VariantPlacement
Defined in file variation.asn
C++ class: CVariantPlacement
VariantPlacement ::= SEQUENCE
{
-- actual concrete placement we are considering
loc Seq-loc,
mol INTEGER {
unknown(0),
genomic(1), --"g." coordinates in HGVS
cdna(2), --"c." coordinates in HGVS
rna(3), --"n." coordinates in HGVS
protein(4), --"p." coordinates in HGVS
mitochondrion(5) --"mt." coordinates in HGVS
},
-- location flags
placement-method INTEGER {
projected(1),
asserted(2),
aligned(3)
} OPTIONAL,
-- location refinements, describing offsets into introns from product coordinates.
-- Biological semantics: start-offset/stop-offset apply to bio-start/bio-stop respectively.
-- positive = downstream; negative = upstream.
start-offset INTEGER OPTIONAL,
start-offset-fuzz Int-fuzz OPTIONAL,
stop-offset INTEGER OPTIONAL,
stop-offset-fuzz Int-fuzz OPTIONAL,
-- 0-based position of bio-start relative to containing codon
frame INTEGER OPTIONAL,
-- for situations in which a raw location isn't sufficient
seq Seq-literal OPTIONAL,
-- reference to the assembly (GenColl ID) for this location
assembly Dbtag OPTIONAL,
hgvs-name VisibleString OPTIONAL,
-- the reference location for this variant
comment VisibleString OPTIONAL,
exceptions SET OF VariationException OPTIONAL,
dbxrefs SET OF Dbtag OPTIONAL, --e.g. rs#, that are placement-specific
ext SET OF User-object OPTIONAL, --for process-specific placement tags/labels
gene-location INTEGER OPTIONAL, --Same semantics as VariantProperties.gene-location, except placement-specific
id Object-id OPTIONAL,
parent-id Object-id OPTIONAL, --id of the placement from which this one was derived
so-terms SEQUENCE OF INTEGER OPTIONAL --Sequence Ontology terms for this placement
}