/usr/lib/R/site-library/Biostrings/unitTests/test_XStringSetList.R is in r-bioc-biostrings 2.42.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 | ## TODO : add tests for append, subset
## WARNING: Do *NOT* use checkIdentical() on XString, XStringSet, or
## XStringSetList objects. It is *NOT* reliable. Use checkTrue(all.equal())
## instead.
## TODO: Maybe "all.equal" should be made an S4 generic with S4/S3 method
## combos for XVector and XVectorList object?
## Unclass the XStringSet object by setting its "pool" and "ranges" slots
## to NULL first.
.unclass_XStringSet <- function(x)
{
slot(x, "pool", check=FALSE) <- NULL
slot(x, "ranges", check=FALSE) <- NULL
unclass(x)
}
all.equal.XStringSet <- function(target, current, ...)
{
## Compare the sequences (and their names if they have).
target_seqs <- as.character(target)
current_seqs <- as.character(current)
ok1 <- all.equal(target_seqs, current_seqs)
## Compare the rest.
# .unclass_XStringSet() works interactively but fails when run in the
# context of the unit tests.
#target <- .unclass_XStringSet(target)
#current <- .unclass_XStringSet(current)
#ok2 <- all.equal(target, current)
ok2 <- identical(class(target), class(current))
if (!ok2)
ok2 <- "class mismatch"
ok3 <- all.equal(target@metadata, current@metadata)
ok4 <- all.equal(target@elementMetadata, current@elementMetadata)
ans <- character(0)
if (!isTRUE(ok1))
ans <- c(ans, ok1)
if (!isTRUE(ok2))
ans <- c(ans, ok2)
if (!isTRUE(ok3))
ans <- c(ans, ok3)
if (!isTRUE(ok4))
ans <- c(ans, ok4)
if (length(ans) == 0L)
return(TRUE)
ans
}
all.equal.XStringSetList <- function(target, current, ...)
{
ok1 <- identical(class(target), class(current))
if (!ok1)
ok1 <- "class mismatch"
target2 <- as(target, "CharacterList")
current2 <- as(current, "CharacterList")
## Temporary workaround until coercion from XStringSet to CharacterList
## is fixed to propagate metadata and metadata columns.
metadata(target2) <- metadata(target)
mcols(target2) <- mcols(target)
metadata(current2) <- metadata(current)
mcols(current2) <- mcols(current)
ok2 <- all.equal(target2, current2)
ans <- character(0)
if (!isTRUE(ok1))
ans <- c(ans, ok1)
if (!isTRUE(ok2))
ans <- c(ans, ok2)
if (length(ans) == 0L)
return(TRUE)
ans
}
.XStringSetList_constructor <-
function(XStringSetFUN, XStringSetListFUN, XS_ALPHABET)
{
xs1 <- XStringSetFUN(XS_ALPHABET[1:8])
xs2 <- XStringSetFUN(XS_ALPHABET[9:17])
lst1 <- XStringSetListFUN(xs1, xs2)
lst2 <- XStringSetListFUN(as.character(XS_ALPHABET[1:8]),
as.character(XS_ALPHABET[9:17]))
checkTrue(all.equal.XStringSetList(lst1, lst2))
checkTrue(length(XStringSetListFUN()) == 0)
}
.XStringSetList_unlist <-
function(XStringSetFUN, XStringSetListFUN, XS_ALPHABET)
{
lst <- XStringSetListFUN(XS_ALPHABET, XS_ALPHABET)
expected <- XStringSetFUN(c(XS_ALPHABET, XS_ALPHABET))
checkTrue(all.equal.XStringSet(unlist(lst), expected))
}
.XStringSetList_append <-
function(XStringSetFUN, XStringSetListFUN, XS_ALPHABET)
{
xs <- XStringSetFUN(XS_ALPHABET)
lst <- XStringSetListFUN(XS_ALPHABET, XS_ALPHABET)
elementMetadata(lst) <- DataFrame(C1=c("list1", "list2"))
xs2a <- c(lst, lst)
xs2b <- rep(lst, 2L)
xs2c <- append(lst, lst)
checkTrue(all.equal.XStringSetList(xs2a, xs2b))
checkTrue(all.equal.XStringSetList(xs2a, xs2c))
}
## DNAStringSet
test_DNAStringSetList_constructor <- function()
.XStringSetList_constructor(DNAStringSet, DNAStringSetList, DNA_ALPHABET)
test_DNAStringSetList_unlist <- function()
.XStringSetList_unlist(DNAStringSet, DNAStringSetList, DNA_ALPHABET)
test_DNAStringSetList_append <- function()
.XStringSetList_append(DNAStringSet, DNAStringSetList, DNA_ALPHABET)
## AAStringSet
test_AAStringSetList_constructor <- function()
.XStringSetList_constructor(AAStringSet, AAStringSetList, AA_ALPHABET)
test_AAStringSetList_unlist <- function()
.XStringSetList_unlist(AAStringSet, AAStringSetList, AA_ALPHABET)
test_AAStringSetList_append <- function()
.XStringSetList_append(AAStringSet, AAStringSetList, AA_ALPHABET)
test_DNAStringSetList_showAsCell <- function()
{
dna <- showAsCell(DNAStringSetList())
checkTrue(is(dna, "character"))
dna <- showAsCell(DNAStringSetList(DNA_ALPHABET))
checkTrue(is(dna, "character"))
}
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