tests/testthat/test-letter.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

## letter.R exports `letter` for the following classes:
## - character
## - XString
## - XStringViews
## - MaskedXString


test_that("letter generic works properly for all classes", {
    s <- paste(letters, collapse="")
    sdna <- sample(DNA_BASES, 20L, replace=TRUE)

    dna <- DNAString(paste(sdna, collapse=""))
    viewdna <- Views(dna, start=rep(1L,3L), width=10)

    m <- Mask(mask.width=20L, start=1, end=5L)
    maskdna <- dna
    masks(maskdna) <- m

    ## happy path testing
    test_cases <- list(1.0, 1:3, 1:3*2L, integer(0L))
    for (i in seq_along(test_cases)) {
        ## character
        expect_equal(letter(s, test_cases[[i]]),
                     paste(letters[test_cases[[i]]], collapse=""))

        ## XString
        expect_equal(letter(dna, test_cases[[i]]),
                     paste(sdna[test_cases[[i]]], collapse=""))

        ## XStringViews
        expect_equal(letter(viewdna, test_cases[[i]]),
                     rep(paste(sdna[test_cases[[i]]], collapse=""), 3L))

        ## MaskedXString -- note that this ignores the mask
        expect_equal(letter(maskdna, test_cases[[i]]),
                     paste(sdna[test_cases[[i]]], collapse=""))
    }

    ## sad path testing
    sad_list <- list("a", NA_real_, 10000)
    error_msgs <- c("must be an NA-free numeric vector",
                    "must be an NA-free numeric vector",
                    "out of bounds")
    for (i in seq_along(sad_list)) {
        expect_error(letter(s, sad_list[[i]]), error_msgs[i])
        expect_error(letter(dna, sad_list[[i]]), error_msgs[i])
        expect_error(letter(viewdna, sad_list[[i]]), error_msgs[i])
        expect_error(letter(maskdna, sad_list[[i]]), error_msgs[i])
    }
})