Note: All ids are coding started from 0. Nucleotides, A, G, C, T, and - have codes 0, 1, 2, 3, and 4.
SNPs, 1, 2, and - have code codes 0, 1, and 2.
These are objects are in data frames unlike other internal objects due
to heavily used in processing data. The original data should be transfered
to numerical codes in order to be passed to C codes. In C codes, we use
integers, 0, 1, 2, ..., for coding nucleotides or SNPs and so on.
Now, models and methods are implemented only for .nucleotide and
.snp. Other objects are leaved for further extension.
Data frames use factor formats as the default, and as.character is
the way to transfer to the characters.