R Under development (unstable) (2024-02-29 r86017 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> get_alphabet <- seguid:::get_alphabet
> make_alphabet <- seguid:::make_alphabet
> 
> alphabet <- get_alphabet("{DNA}")
> stopifnot(length(alphabet) == 4L)
> 
> alphabet <- get_alphabet("{RNA}")
> stopifnot(length(alphabet) == 4L)
> 
> alphabet <- get_alphabet("{DNA-extended}")
> stopifnot(length(alphabet) == 15L)
> 
> alphabet <- get_alphabet("{RNA-extended}")
> stopifnot(length(alphabet) == 15L)
> 
> alphabet <- get_alphabet("{protein}")
> stopifnot(length(alphabet) == 22L)
> 
> alphabet <- get_alphabet("{protein-extended}")
> stopifnot(length(alphabet) == 26L)
> 
> ## Unknown alphabet
> res <- tryCatch({
+   alphabet <- get_alphabet("unknown")
+ }, error = identity)
> stopifnot(inherits(res, "error"))
> 
> 
> truth <- get_alphabet("{DNA}")
> alphabet <- make_alphabet("CG,AT")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> truth <- get_alphabet("{RNA}")
> alphabet <- make_alphabet("CG,AU")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> truth <- get_alphabet("{protein}")
> alphabet <- make_alphabet("A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,O,U")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> truth <- get_alphabet("{DNA-extended}")
> alphabet <- make_alphabet("CG,AT,WW,SS,MK,RY,BV,DH,VB,NN")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> truth <- get_alphabet("{RNA-extended}")
> alphabet <- make_alphabet("CG,AU,WW,SS,MK,RY,BV,DH,VB,NN")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> truth <- get_alphabet("{protein-extended}")
> alphabet <- make_alphabet("A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,O,U,B,J,Z,X")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> ## Invalid components; should be either one or two characters
> res <- tryCatch({
+   alphabet <- make_alphabet("ATT")
+ }, error = identity)
> stopifnot(inherits(res, "error"))
> 
> ## Incompatible components
> res <- tryCatch({
+   alphabet <- make_alphabet("AT,T")
+ }, error = identity)
> stopifnot(inherits(res, "error"))
> 
> truth <- c(get_alphabet("{DNA}"), a = "u", u = "a")
> alphabet <- get_alphabet("{DNA},au,ua")
> stopifnot(identical(sort(alphabet), sort(truth)))
> 
> proc.time()
   user  system elapsed 
   0.15    0.12    0.26