tests/testthat/testDNA.R

In Ward9250/HybridCheck: Detection and dating of Recombinant Regions in DNA sequence data

context("DNA related tests")

test_that("dna reference objects correctly throws error when object has no sequences.", {
  blank <- HybridCheck:::HCseq$new()
  expect_is(blank, "HCseq")
  expect_false(blank$hasDNA())
  expect_error(blank$enforceDNA())
  expect_error(blank$numberOfSequences())
  expect_error(blank$getFullBp())
  expect_error(blank$getInformativeBp())
  expect_error(blank$numberOfSequences())
  expect_error(blank$getFullLength())
  expect_error(blank$getInformativeLength())
  expect_error(blank$getSequenceNames())
  expect_error(blank$textSummary())
  expect_error(blank$htmlSummary())
  expect_error(blank$show())
  expect_error(blank$pullTriplet(c("Seq1", "Seq2", "Seq3")))
})

test_that("dna reference objects correctly load and return information about sequences loaded in.", {
  data(MySequences)
  tenSeqs <- HybridCheck:::HCseq$new(MySequences)
  expect_is(tenSeqs, "HCseq")
  expect_true(tenSeqs$hasDNA())
  expect_is(tenSeqs$numberOfSequences(), "integer")
  expect_equal(tenSeqs$numberOfSequences(), 10)
  expect_is(tenSeqs$getFullLength(), "integer")
  expect_equal(tenSeqs$getFullLength(), 400000)
  expect_is(tenSeqs$getFullBp(), "integer")
  expect_equal(tenSeqs$getFullBp(), 1:400000)
  expect_is(tenSeqs$getInformativeBp(), "integer")
  expect_less_than(tenSeqs$getInformativeLength(), tenSeqs$getFullLength())
  seqnames <- tenSeqs$getSequenceNames()
  expect_is(seqnames, "character")
  expect_equal(length(seqnames), tenSeqs$numberOfSequences())
  expect_is(tenSeqs$textSummary(), "character")
  expect_is(tenSeqs$htmlSummary(), "character")
  triplet <- tenSeqs$pullTriplet(c("Seq1", "Seq2", "Seq3"))
  expect_is(triplet, "DNAStringSet")
  expect_equal(length(triplet), 3)
  expect_equal(names(triplet), c("Seq1", "Seq2", "Seq3"))
})