tests/testthat/test-XStringSetList.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

## XStringSetList-class.R exports the following:
## - DNAStringSetList
## - AAStringSetList
## note that RNAStringSetList and BStringSetList are not supported


test_that("XStringSetList constuctors work properly", {
    seq_lengths <- 2:4
    seqs <- list(DNA=paste(DNA_ALPHABET, collapse=""),
                 RNA=paste(RNA_ALPHABET, collapse=""),
                 AA=paste(AA_ALPHABET, collapse=""),
                 B=rawToChar(as.raw(32:126)))

    for (s in c("DNA", "RNA", "AA", "B")) {
        seq <- seqs[[s]]
        all_seqs <- lapply(seq_along(seq_lengths),
            function(i) get(paste0(s, "StringSet"))(rep(seq, seq_lengths[i])))
        cl_name <- paste0(s, "StringSetList")
        CONSTRUCTOR <- get(cl_name)
        expect_s4_class(CONSTRUCTOR(all_seqs), cl_name)

        seqlist <- CONSTRUCTOR(all_seqs)
        expect_equal(length(seqlist), length(seq_lengths))
        expect_equal(lengths(seqlist), seq_lengths)
        expect_equal(as.list(seqlist), all_seqs)
        expect_equal(seqtype(seqlist), s)

        # empty constructor
        expect_equal(length(CONSTRUCTOR()), 0L)

        names(all_seqs) <- LETTERS[seq_along(seq_lengths)]
        expect_equal(names(CONSTRUCTOR(all_seqs)), names(all_seqs))
        expect_null(names(CONSTRUCTOR(all_seqs, use.names=FALSE)))
    }
})