MolecularSequenceQuality class

MolecularSequenceQuality Raw data describing a biological sequence.

Annotations

• @freezed

Constructors

MolecularSequenceQuality({@JsonKey(name: 'id') FhirId? fhirId, @JsonKey(name: 'extension') List<FhirExtension>? extension_, List<FhirExtension>? modifierExtension, FhirCode? type, @JsonKey(name: '_type') Element? typeElement, CodeableConcept? standardSequence, FhirInteger? start, @JsonKey(name: '_start') Element? startElement, FhirInteger? end, @JsonKey(name: '_end') Element? endElement, Quantity? score, CodeableConcept? method, FhirDecimal? truthTP, @JsonKey(name: '_truthTP') Element? truthTPElement, FhirDecimal? queryTP, @JsonKey(name: '_queryTP') Element? queryTPElement, FhirDecimal? truthFN, @JsonKey(name: '_truthFN') Element? truthFNElement, FhirDecimal? queryFP, @JsonKey(name: '_queryFP') Element? queryFPElement, FhirDecimal? gtFP, @JsonKey(name: '_gtFP') Element? gtFPElement, FhirDecimal? precision, @JsonKey(name: '_precision') Element? precisionElement, FhirDecimal? recall, @JsonKey(name: '_recall') Element? recallElement, FhirDecimal? fScore, @JsonKey(name: '_fScore') Element? fScoreElement, MolecularSequenceRoc? roc})

MolecularSequenceQuality Raw data describing a biological sequence.

const

factory

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

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

factory

MolecularSequenceQuality.fromJsonString(String source)

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

factory

MolecularSequenceQuality.fromYaml(dynamic yaml)

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

factory

Properties

copyWith → $MolecularSequenceQualityCopyWith<MolecularSequenceQuality>

no setter, inherited

end → FhirInteger?

end End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

no setter, inherited

endElement → Element?

endElement Extensions for end

no setter, inherited

extension_ → List<FhirExtension>?

extension_ 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 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 → FhirId?

id Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

no setter, inherited

fScore → FhirDecimal?

fScore Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

no setter, inherited

fScoreElement → Element?

fScoreElement Extensions for fScore

no setter, inherited

gtFP → FhirDecimal?

gtFP The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

no setter, inherited

gtFPElement → Element?

gtFPElement Extensions for gtFP

no setter, inherited

hashCode → int

The hash code for this object.

no setter, inherited

method → CodeableConcept?

method Which method is used to get sequence quality.

no setter, inherited

modifierExtension → List<FhirExtension>?

modifierExtension 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 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 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).

no setter, inherited

precision → FhirDecimal?

precision QUERY.TP / (QUERY.TP + QUERY.FP).

no setter, inherited

precisionElement → Element?

precisionElement Extensions for precision

no setter, inherited

queryFP → FhirDecimal?

queryFP False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

no setter, inherited

queryFPElement → Element?

queryFPElement Extensions for queryFP

no setter, inherited

queryTP → FhirDecimal?

queryTP True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

no setter, inherited

queryTPElement → Element?

queryTPElement Extensions for queryTP

no setter, inherited

recall → FhirDecimal?

recall TRUTH.TP / (TRUTH.TP + TRUTH.FN).

no setter, inherited

recallElement → Element?

recallElement Extensions for recall

no setter, inherited

roc → MolecularSequenceRoc?

roc Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.

no setter, inherited

runtimeType → Type

A representation of the runtime type of the object.

no setter, inherited

score → Quantity?

score The score of an experimentally derived feature such as a p-value (SO:0001685).

no setter, inherited

standardSequence → CodeableConcept?

standardSequence Gold standard sequence used for comparing against.

no setter, inherited

start → FhirInteger?

start Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

no setter, inherited

startElement → Element?

startElement Extensions for start

no setter, inherited

truthFN → FhirDecimal?

truthFN False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

no setter, inherited

truthFNElement → Element?

truthFNElement Extensions for truthFN

no setter, inherited

truthTP → FhirDecimal?

truthTP True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

no setter, inherited

truthTPElement → Element?

truthTPElement Extensions for truthTP

no setter, inherited

type → FhirCode?

type INDEL / SNP / Undefined variant.

no setter, inherited

typeElement → Element?

typeElement Extensions for type

no setter, inherited

Methods

noSuchMethod(Invocation invocation) → dynamic

Invoked when a nonexistent method or property is accessed.

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

toString() → String

A string representation of this object.

inherited

toYaml() → String

Produces a Yaml formatted String version of the object

Operators

operator ==(Object other) → bool

The equality operator.

inherited