Data Model Libraries
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    Class MolecularSequenceRelativeStartingSequenceComponent

    MolecularSequenceRelativeStartingSequenceComponent Class

    FHIR Specification

    • Short: A sequence used as starting sequence
    • Definition: A sequence that is used as a starting sequence to describe variants that are present in a sequence analyzed.

    Hierarchy (View Summary)

    Implements

    Index

    Constructors

    Properties

    genomeAssembly?: CodeableConcept

    MolecularSequence.relative.startingSequence.genomeAssembly Element

    FHIR Specification

    • Short: The genome assembly used for starting sequence, e.g. GRCh38
    • Definition: The genome assembly used for starting sequence, e.g. GRCh38.
    • FHIR Type: CodeableConcept
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    chromosome?: CodeableConcept

    MolecularSequence.relative.startingSequence.chromosome Element

    FHIR Specification

    • Short: Chromosome Identifier
    • Definition: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340).
    • FHIR Type: CodeableConcept
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    sequence?: IDataType

    MolecularSequence.relative.startingSequence.sequence[x] Element

    @ChoiceDataTypesMeta('MolecularSequence.relative.startingSequence.sequence[x]', ['CodeableConcept','string','Reference',]

    FHIR Specification

    • Short: The reference sequence that represents the starting sequence
    • Definition: The reference sequence that represents the starting sequence.
    • Comment: A starting sequence may be represented in one of three ways: 1. CodeableConcept, using NCBI, LRG or other appropriate code systems 1. a simple string of IUPAC codes 1. a reference to another MolecularSequence resource.
    • FHIR Types: 'CodeableConcept', 'string', 'Reference',
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    windowStart?: IntegerType

    MolecularSequence.relative.startingSequence.windowStart Element

    FHIR Specification

    • Short: Start position of the window on the starting sequence
    • Definition: Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.
    • FHIR Type: integer
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    windowEnd?: IntegerType

    MolecularSequence.relative.startingSequence.windowEnd Element

    FHIR Specification

    • Short: End position of the window on the starting sequence
    • Definition: End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.
    • FHIR Type: integer
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    orientationTypeEnum: OrientationTypeEnum

    FHIR CodeSystem: OrientationType

    orientation?: EnumCodeType

    MolecularSequence.relative.startingSequence.orientation Element

    FHIR Specification

    • Short: sense | antisense
    • Definition: A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.
    • FHIR Type: code
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    CodeSystem Enumeration: OrientationTypeEnum

    strandTypeEnum: StrandTypeEnum

    FHIR CodeSystem: StrandType

    strand?: EnumCodeType

    MolecularSequence.relative.startingSequence.strand Element

    FHIR Specification

    • Short: watson | crick
    • Definition: An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.
    • FHIR Type: code
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    CodeSystem Enumeration: StrandTypeEnum

    Methods

    • Parse the provided MolecularSequenceRelativeStartingSequenceComponent JSON to instantiate the MolecularSequenceRelativeStartingSequenceComponent data model.

      Parameters

      • sourceJson: Value

        JSON representing FHIR MolecularSequenceRelativeStartingSequenceComponent

      • OptionaloptSourceField: string

        Optional data source field (e.g. <complexTypeName>.<complexTypeFieldName>); defaults to MolecularSequenceRelativeStartingSequenceComponent

      Returns undefined | MolecularSequenceRelativeStartingSequenceComponent

      MolecularSequenceRelativeStartingSequenceComponent data model or undefined for MolecularSequenceRelativeStartingSequenceComponent

      JsonError if the provided JSON is not a valid JSON object

    • 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; false otherwise

      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.

      AssertionError for invalid url

    • Returns undefined | string

      the id property value

    • Assigns the provided value to the id property.

      Parameters

      • value: undefined | string

        the id value

      Returns this

      this

      PrimitiveTypeError for invalid value

    • Returns boolean

      true if id exists and has a value; false otherwise

    • 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

      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.

      AssertionError for invalid url

    • Determines if the extension property exists.

      Parameters

      • url: string

        the url that identifies a specific Extension

      Returns undefined | IExtension

      an Extension having the provided url

      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.

      AssertionError for invalid url

    • 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

    • 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

      AssertionError for invalid url

    • 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

    • Returns boolean

      true if the instance is a FHIR complex or primitive datatype; false otherwise