tests/testthat/test-XStringViews.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

## XStringViews-class.R exports the following:
## - `==` for XStringViews against XStringViews, XString, character
## - `!=` for the same as above
## - as.character
## - as.matrix
## - toString


slen <- 25L
dnas <- sample(DNA_BASES, slen, replace=TRUE)
d <- DNAString(paste(dnas, collapse=""))

test_that("XStringViews equality works correctly", {
    n_ranges <- 5L
    starts <- sample(slen-5L, n_ranges)
    ends <- starts + sample(5L, n_ranges)
    strs <- vapply(seq_len(n_ranges),
        function(i) paste(dnas[seq(starts[i], ends[i])], collapse=""),
        character(1L)
    )
    v <- Views(d, start=starts, end=ends)
    expect_equal(seqtype(v), seqtype(d))

    ## only the diagonal should be true
    exp_opt <- matrix(FALSE, nrow=n_ranges, ncol=n_ranges)
    diag(exp_opt) <- TRUE
    test1 <- matrix(unlist(v == DNAStringSet(strs)), nrow=n_ranges, byrow=TRUE)
    expect_identical(test1, exp_opt)

    ## only the diagonal should be false
    exp_opt <- !exp_opt
    test2 <- matrix(unlist(v != DNAStringSet(strs)), nrow=n_ranges, byrow=TRUE)
    expect_identical(test2, exp_opt)

    ## comparison against Views objects should be supported
    expect_identical(v==v, rep(TRUE, n_ranges))

    ## comparison with non-BString is not supported
    expect_error(v == strs, "is not supported")
    expect_error(strs == v, "is not supported")

    ## comparing BString against character
    v2 <- v
    expect_identical((seqtype(v2) <- "B"), "B")
    expect_identical(v2 == strs, rep(TRUE, n_ranges))
    expect_identical(strs == v2, rep(TRUE, n_ranges))
    expect_identical(v2 != strs, rep(FALSE, n_ranges))
    expect_identical(strs != v2, rep(FALSE, n_ranges))

    expect_identical(toString(v2), paste(strs, collapse=", "))
    expect_identical(nchar(v2), nchar(strs))
})