/usr/lib/R/site-library/Biostrings/UnitTests/runit-XStringSet.R is in r-bioc-biostrings 2.32.1-1.
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 | ### -------------------------------------------------------------------------
### Helper functions
###
### In R 2.14 (and maybe before that), 2 external pointers are always
### considered identical so the identical() function cannot be used to
### compare the "pool" slots of 2 XVectorList objects. The workaround we
### use below is to extract the adresses in each pool as a character vector,
### and then to compare the 2 character vectors.
### '.eltAddresses(x)' collects the addresses of the elements in 'x' (in
### practice 'x' will be a list of external pointers or environments).
.eltAddresses <- function(x) sapply(x, XVector:::address)
### 'x' and 'y' must be XVectorList vectors.
.haveIdenticalPools <- function(x, y)
identical(.eltAddresses(x@pool@xp_list), .eltAddresses(y@pool@xp_list))
### 'x' must be an XVectorList vector.
.poolEltLengths <- function(x)
{
pool_len <- length(x@pool)
if (pool_len == 0L)
return(integer(0))
sapply(seq_len(pool_len), function(i) length(x@pool[[i]]))
}
### -------------------------------------------------------------------------
test_DNAStringSet_constructor <- function()
{
dna <- DNAStringSet(DNA_ALPHABET)
## Checking internal representation.
checkIdentical(.poolEltLengths(dna), length(DNA_ALPHABET))
}
test_DNAStringSet_width <- function()
{
dna <- DNAStringSet(DNA_ALPHABET)
checkIdentical(width(dna), width(DNA_ALPHABET))
}
test_DNAStringSet_subsetting <- function()
{
dna <- DNAStringSet(DNA_ALPHABET)
elementMetadata(dna) <- DataFrame(C1=dna)
dna0 <- dna[FALSE]
checkIdentical(length(dna0), 0L)
## Checking internal representation.
checkIdentical(.poolEltLengths(dna0), integer(0))
checkIdentical(.haveIdenticalPools(elementMetadata(dna0)$C1, dna0),
TRUE)
checkIdentical(elementMetadata(dna0)$C1@ranges, dna0@ranges)
idx <- rep.int((8:6)*2L, 100L)
dna300 <- dna[idx]
checkIdentical(length(dna300), length(idx))
## Checking internal representation.
checkIdentical(.haveIdenticalPools(dna300, dna), TRUE)
checkIdentical(.haveIdenticalPools(elementMetadata(dna300)$C1, dna300),
TRUE)
checkIdentical(elementMetadata(dna300)$C1@ranges, dna300@ranges)
}
test_DNAStringSet_combining <- function()
{
dna <- DNAStringSet(DNA_ALPHABET)
elementMetadata(dna) <- DataFrame(C1=dna)
dna2a <- c(dna, dna)
dna2b <- rep(dna, 2L)
checkIdentical(dna2a, dna2b)
## Checking internal representation.
checkIdentical(.haveIdenticalPools(dna2a, dna), TRUE)
checkIdentical(.haveIdenticalPools(dna2a, dna2b), TRUE)
checkIdentical(.haveIdenticalPools(elementMetadata(dna2a)$C1, dna2a),
TRUE)
checkIdentical(elementMetadata(dna2a)$C1@ranges, dna2a@ranges)
}
test_DNAStringSet_unlist <- function()
{
dna <- DNAStringSet(DNA_ALPHABET)
checkIdentical(as.character(unlist(dna)), paste(DNA_ALPHABET, collapse=""))
}
test_DNAStringSet_compaction <- function()
{
dna <- DNAStringSet(DNA_ALPHABET)
elementMetadata(dna) <- DataFrame(C1=dna)
idx <- rep.int((8:6)*2L, 100L)
dna300 <- dna[idx]
compact_dna300 <- compact(dna300)
checkIdentical(as.character(compact_dna300), as.character(dna300))
## Checking internal representation.
checkIdentical(.poolEltLengths(compact_dna300), 3L)
checkIdentical(.poolEltLengths(elementMetadata(compact_dna300)$C1),
.poolEltLengths(compact_dna300))
checkIdentical(elementMetadata(compact_dna300)$C1@ranges,
compact_dna300@ranges)
}
|