context("exportMsd")
m <- createMassSpectrum(mass=1:5, intensity=6:10,
metaData=list(owner="OWNER", institution="INSTITUTION",
instrument="INSTRUMENT"))
p <- createMassPeaks(mass=4:5, intensity=9:10, snr=1:2)
tmp <- tempdir()
msd <- c(
"<?xml version=\"1.0\" encoding=\"utf-8\"?>",
"<mSD version=\"2.2\">",
" <description>",
" <title>tmp.msd</title>",
" <date value=\"1970-01-01 00:00:00 UTC\"/>",
" <operator value=\"OWNER\"/>",
" <contact value=\"OWNER\"/>",
" <institution value=\"INSTITUTION\"/>",
" <instrument value=\"INSTRUMENT\"/>",
" <notes></notes>",
" </description>",
" <spectrum points=\"5\" msLevel=\"1\" polarity=\"\">",
" <mzArray precision=\"64\" compression=\"zlib\" endian=\"little\">eJxjYACBD/YMEOAAoTigtACUFnEAADZ/Alw=</mzArray>",
" <intArray precision=\"64\" compression=\"zlib\" endian=\"little\">eJxjYAABCQcwxSADpRWgtBKUVnEAAB9MAds=</intArray>",
" </spectrum>",
" <peaklist>",
" <peak mz=\"4\" intensity=\"9\" baseline=\"0\" sn=\"1\"/>",
" <peak mz=\"5\" intensity=\"10\" baseline=\"0\" sn=\"2\"/>",
" </peaklist>",
"</mSD>")
if (.Platform$endian == "big") {
msd[13:14] <- c(
" <mzArray precision=\"64\" compression=\"zlib\" endian=\"big\">eJyz/8AABg4MUJoDSgtAaREIDQBExAJc</mzArray>",
" <intArray precision=\"64\" compression=\"zlib\" endian=\"big\">eJxzkGAAAwcZKK0ApZWgtAqEBgArDgHb</intArray>")
}
test_that(".exportMsd", {
MALDIquantForeign:::.exportMsd(m, file=file.path(tmp, "m.msd"), peaks=p)
expect_equal(readLines(file.path(tmp, "m.msd"))[-c(4:5)], msd[-c(4:5)])
})
test_that("exportMsd,MassSpectrum", {
MALDIquantForeign::exportMsd(m, file=file.path(tmp, "msp.msd"), peaks=p)
expect_equal(readLines(file.path(tmp, "msp.msd"))[-c(4:5)], msd[-c(4:5)])
MALDIquantForeign::exportMsd(m, file=file.path(tmp, "ms.msd"))
expect_equal(readLines(file.path(tmp, "ms.msd"))[-c(4:5)], msd[-c(4:5, 16:19)])
})
test_that("exportMsd,list", {
spectra <- list(m, m)
peaks <- list(p, p)
MALDIquantForeign::exportMsd(spectra, path=tmp, force=TRUE, peaks=peaks)
expect_equal(readLines(file.path(tmp, "1.msd"))[-c(4:5)], msd[-c(4:5)])
expect_equal(readLines(file.path(tmp, "2.msd"))[-c(4:5)], msd[-c(4:5)])
MALDIquantForeign::exportMsd(spectra, path=tmp, force=TRUE)
expect_equal(readLines(file.path(tmp, "1.msd"))[-c(4:5)], msd[-c(4:5, 16:19)])
expect_equal(readLines(file.path(tmp, "2.msd"))[-c(4:5)], msd[-c(4:5, 16:19)])
})
test_that(".createMsdTitle", {
f <- file(file.path(tempdir(), "test.msd"))
expect_true(MALDIquantForeign:::.createMsdTitle(f) == "test")
close(f)
})
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