tests/testthat/test_importMzXml-functions.R

In MALDIquantForeign: Import/Export Routines for 'MALDIquant'

context("importMzXml")

test_that("importMzXml", {
  expect_error(MALDIquantForeign:::.importMzXml("tmp.tmp"))

  path <- system.file(file.path("exampledata", "tiny1.mzXML3.0.mzXML"),
                      package="MALDIquantForeign")

  s <- MALDIquantForeign:::.importMzXml(path, verbose=FALSE)

  expect_equal(s, import(path, verbose=FALSE))
  expect_equal(s, importMzXml(path, verbose=FALSE))
  expect_equal(s, import(path, type="mzXML", verbose=FALSE))

  expect_true(isMassSpectrum(s[[1]]))
  expect_equal(mass(s[[1]]), 1:5)
  expect_equal(intensity(s[[1]]), 6:10)
  expect_equal(basename(metaData(s[[1]])$file), "tiny1.mzXML3.0.mzXML")
})

test_that("importMzXml compressed", {
  expect_error(MALDIquantForeign:::.importMzXml("tmp.tmp"))

  path <- system.file(file.path("exampledata", "tiny1-compressed.mzXML3.0.mzXML"),
                      package="MALDIquantForeign")

  s <- MALDIquantForeign:::.importMzXml(path, verbose=FALSE)

  expect_equal(s, import(path, verbose=FALSE))
  expect_equal(s, importMzXml(path, verbose=FALSE))
  expect_equal(s, import(path, type="mzXML", verbose=FALSE))

  expect_true(isMassSpectrum(s[[1]]))
  expect_equal(mass(s[[1]]), 1:5)
  expect_equal(intensity(s[[1]]), 6:10)
  expect_equal(basename(metaData(s[[1]])$file),
               "tiny1-compressed.mzXML3.0.mzXML")
})

test_that("importMzXml centroided", {
  expect_error(MALDIquantForeign:::.importMzXml("tmp.tmp"))

  path <- system.file(file.path("exampledata", "tiny1-centroided.mzXML3.0.mzXML"),
                      package="MALDIquantForeign")

  p <- MALDIquantForeign:::.importMzXml(path, centroided=TRUE, verbose=FALSE)

  expect_equal(p, import(path, centroided=TRUE, verbose=FALSE))
  expect_equal(p, importMzXml(path, centroided=TRUE, verbose=FALSE))
  expect_equal(p, import(path, type="mzXML", centroided=TRUE, verbose=FALSE))

  expect_true(isMassPeaks(p[[1]]))
  expect_equal(mass(p[[1]]), 1:5)
  expect_equal(intensity(p[[1]]), 6:10)
  expect_equal(basename(metaData(p[[1]])$file),
               "tiny1-centroided.mzXML3.0.mzXML")
})