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-- ==========================================================================
-- Objects for sequence coordinate remapping
-- ==========================================================================



IMPORTS User-object FROM NCBI-General;

HGVS-Coordinate ::= SEQUENCE {
    -- actual marker position
    -- this is supplied because this is the position of the marker in the main
    -- sequence's coordinate space; this is different than the mapped
    -- coordinate space.
    marker-pos INTEGER,

    -- pretty-printed name for the object
    -- in general, this should be the "best" seq-id for the product
    -- of a feature represented at a position
    title VisibleString,

    -- the fingerprint of the object in question
    -- this is a complex reversible hash
    object-id VisibleString OPTIONAL,

    -- the mapped position in the object's coordinate space
    -- it's not valid for DNA coordinate in UTR and intergenic region,
    -- while hgvs-position can be meaningful, that is why OPTIONAL.
    pos-mapped INTEGER OPTIONAL,

    -- a label for this position
    -- this shall always be in HGVS nomenclature
    hgvs-position VisibleString,

    -- a sequence for this position
    sequence VisibleString

HGVS-Coordinate-Set ::= SET OF HGVS-Coordinate