Data Model Libraries
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    MolecularSequenceVariantComponent Class

    FHIR Specification

    • Short: Variant in sequence
    • Definition: 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.

    Hierarchy (View Summary)

    Implements

    Index

    Constructors

    Properties

    start?: IntegerType

    MolecularSequence.variant.start Element

    FHIR Specification

    • Short: Start position of the variant on the reference sequence
    • Definition: Start position of the variant 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

    MolecularSequence.variant.end Element

    FHIR Specification

    • Short: End position of the variant on the reference sequence
    • Definition: End position of the variant 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
    observedAllele?: StringType

    MolecularSequence.variant.observedAllele Element

    FHIR Specification

    • Short: Allele that was observed
    • Definition: An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
    • FHIR Type: string
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    referenceAllele?: StringType

    MolecularSequence.variant.referenceAllele Element

    FHIR Specification

    • Short: Allele in the reference sequence
    • Definition: An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
    • FHIR Type: string
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    cigar?: StringType

    MolecularSequence.variant.cigar Element

    FHIR Specification

    • Short: Extended CIGAR string for aligning the sequence with reference bases
    • Definition: Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here.
    • FHIR Type: string
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    variantPointer?: Reference

    MolecularSequence.variant.variantPointer Element

    FHIR Specification

    • Short: Pointer to observed variant information
    • Definition: A pointer to an Observation containing variant information.
    • FHIR Type: Reference
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true

    Methods

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

      Parameters

      • sourceJson: Value

        JSON representing FHIR MolecularSequenceVariantComponent

      • OptionaloptSourceField: string

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

      Returns undefined | MolecularSequenceVariantComponent

      MolecularSequenceVariantComponent data model or undefined for MolecularSequenceVariantComponent

      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