context("preprocess")

test_that("Check preprocessing", {

  #testthat::skip_if_not_installed("tensorflow")

  testthat::skip_if_not(reticulate::py_module_available("tensorflow"))

  z <- seq_encoding_lm(sequence = c(1,0,5,1,3,4,3,1,4,1,2),

                       maxlen = 5,

                       vocabulary = c("a", "c", "g", "t"),

                       start_ind = c(1,3),

                       ambiguous_nuc = "equal",

                       target_len = 1,

                       output_format = "target_right")

  x <- z[[1]]

  y <- z[[2]]

  expect_equivalent(x[1,1,], c(1,0,0,0))

  expect_equivalent(x[1,2,], c(0,0,0,0))

  expect_equivalent(x[1,3,], rep(0.25, 4))

  expect_equivalent(x[1,4,], c(1,0,0,0))

  expect_equivalent(x[1,5,], c(0,0,1,0))

  expect_equivalent(y[1,], c(0,0,0,1))

  expect_equivalent(x[2,1,], rep(0.25, 4))

  expect_equivalent(x[2,2,], c(1,0,0,0))

  expect_equivalent(x[2,3,], c(0,0,1,0))

  expect_equivalent(x[2,4,], c(0,0,0,1))

  expect_equivalent(x[2,5,], c(0,0,1,0))

  expect_equivalent(y[2,], c(1,0,0,0))

  # use character string as input

  z <- seq_encoding_lm(sequence = NULL,

                       maxlen = 5,

                       vocabulary = c("a", "c", "g", "t"),

                       start_ind = c(1,3),

                       ambiguous_nuc = "zero",

                       target_len = 1,

                       output_format = "target_right",

                       char_sequence = "ACTaaTNTNaZ")

  x <- z[[1]]

  y <- z[[2]]

  expect_equivalent(apply(x[1,,], 1, which.max), c(1,2,4,1,1))

  expect_equivalent(apply(x[2,,], 1, which.max), c(4,1,1,4,1))

  expect_equivalent(y[1,], c(0,0,0,1))

  expect_equivalent(y[2,], c(0,0,0,1))

  x <- seq_encoding_label(sequence = c(1,0,5,1,3,4,3,1,4,1,2),

                          maxlen = 5,

                          vocabulary = c("a", "c", "g", "t"),

                          start_ind = c(1,3),

                          ambiguous_nuc = "equal")

  expect_equivalent(x[1,1,], c(1,0,0,0))

  expect_equivalent(x[1,2,], c(0,0,0,0))

  expect_equivalent(x[1,3,], rep(0.25, 4))

  expect_equivalent(x[1,4,], c(1,0,0,0))

  expect_equivalent(x[1,5,], c(0,0,1,0))

  expect_equivalent(x[2,1,], rep(0.25, 4))

  expect_equivalent(x[2,2,], c(1,0,0,0))

  expect_equivalent(x[2,3,], c(0,0,1,0))

  expect_equivalent(x[2,4,], c(0,0,0,1))

  expect_equivalent(x[2,5,], c(0,0,1,0))

  # use character string as input

  x <- seq_encoding_label(maxlen = 5,

                          vocabulary = c("a", "c", "g", "t"),

                          start_ind = c(1,3),

                          ambiguous_nuc = "equal",

                          char_sequence = "ACTaaTNTNaZ")

  expect_equivalent(apply(x[1,,], 1, which.max), c(1,2,4,1,1))

  expect_equivalent(apply(x[2,,], 1, which.max), c(4,1,1,4,1))

  expect_equivalent(x[2,5,], rep(0.25, 4))

})