MolecularSequence class

MolecularSequence Raw data describing a biological sequence.

Mixed in types

• Resource

Annotations

• @freezed

Constructors

MolecularSequence({@Default(R4ResourceType.MolecularSequence) @JsonKey(unknownEnumValue: R4ResourceType.MolecularSequence) R4ResourceType resourceType, @JsonKey(includeFromJson: true, includeToJson: false) int? dbId, @JsonKey(name: 'id') String? fhirId, FhirMeta? meta, FhirUri? implicitRules, @JsonKey(name: '_implicitRules') Element? implicitRulesElement, FhirCode? language, @JsonKey(name: '_language') Element? languageElement, Narrative? text, List<Resource>? contained, @JsonKey(name: 'extension') List<FhirExtension>? extension_, List<FhirExtension>? modifierExtension, List<Identifier>? identifier, FhirCode? type, @JsonKey(name: '_type') Element? typeElement, FhirInteger? coordinateSystem, @JsonKey(name: '_coordinateSystem') Element? coordinateSystemElement, Reference? patient, Reference? specimen, Reference? device, Reference? performer, Quantity? quantity, MolecularSequenceReferenceSeq? referenceSeq, List<MolecularSequenceVariant>? variant, String? observedSeq, @JsonKey(name: '_observedSeq') Element? observedSeqElement, List<MolecularSequenceQuality>? quality, FhirInteger? readCoverage, @JsonKey(name: '_readCoverage') Element? readCoverageElement, List<MolecularSequenceRepository>? repository, List<Reference>? pointer, List<MolecularSequenceStructureVariant>? structureVariant})

MolecularSequence Raw data describing a biological sequence.

const

factory

MolecularSequence.fromJson(Map<String, dynamic> json)

Factory constructor, accepts Map<String, dynamic> as an argument

factory

MolecularSequence.fromJsonString(String source)

Acts like a constructor, returns a MolecularSequence, accepts a String as an argument, mostly because I got tired of typing it out

factory

MolecularSequence.fromYaml(dynamic yaml)

Factory constructor that accepts a String in YAML format as an argument

factory

Properties

contained → List<Resource>?

contained 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.

no setter, inherited

coordinateSystem → FhirInteger?

coordinateSystem 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).

no setter, inherited

coordinateSystemElement → Element?

coordinateSystemElement Extensions for coordinateSystem

no setter, inherited

copyWith → $MolecularSequenceCopyWith<MolecularSequence>

no setter, inherited

dbId → int?

no setter, inherited

device → Reference?

device The method for sequencing, for example, chip information.

no setter, inherited

extension_ → List<FhirExtension>?

extension_ 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.

no setter, inherited

fhirId → String?

id The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

no setter, inherited

hashCode → int

The hash code for this object.

no setter, inherited

identifier → List<Identifier>?

identifier A unique identifier for this particular sequence instance. This is a FHIR-defined id.

no setter, inherited

implicitRules → FhirUri?

implicitRules 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.

no setter, inherited

implicitRulesElement → Element?

implicitRulesElement Extensions for implicitRules

no setter, inherited

language → FhirCode?

language The base language in which the resource is written.

no setter, inherited

languageElement → Element?

languageElement Extensions for language

no setter, inherited

meta → FhirMeta?

meta 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.

no setter, inherited

modifierExtension → List<FhirExtension>?

modifierExtension 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).

no setter, inherited

observedSeq → String?

observedSeq 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.

no setter, inherited

observedSeqElement → Element?

observedSeqElement Extensions for observedSeq

no setter, inherited

path → String

Local Reference for this Resource, form is "ResourceType/Id"

no setter, inherited

patient → Reference?

patient The patient whose sequencing results are described by this resource.

no setter, inherited

performer → Reference?

performer The organization or lab that should be responsible for this result.

no setter, inherited

pointer → List<Reference>?

pointer Pointer to next atomic sequence which at most contains one variant.

no setter, inherited

quality → List<MolecularSequenceQuality>?

quality An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score (SO:0001686).

no setter, inherited

quantity → Quantity?

quantity The number of copies of the sequence of interest. (RNASeq).

no setter, inherited

readCoverage → FhirInteger?

readCoverage Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

no setter, inherited

readCoverageElement → Element?

readCoverageElement Extensions for readCoverage

no setter, inherited

referenceSeq → MolecularSequenceReferenceSeq?

referenceSeq A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

no setter, inherited

repository → List<MolecularSequenceRepository>?

repository Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

no setter, inherited

resourceType → R4ResourceType

no setter, inherited

resourceTypeString → String?

produce a string of the resourceType

no setter, inherited

runtimeType → Type

A representation of the runtime type of the object.

no setter, inherited

specimen → Reference?

specimen Specimen used for sequencing.

no setter, inherited

structureVariant → List<MolecularSequenceStructureVariant>?

structureVariant Information about chromosome structure variation.

no setter, inherited

text → Narrative?

text 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.

no setter, inherited

thisReference → Reference

Convenience method to return a Reference referring to that Resource

no setter, inherited

type → FhirCode?

type Amino Acid Sequence/ DNA Sequence / RNA Sequence.

no setter, inherited

typeElement → Element?

typeElement Extensions for type

no setter, inherited

variant → List<MolecularSequenceVariant>?

variant 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.

no setter, inherited

Methods

newId() → Resource

returns the same resource with a new ID (even if there is already an ID present)

inherited

newIdIfNoId() → Resource

returns the same resource with a new ID if there is no current ID

inherited

noSuchMethod(Invocation invocation) → dynamic

Invoked when a nonexistent method or property is accessed.

inherited

toDbJson() → Map<String, dynamic>

The normal toJson ignores the dbId, and produces the fhirId as the id However, if you're going to use this as a database entry, you have to switch those two ids

inherited

toJson() → Map<String, dynamic>

inherited

toJsonString() → String

Another convenience method because more and more I'm transmitting FHIR data as a String and not a Map

override

toString() → String

A string representation of this object.

inherited

toYaml() → String

Produces a Yaml formatted String version of the object

inherited

updateVersion({FhirMeta? oldMeta}) → Resource

Updates the meta field of this Resource, updates the meta.lastUpdated field, adds 1 to the version number

inherited

Operators

operator ==(Object other) → bool

The equality operator.

inherited