hl7/com.babylonhealth.lit.hl7.model/MolecularSequence

MolecularSequence

object MolecularSequence extends CompanionFor[MolecularSequence]
Companion:
class
class CompanionFor[MolecularSequence]
trait OptionSugar
trait JsonDecoderHelpers
trait BaseFieldDecoders
trait Utils
class Object
trait Matchable
class Any

Type members

Classlikes

@POJOBoilerplate
class Quality(val id: Option[String], val end: Option[Int], `type`: QUALITY_TYPE, val gtFP: Option[BigDecimal], val start: Option[Int], val score: Option[Quantity], val method: Option[CodeableConcept], val recall: Option[BigDecimal], val fScore: Option[BigDecimal], val truthTP: Option[BigDecimal], val queryTP: Option[BigDecimal], val truthFN: Option[BigDecimal], val queryFP: Option[BigDecimal], val extension: LitSeq[Extension], val precision: Option[BigDecimal], val standardSequence: Option[CodeableConcept], val modifierExtension: LitSeq[Extension], val roc: Option[Roc], val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]) extends BackboneElement
Companion:
object
object Quality extends CompanionFor[Quality]
Companion:
class
@POJOBoilerplate
class ReferenceSeq(val id: Option[String], val strand: Option[STRAND_TYPE], val extension: LitSeq[Extension], val windowEnd: Option[Int], val chromosome: Option[CodeableConcept], val genomeBuild: Option[String], val orientation: Option[ORIENTATION_TYPE], val windowStart: Option[Int], val referenceSeqId: Option[CodeableConcept], val modifierExtension: LitSeq[Extension], val referenceSeqString: Option[String], val referenceSeqPointer: Option[Reference], val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]) extends BackboneElement
Companion:
object
object ReferenceSeq extends CompanionFor[ReferenceSeq]
Companion:
class
@POJOBoilerplate
class Repository(val id: Option[String], val url: Option[UriStr], `type`: REPOSITORY_TYPE, val name: Option[String], val extension: LitSeq[Extension], val datasetId: Option[String], val readsetId: Option[String], val variantsetId: Option[String], val modifierExtension: LitSeq[Extension], val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]) extends BackboneElement
Companion:
object
object Repository extends CompanionFor[Repository]
Companion:
class
@POJOBoilerplate
class StructureVariant(val id: Option[String], val exact: Option[Boolean], val length: Option[Int], val extension: LitSeq[Extension], val variantType: Option[CodeableConcept], val modifierExtension: LitSeq[Extension], val outer: Option[Outer], val inner: Option[Inner], val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]) extends BackboneElement
Companion:
object
object StructureVariant extends CompanionFor[StructureVariant]
Companion:
class
@POJOBoilerplate
class Variant(val id: Option[String], val end: Option[Int], val start: Option[Int], val cigar: Option[String], val extension: LitSeq[Extension], val observedAllele: Option[String], val variantPointer: Option[Reference], val referenceAllele: Option[String], val modifierExtension: LitSeq[Extension], val primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]) extends BackboneElement
Companion:
object
object Variant extends CompanionFor[Variant]
Companion:
class

Inherited classlikes

implicit class RichCursor(cursor: ACursor)
Inherited from:
JsonDecoderHelpers
implicit class RichSeqT[T](val s1: Seq[T])
Inherited from:
OptionSugar
implicit class RichT[T](val t: T)
Inherited from:
OptionSugar

Types

Value members

Concrete methods

def apply(id: Option[String], meta: Option[Meta], text: Option[Narrative], `type`: Option[SEQUENCE_TYPE], device: Option[Reference], patient: Option[Reference], pointer: LitSeq[Reference], language: Option[LANGUAGES], specimen: Option[Reference], quantity: Option[Quantity], contained: LitSeq[Resource], extension: LitSeq[Extension], performer: Option[Reference], identifier: LitSeq[Identifier], observedSeq: Option[String], readCoverage: Option[Int], implicitRules: Option[UriStr], coordinateSystem: Int, modifierExtension: LitSeq[Extension], variant: LitSeq[Variant], repository: LitSeq[Repository], quality: LitSeq[Quality], referenceSeq: Option[ReferenceSeq], structureVariant: LitSeq[StructureVariant], primitiveAttributes: TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]): MolecularSequence
def decodeThis(cursor: HCursor)(implicit params: DecoderParams): Try[MolecularSequence]
def extractContained(t: MolecularSequence): LitSeq[Resource]
def extractDevice(t: MolecularSequence): Option[Reference]
def extractExtension(t: MolecularSequence): LitSeq[Extension]
def extractId(t: MolecularSequence): Option[String]
def extractIdentifier(t: MolecularSequence): LitSeq[Identifier]
def extractImplicitRules(t: MolecularSequence): Option[UriStr]
def extractLanguage(t: MolecularSequence): Option[LANGUAGES]
def extractMeta(t: MolecularSequence): Option[Meta]
def extractModifierExtension(t: MolecularSequence): LitSeq[Extension]
def extractObservedSeq(t: MolecularSequence): Option[String]
def extractPatient(t: MolecularSequence): Option[Reference]
def extractPerformer(t: MolecularSequence): Option[Reference]
def extractPointer(t: MolecularSequence): LitSeq[Reference]
def extractQuantity(t: MolecularSequence): Option[Quantity]
def extractSpecimen(t: MolecularSequence): Option[Reference]
override def fields(t: MolecularSequence): Seq[FHIRComponentField[_]]
Definition Classes
CompanionFor
override def fieldsFromParent(t: ResourceType): Try[Seq[FHIRComponentField[_]]]
Definition Classes
CompanionFor

Inherited methods

def cast(t: ResourceType): Try[MolecularSequence]
Inherited from:
CompanionFor
def checkUnknownFields(cursor: HCursor, keys: Set[String], keyPrefixes: Seq[Set[String]])(implicit decoderParams: DecoderParams): Try[Unit]
Inherited from:
CompanionFor
def companionClassName[T](tag: LTag[T]): String
Inherited from:
Utils
def companionOf[T <: FHIRObject : ClassTag](implicit evidence$1: ClassTag[T], tag: LTag[T]): CompanionFor[T]
Inherited from:
Utils
def decodeAttributes(cursor: HCursor)(implicit params: DecoderParams): TreeMap[FHIRComponentFieldMeta[_], PrimitiveElementInfo]
Inherited from:
CompanionFor
def decodeMethodFor[T <: FHIRObject : ClassTag](implicit evidence$2: ClassTag[T], tag: LTag[T], params: DecoderParams): HCursor => Try[T]
Inherited from:
Utils
def decoder(implicit params: DecoderParams): Decoder[MolecularSequence]
Inherited from:
CompanionFor
def extract[O](fn: MolecularSequence.type => FHIRComponentFieldMeta[O])(t: MolecularSequence): O
Inherited from:
CompanionFor
def isSubTypeOf(other: CompanionFor[_]): Boolean
Inherited from:
CompanionFor
protected def otherMetas: Set[String]
Inherited from:
CompanionFor
def parameterisedDecode(x: HCursor, params: DecoderParams): Try[MolecularSequence]
Inherited from:
CompanionFor
protected def refMetas: Seq[Set[String]]
Inherited from:
CompanionFor
def tryDecode[T](fn: => T, c: HCursor): Either[DecodingFailure, T]
Inherited from:
BaseFieldDecoders

Concrete fields

val `type`: FHIRComponentFieldMeta[Option[SEQUENCE_TYPE]]
override val baseType: CompanionFor[ResourceType]
val contained: FHIRComponentFieldMeta[LitSeq[Resource]]
val coordinateSystem: FHIRComponentFieldMeta[Int]
val device: FHIRComponentFieldMeta[Option[Reference]]
val extension: FHIRComponentFieldMeta[LitSeq[Extension]]
val fieldsMeta: Seq[FHIRComponentFieldMeta[_]]
val id: FHIRComponentFieldMeta[Option[String]]
val identifier: FHIRComponentFieldMeta[LitSeq[Identifier]]
val implicitRules: FHIRComponentFieldMeta[Option[UriStr]]
val language: FHIRComponentFieldMeta[Option[LANGUAGES]]
val meta: FHIRComponentFieldMeta[Option[Meta]]
val modifierExtension: FHIRComponentFieldMeta[LitSeq[Extension]]
val observedSeq: FHIRComponentFieldMeta[Option[String]]
override val parentType: CompanionFor[ParentType]
val patient: FHIRComponentFieldMeta[Option[Reference]]
val performer: FHIRComponentFieldMeta[Option[Reference]]
val pointer: FHIRComponentFieldMeta[LitSeq[Reference]]
override val profileUrl: Option[String]
val quality: FHIRComponentFieldMeta[LitSeq[Quality]]
val quantity: FHIRComponentFieldMeta[Option[Quantity]]
val readCoverage: FHIRComponentFieldMeta[Option[Int]]
val referenceSeq: FHIRComponentFieldMeta[Option[ReferenceSeq]]
val repository: FHIRComponentFieldMeta[LitSeq[Repository]]
override val searchParams: Map[String, MolecularSequence => Seq[Any]]
val specimen: FHIRComponentFieldMeta[Option[Reference]]
val structureVariant: FHIRComponentFieldMeta[LitSeq[StructureVariant]]
val text: FHIRComponentFieldMeta[Option[Narrative]]
override val thisName: String
val variant: FHIRComponentFieldMeta[LitSeq[Variant]]

Inherited fields

val classConstructor: Constructor[MolecularSequence]
Inherited from:
CompanionFor
val thisClassTag: ClassTag[MolecularSequence]
Inherited from:
CompanionFor
val thisTypeTag: LTag[MolecularSequence]
Inherited from:
CompanionFor
val yearsAndMonths: Regex
Inherited from:
BaseFieldDecoders
val yearsMonthsAndDays: Regex
Inherited from:
BaseFieldDecoders
val yearsOnly: Regex
Inherited from:
BaseFieldDecoders

Implicits

Implicits

Inherited implicits

final implicit def RichCursor(cursor: ACursor): RichCursor
Inherited from:
JsonDecoderHelpers
final implicit def RichSeqT[T](s1: Seq[T]): RichSeqT[T]
Inherited from:
OptionSugar
final implicit def RichT[T](t: T): RichT[T]
Inherited from:
OptionSugar
implicit val base64BinaryDecoder: Decoder[Base64Binary]
Inherited from:
BaseFieldDecoders
implicit val base64BinaryEncoder: Encoder[Base64Binary]
Inherited from:
BaseFieldDecoders
implicit val canonicalDecoder: Decoder[Canonical]
Inherited from:
BaseFieldDecoders
implicit val canonicalEncoder: Encoder[Canonical]
Inherited from:
BaseFieldDecoders
implicit val codeDecoder: Decoder[Code]
Inherited from:
BaseFieldDecoders
implicit val codeEncoder: Encoder[Code]
Inherited from:
BaseFieldDecoders
implicit def decodeEither[A, B](implicit decoderA: Decoder[A], decoderB: Decoder[B]): Decoder[Either[A, B]]
Inherited from:
BaseFieldDecoders
implicit val decodeFHIRDate: Decoder[FHIRDate]
Inherited from:
BaseFieldDecoders
implicit val decodeFHIRDateTime: Decoder[FHIRDateTime]
Inherited from:
BaseFieldDecoders
implicit def decodeLitSeq[T](implicit decoder: Decoder[T]): Decoder[LitSeq[T]]
Inherited from:
BaseFieldDecoders
implicit def decodeNonEmptyLitSeq[T](implicit decoder: Decoder[LitSeq[T]]): Decoder[NonEmptyLitSeq[T]]
Inherited from:
BaseFieldDecoders
implicit val decodeZonedDateTime: Decoder[ZonedDateTime]
Inherited from:
BaseFieldDecoders
implicit def encodeEither[A, B](implicit encoderA: Encoder[A], encoderB: Encoder[B]): Encoder[Either[A, B]]
Inherited from:
BaseFieldDecoders
implicit def encodeLitSeq[T](implicit encoder: Encoder[T]): Encoder[LitSeq[T]]
Inherited from:
BaseFieldDecoders
implicit val encodeZonedDateTime: Encoder[ZonedDateTime]
Inherited from:
BaseFieldDecoders
implicit val encoderFHIRDate: Encoder[FHIRDate]
Inherited from:
BaseFieldDecoders
implicit val encoderFHIRDateTime: Encoder[FHIRDateTime]
Inherited from:
BaseFieldDecoders
implicit val idDecoder: Decoder[Id]
Inherited from:
BaseFieldDecoders
implicit val idEncoder: Encoder[Id]
Inherited from:
BaseFieldDecoders
implicit val markdownDecoder: Decoder[Markdown]
Inherited from:
BaseFieldDecoders
implicit val markdownEncoder: Encoder[Markdown]
Inherited from:
BaseFieldDecoders
implicit val oidDecoder: Decoder[OID]
Inherited from:
BaseFieldDecoders
implicit val oidEncoder: Encoder[OID]
Inherited from:
BaseFieldDecoders
implicit val positiveIntDecoder: Decoder[PositiveInt]
Inherited from:
BaseFieldDecoders
implicit val positiveIntEncoder: Encoder[PositiveInt]
Inherited from:
BaseFieldDecoders
implicit val unsignedIntDecoder: Decoder[UnsignedInt]
Inherited from:
BaseFieldDecoders
implicit val unsignedIntEncoder: Encoder[UnsignedInt]
Inherited from:
BaseFieldDecoders
implicit val uriDecoder: Decoder[UriStr]
Inherited from:
BaseFieldDecoders
implicit val uriEncoder: Encoder[UriStr]
Inherited from:
BaseFieldDecoders
implicit val urlDecoder: Decoder[UrlStr]
Inherited from:
BaseFieldDecoders
implicit val urlEncoder: Encoder[UrlStr]
Inherited from:
BaseFieldDecoders
implicit val xhtmlDecoder: Decoder[XHTML]
Inherited from:
BaseFieldDecoders
implicit val xhtmlEncoder: Encoder[XHTML]
Inherited from:
BaseFieldDecoders