Data Model Libraries
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    Class MolecularSequenceReferenceSeqComponent

    MolecularSequenceReferenceSeqComponent Class

    FHIR Specification

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

    Hierarchy (View Summary)

    Implements

    Index

    Constructors

    Properties

    Methods

    Constructors

    Properties

    chromosome?: CodeableConcept

    MolecularSequence.referenceSeq.chromosome Element

    FHIR Specification

    • Short: Chromosome containing genetic finding
    • 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
    genomeBuild?: StringType

    MolecularSequence.referenceSeq.genomeBuild Element

    FHIR Specification

    • Short: The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    • Definition: The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
    • FHIR Type: string
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    orientationTypeEnum: OrientationTypeEnum

    FHIR CodeSystem: OrientationType

    orientation?: EnumCodeType

    MolecularSequence.referenceSeq.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

    referenceSeqId?: CodeableConcept

    MolecularSequence.referenceSeq.referenceSeqId Element

    FHIR Specification

    • Short: Reference identifier
    • Definition: Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, "NG_" identifies reference sequence for genes, "NM_" for messenger RNA transcripts, and "NP_" for amino acid sequences.
    • FHIR Type: CodeableConcept
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    referenceSeqPointer?: Reference

    MolecularSequence.referenceSeq.referenceSeqPointer Element

    FHIR Specification

    • Short: A pointer to another MolecularSequence entity as reference sequence
    • Definition: A pointer to another MolecularSequence entity as reference sequence.
    • FHIR Type: Reference
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    referenceSeqString?: StringType

    MolecularSequence.referenceSeq.referenceSeqString Element

    FHIR Specification

    • Short: A string to represent reference sequence
    • Definition: A string like "ACGT".
    • FHIR Type: string
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    strandTypeEnum: StrandTypeEnum

    FHIR CodeSystem: StrandType

    strand?: EnumCodeType

    MolecularSequence.referenceSeq.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

    windowStart?: IntegerType

    MolecularSequence.referenceSeq.windowStart Element

    FHIR Specification

    • Short: Start position of the window on the reference sequence
    • Definition: Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
    • FHIR Type: integer
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    windowEnd?: IntegerType

    MolecularSequence.referenceSeq.windowEnd Element

    FHIR Specification

    • Short: End position of the window on the reference sequence
    • Definition: End position of the window on the reference 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.
    • FHIR Type: integer
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    Methods

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

      Parameters

      • sourceJson: Value

        JSON representing FHIR MolecularSequenceReferenceSeqComponent

      • OptionaloptSourceField: string

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

      Returns undefined | MolecularSequenceReferenceSeqComponent

      MolecularSequenceReferenceSeqComponent data model or undefined for MolecularSequenceReferenceSeqComponent

      JsonError if the provided JSON is not a valid JSON object

    • Assigns the provided ReferenceSeqPointer object value to the referenceSeqPointer property.

      Parameters

      • value: undefined | Reference

        the referenceSeqPointer object value

      Returns this

      this

      @ReferenceTargets('MolecularSequence.referenceSeq.referenceSeqPointer', ['MolecularSequence',])

      InvalidTypeError for invalid data type or reference value

    • 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