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@DominikRafacz
DominikRafacz committed Sep 26, 2024
2 parents 50b0ae5 + 740acbf commit b0421ca
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198 changes: 99 additions & 99 deletions tests/testthat/test-substitute_letters.R
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# SETUP ----
sq_dna <- sq(c("ACTGTC", "CGCGTTA"), alphabet = "dna_bsc")
sq_ami <- sq(c("APOPNIQEV", "CSVMIBF"), alphabet = "ami_ext")
# sq_unt <- sq(c("GO%NC@E(123)RO", "NFI%(#)VT;"), alphabet = "unt")

str_dna <- c("ACBGBC", "CGCGBBA")
str_dna_num <- c("AC6G6C", "CGCG66A")
str_ami <- c("AQWQXEQEV", "CSVZECF")
str_ami_num <- c("A11O11NIQ3322", "CS22MI7F")

# CORRECT PROTOTYPE OF RETURNED VALUE ----
test_that("substitute_letters() returns an sq_atp object", {
expect_s3_class(substitute_letters(sq_dna, c(T = "B")),
class = "sq_atp",
exact = FALSE)
expect_s3_class(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C")),
class = "sq_atp",
exact = FALSE)
})

test_that("substitute_letters() returns an object with trimmed alphabet attribute", {
expect_setequal(
alphabet(substitute_letters(sq_dna, c(T = "B"))),
c("A", "C", "G", "B", "-")
)
expect_setequal(
alphabet(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C"))),
setdiff(alphabet(sq_ami), c("P", "O", "I", "U", "Y", "G", "L", "K", "J", "H", "M", "N", "B"))
)
})

test_that("substitute_letters() does not remove nor add sequences", {
expect_length(substitute_letters(sq_dna, c(T = "B")),
length(sq_dna))
expect_length(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C")),
length(sq_ami))
})

test_that("substitute_letters() keep original_lengths unchanged", {
expect_equal(
get_sq_lengths(substitute_letters(sq_dna, c(T = "B"))),
get_sq_lengths(sq_dna)
)
expect_equal(
get_sq_lengths(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C"))),
get_sq_lengths(sq_ami)
)
})

# ARGUMENT PREREQUISITES ----
test_sq_only(substitute_letters, encoding = c(S = "H"))

test_that("encoding must be either numeric or character", {
expect_error(substitute_letters(sq_dna, c(A = TRUE, T = FALSE)),
"encoding must be either numeric of character vector")
expect_error(substitute_letters(sq_dna, list(G = mean, C = sum)))
})

# CORRECT RETURN VALUE ----
test_that("substitute_letters() correctly computes value", {
expect_equal(
as.character(substitute_letters(sq_dna, c(T = "B"))),
str_dna
)
expect_equal(
as.character(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C"))),
str_ami
)
})

# COERCING NUMERIC VECTORS TO CHARACTERS ----
test_that("substitute_letters() coerces numeric encodings to string vectors", {
expect_equal(
as.character(substitute_letters(sq_dna, c(T = 6))),
str_dna_num
)
expect_equal(
as.character(substitute_letters(sq_ami, c(P = 11, V = 22, E = 33, X = 6, B = 7))),
str_ami_num
)
})

# SURJECTIVITY OF SUBSTITUTION ----
test_that("substitute_letters() is a surjection regarding the alphabets", {
expect_lte(
vec_size(alphabet(substitute_letters(sq_dna, c(T = "B")))),
vec_size(alphabet(sq_dna))
)
expect_lte(
vec_size(alphabet(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C")))),
vec_size(alphabet(sq_ami))
)
})
# SETUP ----
sq_dna <- sq(c("ACTGTC", "CGCGTTA"), alphabet = "dna_bsc")
sq_ami <- sq(c("APOPNIQEV", "CSVMIBF"), alphabet = "ami_ext")
# sq_unt <- sq(c("GO%NC@E(123)RO", "NFI%(#)VT;"), alphabet = "unt")

str_dna <- c("ACBGBC", "CGCGBBA")
str_dna_num <- c("AC6G6C", "CGCG66A")
str_ami <- c("AQWQXEQEV", "CSVZECF")
str_ami_num <- c("A11O11NIQ3322", "CS22MI7F")

# CORRECT PROTOTYPE OF RETURNED VALUE ----
test_that("substitute_letters() returns an sq_atp object", {
expect_s3_class(substitute_letters(sq_dna, c(T = "B")),
class = "sq_atp",
exact = FALSE)
expect_s3_class(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C")),
class = "sq_atp",
exact = FALSE)
})

test_that("substitute_letters() returns an object with trimmed alphabet attribute", {
expect_setequal(
alphabet(substitute_letters(sq_dna, c(T = "B"))),
c("A", "C", "G", "B", "-")
)
expect_setequal(
alphabet(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C"))),
setdiff(as.character(alphabet(sq_ami)), c("P", "O", "I", "U", "Y", "G", "L", "K", "J", "H", "M", "N", "B"))
)
})

test_that("substitute_letters() does not remove nor add sequences", {
expect_length(substitute_letters(sq_dna, c(T = "B")),
length(sq_dna))
expect_length(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C")),
length(sq_ami))
})

test_that("substitute_letters() keep original_lengths unchanged", {
expect_equal(
get_sq_lengths(substitute_letters(sq_dna, c(T = "B"))),
get_sq_lengths(sq_dna)
)
expect_equal(
get_sq_lengths(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C"))),
get_sq_lengths(sq_ami)
)
})

# ARGUMENT PREREQUISITES ----
test_sq_only(substitute_letters, encoding = c(S = "H"))

test_that("encoding must be either numeric or character", {
expect_error(substitute_letters(sq_dna, c(A = TRUE, T = FALSE)),
"encoding must be either numeric of character vector")
expect_error(substitute_letters(sq_dna, list(G = mean, C = sum)))
})

# CORRECT RETURN VALUE ----
test_that("substitute_letters() correctly computes value", {
expect_equal(
as.character(substitute_letters(sq_dna, c(T = "B"))),
str_dna
)
expect_equal(
as.character(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C"))),
str_ami
)
})

# COERCING NUMERIC VECTORS TO CHARACTERS ----
test_that("substitute_letters() coerces numeric encodings to string vectors", {
expect_equal(
as.character(substitute_letters(sq_dna, c(T = 6))),
str_dna_num
)
expect_equal(
as.character(substitute_letters(sq_ami, c(P = 11, V = 22, E = 33, X = 6, B = 7))),
str_ami_num
)
})

# SURJECTIVITY OF SUBSTITUTION ----
test_that("substitute_letters() is a surjection regarding the alphabets", {
expect_lte(
vec_size(alphabet(substitute_letters(sq_dna, c(T = "B")))),
vec_size(alphabet(sq_dna))
)
expect_lte(
vec_size(alphabet(substitute_letters(sq_ami, c(P = "Q", O = "W", I = "E", U = "R", Y = "T", G = "V",
L = "A", K = "S", J = "D", H = "F", M = "Z", N = "X", B = "C")))),
vec_size(alphabet(sq_ami))
)
})

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