Scope and Usage
ComplexCanonicalAllele is an abstract class; any instance of ComplexCanonicalAllele must be either a ComplexNucleotideCanonicalAllele or a ComplexAminoAcidCanonicalAllele.
A ComplexCanonicalAllele is an aggregation of two or more SimpleCanonicalAlleles, and provides a way to attach assertions or observations to the that collection. The assertion that a particular person has a ComplexCanonicalAllele is equivalent to the assertion that they contain all of the SimpleCanonicalAlleles in cis (i.e. on the same copy of the chromosome).
ComplexCanonicalAllele is a suitable class for describing pharmacogenomic star alleles or other haplotypes.
Because the ComplexCanonicalAllele is defined as an aggregation of SimpleCanonicalAlleles, canonicalization of the complex alleles is straightforward: every unique combination of SimpleCanonicalAlleles is already canonicalized.
Exclusions and Limitations
ComplexCanonicalAllele is exclusivly used for alleles in cis. It can not be used to represent, e.g. compound heterozygotes.
Concrete aggregation must occur at either the nucleotide or protein level; there is no way to build a complex allele that involves one SimpleNucleotideCanonicalAllele and one SimpleAminoAcidCanonicalAllele.
There is exactly one level of aggregation: SimpleCanonicalAlleles are aggregated to ComplexCanonicalAlleles, but ComplexCanonicalAlleles cannot be further aggregated to new ComplexCanonicalAlleles. In this case, a new ComplexCanonicalAllele must be created based on the union of all of the involved SimpleCanonicalAlleles.
See Also
Related Resources: CanonicalAllele