context("Testing seqaln")


test_that("seqaln works", {
  skip_on_cran()
  skip_on_travis()
  skip_if_not(check.utility("muscle"), 
              message = "Need MUSCLE installed to run the test")
  
  ## seqaln with one sequence. should remove gaps
  seqs <- c("X", "-", "-", "A", "C", "A", "G", "K", "-")
  suppressWarnings( aln <- seqaln(seqs) )
  expected <- c("X", "A", "C", "A", "G", "K")
  expect_identical(c(aln$ali), expected)
  

  ## align two sequences
  seqs <- seqbind(seqs,
                c("C", "A", "G", "G", "A", "G", "K"))
  aln <- seqaln(seqs)
  expected <- seqbind(c("-", "X", "A", "C", "A", "G", "K"),
                      c("C", "A", "G", "G", "A", "G", "K"))
  expect_identical(aln$ali, expected$ali)

    
  ## add a sequence to the (profile) alignment
  seq <- c("G", "A", "G", "K", "-")
  aln <- seqaln(seq, profile=aln)
  rownames(aln$ali) <- paste0("seq", 1:3)
  expected <- seqbind(c("-", "X", "A", "C", "A", "G", "K", "-"),
                      c("C", "A", "G", "G", "A", "G", "K", "-"),
                      c("-", "-", "-", "G", "A", "G", "K", "-"))
  expect_identical(aln$ali, expected$ali)

  ## test 'msa' option
  if( requireNamespace("msa", quietly=TRUE) ) { 
     capture.output( seqs <- get.seq(c("4q21_A", "1ftn_A"), outfile=tempfile()) )
     aln <- seqaln(seqs, outfile=tempfile())
     aln2 <- seqaln(seqs, outfile=tempfile(), exefile="msa")
     aln$call <- NULL; aln2$call <- NULL
     expect_identical(aln, aln2)
  }
})