  Optional data source field (e.g. <complexTypeName>.<complexTypeFieldName>); defaults to MolecularSequence
Returns undefined | MolecularSequence
MolecularSequence data model or undefined for MolecularSequence

Throws
JsonError if the provided JSON is not a valid JSON object
Overrides DomainResource.parse
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:135

getIdentifier

getIdentifier(): Identifier[]
Returns Identifier[]
the identifier property value as a Identifier array
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:589

setIdentifier

setIdentifier(value: undefined | Identifier[]): this
Assigns the provided Identifier array value to the identifier property.
Parameters
- value: undefined | Identifier[]
  the identifier array value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:600

addIdentifier

addIdentifier(value: undefined | Identifier): this
Add the provided Identifier value to the identifier array property.
Parameters
- value: undefined | Identifier
  the identifier value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:618

hasIdentifier

hasIdentifier(): boolean
Returns boolean
true if the identifier property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:631

getTypeEnumType

getTypeEnumType(): undefined | EnumCodeType
Returns undefined | EnumCodeType
the type_ property value as a EnumCodeType if defined; else undefined

See
CodeSystem Enumeration: SequenceTypeEnum
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:649

setTypeEnumType

setTypeEnumType(enumType: undefined | EnumCodeType): this
Assigns the provided EnumCodeType value to the type_ property.
Parameters
- enumType: undefined | EnumCodeType
  the type_ value
Returns this
this

Throws
InvalidCodeError for invalid code values

Throws
InvalidTypeError for invalid data types

See
CodeSystem Enumeration: SequenceTypeEnum
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:663

hasTypeEnumType

hasTypeEnumType(): boolean
Returns boolean
true if the type_ property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:677

getTypeElement

getTypeElement(): undefined | CodeType
Returns undefined | CodeType
the type_ property value as a CodeType if defined; else undefined

See
CodeSystem Enumeration: SequenceTypeEnum
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:686

setTypeElement

setTypeElement(element: undefined | CodeType): this
Assigns the provided PrimitiveType value to the type_ property.
Parameters
- element: undefined | CodeType
  the type_ value
Returns this
this

Throws
InvalidCodeError for invalid code value

Throws
InvalidTypeError for invalid data types

See
CodeSystem Enumeration: SequenceTypeEnum
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:703

hasTypeElement

hasTypeElement(): boolean
Returns boolean
true if the type_ property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:717

getType

getType(): undefined | string
Returns undefined | string
the type_ property value as a fhirCode if defined; else undefined

See
CodeSystem Enumeration: SequenceTypeEnum
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:726

setType

setType(value: undefined | string): this
Assigns the provided primitive value to the type_ property.
Parameters
- value: undefined | string
  the type_ value
Returns this
this

Throws
InvalidCodeError for invalid code value

Throws
PrimitiveTypeError for invalid primitive types

See
CodeSystem Enumeration: SequenceTypeEnum
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:743

hasType

hasType(): boolean
Returns boolean
true if the type_ property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:756

getCoordinateSystemElement

getCoordinateSystemElement(): IntegerType
Returns IntegerType
the coordinateSystem property value as a IntegerType object if defined; else an empty IntegerType object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:763

setCoordinateSystemElement

setCoordinateSystemElement(element: undefined | null | IntegerType): this
Assigns the provided PrimitiveType value to the coordinateSystem property.
Parameters
- element: undefined | null | IntegerType
  the coordinateSystem value
Returns this
this

Throws
InvalidTypeError for invalid data types

Throws
PrimitiveTypeError for invalid primitive types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:775

hasCoordinateSystemElement

hasCoordinateSystemElement(): boolean
Returns boolean
true if the coordinateSystem property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:789

getCoordinateSystem

getCoordinateSystem(): null | number
Returns null | number
the coordinateSystem property value as a fhirInteger if defined; else null
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:796

setCoordinateSystem

setCoordinateSystem(value: undefined | null | number): this
Assigns the provided primitive value to the coordinateSystem property.
Parameters
- value: undefined | null | number
  the coordinateSystem value
Returns this
this

Throws
PrimitiveTypeError for invalid primitive types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:811

hasCoordinateSystem

hasCoordinateSystem(): boolean
Returns boolean
true if the coordinateSystem property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:824

getPatient

getPatient(): Reference
Returns Reference
the patient property value as a Reference object; else an empty Reference object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:831

setPatient

setPatient(value: undefined | Reference): this
Assigns the provided Patient object value to the patient property.
Parameters
- value: undefined | Reference
  the patient object value
Returns this
this

Decorator
@ReferenceTargets('MolecularSequence.patient', ['Patient',])

Throws
InvalidTypeError for invalid data type or reference value
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:847

hasPatient

hasPatient(): boolean
Returns boolean
true if the patient property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:860

getSpecimen

getSpecimen(): Reference
Returns Reference
the specimen property value as a Reference object; else an empty Reference object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:867

setSpecimen

setSpecimen(value: undefined | Reference): this
Assigns the provided Specimen object value to the specimen property.
Parameters
- value: undefined | Reference
  the specimen object value
Returns this
this

Decorator
@ReferenceTargets('MolecularSequence.specimen', ['Specimen',])

Throws
InvalidTypeError for invalid data type or reference value
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:883

hasSpecimen

hasSpecimen(): boolean
Returns boolean
true if the specimen property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:896

getDevice

getDevice(): Reference
Returns Reference
the device property value as a Reference object; else an empty Reference object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:903

setDevice

setDevice(value: undefined | Reference): this
Assigns the provided Device object value to the device property.
Parameters
- value: undefined | Reference
  the device object value
Returns this
this

Decorator
@ReferenceTargets('MolecularSequence.device', ['Device',])

Throws
InvalidTypeError for invalid data type or reference value
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:919

hasDevice

hasDevice(): boolean
Returns boolean
true if the device property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:932

getPerformer

getPerformer(): Reference
Returns Reference
the performer property value as a Reference object; else an empty Reference object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:939

setPerformer

setPerformer(value: undefined | Reference): this
Assigns the provided Performer object value to the performer property.
Parameters
- value: undefined | Reference
  the performer object value
Returns this
this

Decorator
@ReferenceTargets('MolecularSequence.performer', ['Organization',])

Throws
InvalidTypeError for invalid data type or reference value
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:955

hasPerformer

hasPerformer(): boolean
Returns boolean
true if the performer property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:968

getQuantity

getQuantity(): Quantity
Returns Quantity
the quantity property value as a Quantity object if defined; else an empty Quantity object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:975

setQuantity

setQuantity(value: undefined | Quantity): this
Assigns the provided Quantity object value to the quantity property.
Parameters
- value: undefined | Quantity
  the quantity object value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:986

hasQuantity

hasQuantity(): boolean
Returns boolean
true if the quantity property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1000

getReferenceSeq

getReferenceSeq(): MolecularSequenceReferenceSeqComponent
Returns MolecularSequenceReferenceSeqComponent
the referenceSeq property value as a MolecularSequenceReferenceSeqComponent object if defined; else an empty MolecularSequenceReferenceSeqComponent object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1007

setReferenceSeq

setReferenceSeq(value: undefined | MolecularSequenceReferenceSeqComponent): this
Assigns the provided ReferenceSeq object value to the referenceSeq property.
Parameters
- value: undefined | MolecularSequenceReferenceSeqComponent
  the referenceSeq object value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1018

hasReferenceSeq

hasReferenceSeq(): boolean
Returns boolean
true if the referenceSeq property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1032

getVariant

getVariant(): MolecularSequenceVariantComponent[]
Returns MolecularSequenceVariantComponent[]
the variant property value as a MolecularSequenceVariantComponent array
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1039

setVariant

setVariant(value: undefined | MolecularSequenceVariantComponent[]): this
Assigns the provided MolecularSequenceVariantComponent array value to the variant property.
Parameters
- value: undefined | MolecularSequenceVariantComponent[]
  the variant array value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1050

addVariant

addVariant(value: undefined | MolecularSequenceVariantComponent): this
Add the provided MolecularSequenceVariantComponent value to the variant array property.
Parameters
- value: undefined | MolecularSequenceVariantComponent
  the variant value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1068

hasVariant

hasVariant(): boolean
Returns boolean
true if the variant property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1081

getObservedSeqElement

getObservedSeqElement(): StringType
Returns StringType
the observedSeq property value as a StringType object if defined; else an empty StringType object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1097

setObservedSeqElement

setObservedSeqElement(element: undefined | StringType): this
Assigns the provided PrimitiveType value to the observedSeq property.
Parameters
- element: undefined | StringType
  the observedSeq value
Returns this
this

Throws
InvalidTypeError for invalid data types

Throws
PrimitiveTypeError for invalid primitive types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1109

hasObservedSeqElement

hasObservedSeqElement(): boolean
Returns boolean
true if the observedSeq property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1123

getObservedSeq

getObservedSeq(): undefined | string
Returns undefined | string
the observedSeq property value as a fhirString if defined; else undefined
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1130

setObservedSeq

setObservedSeq(value: undefined | string): this
Assigns the provided primitive value to the observedSeq property.
Parameters
- value: undefined | string
  the observedSeq value
Returns this
this

Throws
PrimitiveTypeError for invalid primitive types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1141

hasObservedSeq

hasObservedSeq(): boolean
Returns boolean
true if the observedSeq property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1154

getQuality

getQuality(): MolecularSequenceQualityComponent[]
Returns MolecularSequenceQualityComponent[]
the quality property value as a MolecularSequenceQualityComponent array
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1161

setQuality

setQuality(value: undefined | MolecularSequenceQualityComponent[]): this
Assigns the provided MolecularSequenceQualityComponent array value to the quality property.
Parameters
- value: undefined | MolecularSequenceQualityComponent[]
  the quality array value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1172

addQuality

addQuality(value: undefined | MolecularSequenceQualityComponent): this
Add the provided MolecularSequenceQualityComponent value to the quality array property.
Parameters
- value: undefined | MolecularSequenceQualityComponent
  the quality value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1190

hasQuality

hasQuality(): boolean
Returns boolean
true if the quality property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1203

getReadCoverageElement

getReadCoverageElement(): IntegerType
Returns IntegerType
the readCoverage property value as a IntegerType object if defined; else an empty IntegerType object
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1219

setReadCoverageElement

setReadCoverageElement(element: undefined | IntegerType): this
Assigns the provided PrimitiveType value to the readCoverage property.
Parameters
- element: undefined | IntegerType
  the readCoverage value
Returns this
this

Throws
InvalidTypeError for invalid data types

Throws
PrimitiveTypeError for invalid primitive types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1231

hasReadCoverageElement

hasReadCoverageElement(): boolean
Returns boolean
true if the readCoverage property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1245

getReadCoverage

getReadCoverage(): undefined | number
Returns undefined | number
the readCoverage property value as a fhirInteger if defined; else undefined
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1252

setReadCoverage

setReadCoverage(value: undefined | number): this
Assigns the provided primitive value to the readCoverage property.
Parameters
- value: undefined | number
  the readCoverage value
Returns this
this

Throws
PrimitiveTypeError for invalid primitive types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1263

hasReadCoverage

hasReadCoverage(): boolean
Returns boolean
true if the readCoverage property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1276

getRepository

getRepository(): MolecularSequenceRepositoryComponent[]
Returns MolecularSequenceRepositoryComponent[]
the repository property value as a MolecularSequenceRepositoryComponent array
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1283

setRepository

setRepository(value: undefined | MolecularSequenceRepositoryComponent[]): this
Assigns the provided MolecularSequenceRepositoryComponent array value to the repository property.
Parameters
- value: undefined | MolecularSequenceRepositoryComponent[]
  the repository array value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1294

addRepository

addRepository(value: undefined | MolecularSequenceRepositoryComponent): this
Add the provided MolecularSequenceRepositoryComponent value to the repository array property.
Parameters
- value: undefined | MolecularSequenceRepositoryComponent
  the repository value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1312

hasRepository

hasRepository(): boolean
Returns boolean
true if the repository property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1325

getPointer

getPointer(): Reference[]
Returns Reference[]
the pointer property value as a Reference array
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1341

setPointer

setPointer(value: undefined | Reference[]): this
Assigns the provided Reference array value to the pointer property.
Parameters
- value: undefined | Reference[]
  the pointer array value
Returns this
this

Decorator
@ReferenceTargets('MolecularSequence.pointer', ['MolecularSequence',])

Throws
InvalidTypeError for invalid data type or reference value
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1357

addPointer

addPointer(value: undefined | Reference): this
Add the provided Reference value to the pointer array property.
Parameters
- value: undefined | Reference
  the pointer value
Returns this
this

Decorator
@ReferenceTargets('MolecularSequence.pointer', ['MolecularSequence',])

Throws
InvalidTypeError for invalid data type or reference value
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1379

hasPointer

hasPointer(): boolean
Returns boolean
true if the pointer property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1391

getStructureVariant

getStructureVariant(): MolecularSequenceStructureVariantComponent[]
Returns MolecularSequenceStructureVariantComponent[]
the structureVariant property value as a MolecularSequenceStructureVariantComponent array
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1407

setStructureVariant

setStructureVariant(
value: undefined | MolecularSequenceStructureVariantComponent[],
): this
Assigns the provided MolecularSequenceStructureVariantComponent array value to the structureVariant property.
Parameters
- value: undefined | MolecularSequenceStructureVariantComponent[]
  the structureVariant array value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1418

addStructureVariant

addStructureVariant(
value: undefined | MolecularSequenceStructureVariantComponent,
): this
Add the provided MolecularSequenceStructureVariantComponent value to the structureVariant array property.
Parameters
- value: undefined | MolecularSequenceStructureVariantComponent
  the structureVariant value
Returns this
this

Throws
InvalidTypeError for invalid data types
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1436

hasStructureVariant

hasStructureVariant(): boolean
Returns boolean
true if the structureVariant property exists and has a value; false otherwise
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1449

fhirType

fhirType(): string
Returns string
the FHIR type defined in the FHIR standard
Implementation of IDomainResource.fhirType
Overrides DomainResource.fhirType
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1467

isEmpty

isEmpty(): boolean
Returns boolean
true if the instance is empty; false otherwise
Implementation of IDomainResource.isEmpty
Overrides DomainResource.isEmpty
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1474

isRequiredFieldsEmpty

isRequiredFieldsEmpty(): boolean
Returns boolean
true if and only if the data model has required fields (min cardinality > 0) and at least one of those required fields in the instance is empty; false otherwise
Implementation of IDomainResource.isRequiredFieldsEmpty
Overrides DomainResource.isRequiredFieldsEmpty
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1499

copy

copy(): MolecularSequence
Creates a copy of the current instance.

Returns MolecularSequence
the a new instance copied from the current instance
Implementation of IDomainResource.copy
Overrides DomainResource.copy
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1510

toJSON

toJSON(): undefined | Value
Returns undefined | Value
the JSON value or undefined if the instance is empty
Implementation of IDomainResource.toJSON
Overrides DomainResource.toJSON
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1551

getText

getText(): Narrative
Returns Narrative
the text property value as a Narrative
Implementation of IDomainResource.getText
Inherited from DomainResource.getText
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:86

setText

setText(value: undefined | Narrative): this
Assigns the provided value to the text property.
Parameters
- value: undefined | Narrative
  the text value
Returns this
this
Implementation of IDomainResource.setText
Inherited from DomainResource.setText
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:93

hasText

hasText(): boolean
Returns boolean
true if the text property exists and has a value; false otherwise
Implementation of IDomainResource.hasText
Inherited from DomainResource.hasText
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:97

getContained

getContained(): IResource[]
Returns IResource[]
the contained property value as a Resource array
Implementation of IDomainResource.getContained
Inherited from DomainResource.getContained
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:101

setContained

setContained(value: undefined | IResource[]): this
Assigns the provided Resource array value to the contained property.
Parameters
- value: undefined | IResource[]
  the contained array value
Returns this
this
Implementation of IDomainResource.setContained
Inherited from DomainResource.setContained
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:108

addContained

addContained(value: undefined | IResource): this
Add the provided Resource value to the contained array property.
Parameters
- value: undefined | IResource
  the contained value
Returns this
this
Implementation of IDomainResource.addContained
Inherited from DomainResource.addContained
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:115

hasContained

hasContained(): boolean
Returns boolean
true if the contained property exists and has a value; false otherwise
Implementation of IDomainResource.hasContained
Inherited from DomainResource.hasContained
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:119

getExtension

getExtension(): IExtension[]
Returns IExtension[]
the array of extension values
Implementation of IDomainResource.getExtension
Inherited from DomainResource.getExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:127

setExtension

setExtension(extension: undefined | IExtension[]): this
Assigns the provided array of Extension values to the extension property.
Parameters
- extension: undefined | IExtension[]
  array of Extensions
Returns this
this
Implementation of IDomainResource.setExtension
Inherited from DomainResource.setExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:134

hasExtension

hasExtension(url?: string): boolean
Determines if the extension property exists.
Parameters
- Optionalurl: string
  the url that identifies a specific Extension
Returns boolean
true if an Extension has the provided url; false otherwise

Remarks
If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the extension property exists and has any values.

Throws
AssertionError for invalid url
Implementation of IDomainResource.hasExtension
Inherited from DomainResource.hasExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:146

getExtensionByUrl

getExtensionByUrl(url: string): undefined | IExtension
Returns the Extension having the provided url.
Parameters
- url: string
  the url that identifies a specific Extension
Returns undefined | IExtension
the Extension having the provided url

Throws
AssertionError for invalid url
Implementation of IDomainResource.getExtensionByUrl
Inherited from DomainResource.getExtensionByUrl
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:154

addExtension

addExtension(extension: undefined | IExtension): this
Adds the provided Extension to the extension property array.
Parameters
- extension: undefined | IExtension
  the Extension value to add to the extension property array
Returns this
this
Implementation of IDomainResource.addExtension
Inherited from DomainResource.addExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:161

removeExtension

removeExtension(url: string): void
Removes the Extension having the provided url from the extension property array.
Parameters
- url: string
  the url that identifies a specific Extension to remove
Returns void
Throws
AssertionError for invalid url
Implementation of IDomainResource.removeExtension
Inherited from DomainResource.removeExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:168

getModifierExtension

getModifierExtension(): IExtension[]
Returns IExtension[]
the array of modifierExtension values
Implementation of IDomainResource.getModifierExtension
Inherited from DomainResource.getModifierExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:182

setModifierExtension

setModifierExtension(extension: undefined | IExtension[]): this
Assigns the provided array of Extension values to the modifierExtension property.
Parameters
- extension: undefined | IExtension[]
  array of Extensions
Returns this
this
Implementation of IDomainResource.setModifierExtension
Inherited from DomainResource.setModifierExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:189

hasModifierExtension

hasModifierExtension(url?: string): boolean
Determines if the modifierExtension property exists.
Parameters
- Optionalurl: string
  the url that identifies a specific Extension
Returns boolean
true if an Extension has the provided url

Remarks
If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the modifierExtension property exists and has any values.

Throws
AssertionError for invalid url
Implementation of IDomainResource.hasModifierExtension
Inherited from DomainResource.hasModifierExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:201

getModifierExtensionByUrl

getModifierExtensionByUrl(url: string): undefined | IExtension
Returns the Extension having the provided url.
Parameters
- url: string
  the url that identifies a specific Extension
Returns undefined | IExtension
the Extension having the provided url

Throws
AssertionError for invalid url
Implementation of IDomainResource.getModifierExtensionByUrl
Inherited from DomainResource.getModifierExtensionByUrl
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:209

addModifierExtension

addModifierExtension(extension: undefined | IExtension): this
Adds the provided Extension to the modifierExtension property array.
Parameters
- extension: undefined | IExtension
  the Extension value to add to the modifierExtension property array
Returns this
this
Implementation of IDomainResource.addModifierExtension
Inherited from DomainResource.addModifierExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:216

removeModifierExtension

removeModifierExtension(url: string): void
Removes the Extension having the provided url from the modifierExtension property array.
Parameters
- url: string
  the url that identifies a specific Extension to remove
Returns void
Throws
AssertionError for invalid url
Implementation of IDomainResource.removeModifierExtension
Inherited from DomainResource.removeModifierExtension
- Defined in packages/fhir-core/lib/base-models/DomainResource.d.ts:223

resourceType

resourceType(): string
Returns string
the FHIR resource type as defined by the FHIR specification
Implementation of IDomainResource.resourceType
Inherited from DomainResource.resourceType
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:67

getIdElement

getIdElement(): IdType
Returns IdType
the id property value as a PrimitiveType
Implementation of IDomainResource.getIdElement
Inherited from DomainResource.getIdElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:127

setIdElement

setIdElement(element: undefined | IdType): this
Assigns the provided PrimitiveType value to the id property.
Parameters
- element: undefined | IdType
  the id value
Returns this
this
Implementation of IDomainResource.setIdElement
Inherited from DomainResource.setIdElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:134

hasIdElement

hasIdElement(): boolean
Returns boolean
true if the id property exists and has a value; false otherwise
Implementation of IDomainResource.hasIdElement
Inherited from DomainResource.hasIdElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:138

getId

getId(): undefined | string
Returns undefined | string
the id property value as a primitive value
Implementation of IDomainResource.getId
Inherited from DomainResource.getId
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:142

setId

setId(value: undefined | string): this
Assigns the provided primitive value to the id property.
Parameters
- value: undefined | string
  the id value
Returns this
this

Throws
PrimitiveTypeError for invalid primitive types
Implementation of IDomainResource.setId
Inherited from DomainResource.setId
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:150

hasId

hasId(): boolean
Returns boolean
true if the id property exists and has a value; false otherwise
Implementation of IDomainResource.hasId
Inherited from DomainResource.hasId
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:154

getMeta

getMeta(): Meta
Returns Meta
the meta property value as a Meta
Implementation of IDomainResource.getMeta
Inherited from DomainResource.getMeta
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:158

setMeta

setMeta(value: undefined | Meta): this
Assigns the provided value to the meta property.
Parameters
- value: undefined | Meta
  the meta value
Returns this
this
Implementation of IDomainResource.setMeta
Inherited from DomainResource.setMeta
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:165

hasMeta

hasMeta(): boolean
Returns boolean
true if the meta property exists and has a value; false otherwise
Implementation of IDomainResource.hasMeta
Inherited from DomainResource.hasMeta
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:169

getImplicitRulesElement

getImplicitRulesElement(): UriType
Returns UriType
the implicitRules property value as a PrimitiveType
Implementation of IDomainResource.getImplicitRulesElement
Inherited from DomainResource.getImplicitRulesElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:173

setImplicitRulesElement

setImplicitRulesElement(element: undefined | UriType): this
Assigns the provided PrimitiveType value to the implicitRules property.
Parameters
- element: undefined | UriType
  the implicitRules value
Returns this
this
Implementation of IDomainResource.setImplicitRulesElement
Inherited from DomainResource.setImplicitRulesElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:180

hasImplicitRulesElement

hasImplicitRulesElement(): boolean
Returns boolean
true if the implicitRules property exists and has a value; false otherwise
Implementation of IDomainResource.hasImplicitRulesElement
Inherited from DomainResource.hasImplicitRulesElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:184

getImplicitRules

getImplicitRules(): undefined | string
Returns undefined | string
the implicitRules property value as a primitive value
Implementation of IDomainResource.getImplicitRules
Inherited from DomainResource.getImplicitRules
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:188

setImplicitRules

setImplicitRules(value: undefined | string): this
Assigns the provided primitive value to the implicitRules property.
Parameters
- value: undefined | string
  the implicitRules value
Returns this
this

Throws
PrimitiveTypeError for invalid primitive types
Implementation of IDomainResource.setImplicitRules
Inherited from DomainResource.setImplicitRules
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:196

hasImplicitRules

hasImplicitRules(): boolean
Returns boolean
true if the system property exists and has a value; false otherwise
Implementation of IDomainResource.hasImplicitRules
Inherited from DomainResource.hasImplicitRules
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:200

getLanguageElement

getLanguageElement(): CodeType
Returns CodeType
the language property value as a PrimitiveType
Implementation of IDomainResource.getLanguageElement
Inherited from DomainResource.getLanguageElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:204

setLanguageElement

setLanguageElement(element: undefined | CodeType): this
Assigns the provided PrimitiveType value to the language property.
Parameters
- element: undefined | CodeType
  the language value
Returns this
this
Implementation of IDomainResource.setLanguageElement
Inherited from DomainResource.setLanguageElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:211

hasLanguageElement

hasLanguageElement(): boolean
Returns boolean
true if the language property exists and has a value; false otherwise
Implementation of IDomainResource.hasLanguageElement
Inherited from DomainResource.hasLanguageElement
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:215

getLanguage

getLanguage(): undefined | string
Returns undefined | string
the language property value as a primitive value
Implementation of IDomainResource.getLanguage
Inherited from DomainResource.getLanguage
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:219

setLanguage

setLanguage(value: undefined | string): this
Assigns the provided primitive value to the language property.
Parameters
- value: undefined | string
  the language value
Returns this
this

Throws
PrimitiveTypeError for invalid primitive types
Implementation of IDomainResource.setLanguage
Inherited from DomainResource.setLanguage
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:227

hasLanguage

hasLanguage(): boolean
Returns boolean
true if the language property exists and has a value; false otherwise
Implementation of IDomainResource.hasLanguage
Inherited from DomainResource.hasLanguage
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:231

isResource

isResource(): boolean
Returns boolean
true if the instance is a FHIR resource; false otherwise
Implementation of IDomainResource.isResource
Inherited from DomainResource.isResource
- Defined in packages/fhir-core/lib/base-models/Resource.d.ts:256

isDataType

isDataType(): boolean
Returns boolean
true if the instance is a FHIR complex or primitive datatype; false otherwise
Implementation of IDomainResource.isDataType
Inherited from DomainResource.isDataType
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:71

isComplexDataType

isComplexDataType(): boolean
Returns boolean
true if the instance is a FHIR complex datatype; false otherwise
Implementation of IDomainResource.isComplexDataType
Inherited from DomainResource.isComplexDataType
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:75

isPrimitive

isPrimitive(): boolean
Returns boolean
true if the instance is a FHIR primitive datatype; false otherwise
Implementation of IDomainResource.isPrimitive
Inherited from DomainResource.isPrimitive
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:79

isBooleanPrimitive

isBooleanPrimitive(): boolean
Returns boolean
true if the instance is a FHIR primitive boolean datatype; false otherwise
Implementation of IDomainResource.isBooleanPrimitive
Inherited from DomainResource.isBooleanPrimitive
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:83

isStringPrimitive

isStringPrimitive(): boolean
Returns boolean
true if the instance is a FHIR primitive string-based datatype; false otherwise
Implementation of IDomainResource.isStringPrimitive
Inherited from DomainResource.isStringPrimitive
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:87

isNumberPrimitive

isNumberPrimitive(): boolean
Returns boolean
true if the instance is a FHIR primitive number-based datatype; false otherwise
Implementation of IDomainResource.isNumberPrimitive
Inherited from DomainResource.isNumberPrimitive
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:91

isBigIntPrimitive

isBigIntPrimitive(): boolean
Returns boolean
true if the instance is a FHIR primitive bigint-based datatype; false otherwise
Implementation of IDomainResource.isBigIntPrimitive
Inherited from DomainResource.isBigIntPrimitive
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:95

isDateTimePrimitive

isDateTimePrimitive(): boolean
Returns boolean
true if the instance is a FHIR primitive datetime-based datatype; false otherwise
Implementation of IDomainResource.isDateTimePrimitive
Inherited from DomainResource.isDateTimePrimitive
- Defined in packages/fhir-core/lib/base-models/Base.d.ts:99

`Protected`copyValues

copyValues(dest: MolecularSequence): void
Protected
Copies the current instance's elements into the provided object.
Parameters
- dest: MolecularSequence
  the copied instance
Returns void
Overrides DomainResource.copyValues
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1522

`Private`initIdentifier

initIdentifier(): void
Initialize the identifier property

Returns void
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:638

`Private`initVariant

initVariant(): void
Initialize the variant property

Returns void
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1088

`Private`initQuality

initQuality(): void
Initialize the quality property

Returns void
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1210

`Private`initRepository

initRepository(): void
Initialize the repository property

Returns void
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1332

`Private`initPointer

initPointer(): void
Initialize the pointer property

Returns void
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1398

`Private`initStructureVariant

initStructureVariant(): void
Initialize the structureVariant property

Returns void
- Defined in packages/r4-datamodels/src/resources/MolecularSequence.ts:1456

Class MolecularSequence

Remarks

See

Hierarchy (View Summary)

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Parameters

Returns MolecularSequence

Properties

Private Optionalidentifier

Remarks

Private ReadonlysequenceTypeEnum

See

Private Optionaltype_

Remarks

See

PrivatecoordinateSystem

Remarks

Private Optionalpatient

Remarks

Private Optionalspecimen

Remarks

Private Optionaldevice

Remarks

Private Optionalperformer

Remarks

Private Optionalquantity

Remarks

Private OptionalreferenceSeq

Remarks

Private Optionalvariant

Remarks

Private OptionalobservedSeq

Remarks

Private Optionalquality

Remarks

Private OptionalreadCoverage

Remarks

Private Optionalrepository

Remarks

Private Optionalpointer

Remarks

Private OptionalstructureVariant

Remarks

Methods

Staticparse

Parameters

Returns undefined | MolecularSequence

Throws

getIdentifier

Returns Identifier[]

setIdentifier

Parameters

Returns this

Throws

addIdentifier

Parameters

Returns this

Throws

hasIdentifier

Returns boolean

getTypeEnumType

Returns undefined | EnumCodeType

See

setTypeEnumType

Parameters

Returns this

Throws

Throws

See

hasTypeEnumType

Returns boolean

getTypeElement

Returns undefined | CodeType

See

`Private` `Optional`identifier

`Private` `Readonly`sequenceTypeEnum

`Private` `Optional`type_

`Private`coordinateSystem

`Private` `Optional`patient

`Private` `Optional`specimen

`Private` `Optional`device

`Private` `Optional`performer

`Private` `Optional`quantity

`Private` `Optional`referenceSeq

`Private` `Optional`variant

`Private` `Optional`observedSeq

`Private` `Optional`quality

`Private` `Optional`readCoverage

`Private` `Optional`repository

`Private` `Optional`pointer

`Private` `Optional`structureVariant

`Static`parse