GetSequenceFromFunc extracts a sequence identifier from a FuncExpr if the function takes a sequence identifier as an arg (a sequence identifier can either be a sequence name or an ID), wrapped in the SeqIdentifier type.

GetUsedSequences returns the identifier of the sequence passed to a call to sequence function in the given expression or nil if no sequence identifiers are found.

ReplaceSequenceNamesWithIDs walks the given expression, and replaces any sequence names in the expression by their IDs instead.

UpgradeSequenceReferenceInExpr upgrades all by-name sequence reference in `expr` to by-ID with a provided id-to-name mapping `usedSequenceIDsToNames`, from which we should be able to uniquely determine the ID of each by-name seq reference.

SeqIdentifier wraps together different ways of identifying a sequence.