MolecularSequence class
MolecularSequence Raw data describing a biological sequence.
- Mixed-in types
- 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.
constfactory
-
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 setterinherited - 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 setterinherited - coordinateSystemElement → Element?
-
coordinateSystemElement
Extensions for coordinateSystemno setterinherited -
copyWith
→ $MolecularSequenceCopyWith<
MolecularSequence> -
no setterinherited
- dbId → int?
-
no setterinherited
- device → Reference?
-
device
The method for sequencing, for example, chip information.no setterinherited -
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 setterinherited - fhirId → String?
-
id The logical id of the resource, as used in the URL for the resource.
Once assigned, this value never changes.
no setterinherited
- hashCode → int
-
The hash code for this object.
no setterinherited
-
identifier
→ List<
Identifier> ? -
identifier
A unique identifier for this particular sequence instance. This is a FHIR-defined id.no setterinherited - 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 setterinherited - implicitRulesElement → Element?
-
implicitRulesElement
Extensions for implicitRulesno setterinherited - language → FhirCode?
-
language
The base language in which the resource is written.no setterinherited - languageElement → Element?
-
languageElement
Extensions for languageno setterinherited - 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 setterinherited -
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 setterinherited - 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 setterinherited - observedSeqElement → Element?
-
observedSeqElement
Extensions for observedSeqno setterinherited - path → String
-
Local Reference for this Resource, form is "ResourceType/Id"
no setterinherited
- patient → Reference?
-
patient
The patient whose sequencing results are described by this resource.no setterinherited - performer → Reference?
-
performer
The organization or lab that should be responsible for this result.no setterinherited -
pointer
→ List<
Reference> ? -
pointer
Pointer to next atomic sequence which at most contains one variant.no setterinherited -
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 setterinherited - quantity → Quantity?
-
quantity
The number of copies of the sequence of interest. (RNASeq).no setterinherited - readCoverage → FhirInteger?
-
readCoverage
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.no setterinherited - readCoverageElement → Element?
-
readCoverageElement
Extensions for readCoverageno setterinherited - referenceSeq → MolecularSequenceReferenceSeq?
-
referenceSeq
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.no setterinherited -
repository
→ List<
MolecularSequenceRepository> ? -
repository
Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.no setterinherited - resourceType → R4ResourceType
-
no setterinherited
- resourceTypeString → String?
-
produce a string of the resourceType
no setterinherited
- runtimeType → Type
-
A representation of the runtime type of the object.
no setterinherited
- specimen → Reference?
-
specimen
Specimen used for sequencing.no setterinherited -
structureVariant
→ List<
MolecularSequenceStructureVariant> ? -
structureVariant
Information about chromosome structure variation.no setterinherited - 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 setterinherited - thisReference → Reference
-
Convenience method to return a Reference referring to that Resource
no setterinherited
- type → FhirCode?
-
type
Amino Acid Sequence/ DNA Sequence / RNA Sequence.no setterinherited - typeElement → Element?
-
typeElement
Extensions for typeno setterinherited -
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 setterinherited
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