inst/unitTests/test_findPalindromes.R

In Biostrings: Efficient manipulation of biological strings

###

test_findPalindromes_on_non_nucleotide_sequence <- function()
{
    text1 <- BString("ABCDCBA")
    current <- findPalindromes(text1, min.armlength=2)
    checkIdentical(IRanges(1, 7), ranges(current))
    current <- findPalindromes(text1, min.armlength=2, max.looplength=0)
    checkIdentical(IRanges(), ranges(current))

    text2 <- BString("xesopeReste etseReposeygohangasalamiImalasagnahogz")
    current <- findPalindromes(text2, max.looplength=2)
    checkIdentical(IRanges(c(2, 24), c(22, 49)), ranges(current))
    checkIdentical(c(10L, 12L), palindromeArmLength(current))

    text3 <- BString("AATAAACTNTCAAATYCCY")
    current <- findPalindromes(text3, min.armlength=2)
    checkIdentical(IRanges(c(1, 3, 16), c(5, 15, 19)), ranges(current))
}

test_findPalindromes_on_nucleotide_sequence <- function()
{
    x1 <- DNAString("AATAAACTNTCAAATYCCY")  # same sequence as 'text3'
    for (class in c("DNAString", "RNAString")) {
        x <- as(x1, class)
        current <- findPalindromes(x, min.armlength=2)
        checkIdentical(IRanges(), ranges(current))
        current <- findPalindromes(x, min.armlength=2, max.looplength=10)
        checkIdentical(IRanges(2, 15), ranges(current))
    }

    x2 <- DNAString("AATTT")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x2, class)
        current <- findPalindromes(x, min.armlength=2)
        target <- IRanges(1, 4:5)
        checkIdentical(target, ranges(current))
        current <- findPalindromes(x, min.armlength=2, max.looplength=0)
        checkIdentical(target[1], ranges(current))
    }

    x3 <- DNAString("TTTAA")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x3, class)
        current <- findPalindromes(x, min.armlength=2)
        target <- IRanges(1:2, 5)
        checkIdentical(target, ranges(current))
        current <- findPalindromes(x, min.armlength=2, max.looplength=0)
        checkIdentical(target[2], ranges(current))
    }

    x4 <- DNAString("AAATTT")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x4, class)
        current <- findPalindromes(x, min.armlength=2)
        target <- IRanges(c(1, 1, 2), c(5, 6, 6))
        checkIdentical(target, ranges(current))
        current <- findPalindromes(x, min.armlength=3)
        checkIdentical(target[2], ranges(current))
        current <- findPalindromes(x, min.armlength=4)
        checkIdentical(target[0], ranges(current))
    }

    ## With nested palindromes.

    x5 <- DNAString("CTTGAAATTTGAAG")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x5, class)
        target0 <- IRanges(c(2, 2, 5,  5,  1,  6,  8,  9),
                           c(6, 7, 9, 10, 14, 10, 13, 13))
        current <- findPalindromes(x, min.armlength=2, max.looplength=0)
        checkIdentical(target0[4], ranges(current))
        current <- findPalindromes(x, min.armlength=2, max.looplength=1)
        checkIdentical(target0[-c(2, 5, 7)], ranges(current))
        for (i in 2:7) {
            current <- findPalindromes(x, min.armlength=2, max.looplength=i)
            checkIdentical(target0[-5], ranges(current))
        }
        current <- findPalindromes(x, min.armlength=2, max.looplength=8)
        checkIdentical(target0, ranges(current))
    }

    x6 <- DNAString("AAGAATTGTT")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x6, class)
        target0 <- IRanges(c(1, 4, 1, 4), c(7, 7, 10, 10))
        for (i in 0:2) {
            current <- findPalindromes(x, min.armlength=2, max.looplength=i)
            checkIdentical(target0[2], ranges(current))
        }
        for (i in 3:5) {
            current <- findPalindromes(x, min.armlength=2, max.looplength=i)
            checkIdentical(target0[-3], ranges(current))
        }
        current <- findPalindromes(x, min.armlength=2, max.looplength=6)
        checkIdentical(target0, ranges(current))
    }

    # With IUPAC ambiguity codes. Ambiguity codes are not allowed in the arms
    # of a palindrome!

    x7 <- DNAString("NNNNNN")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x7, class)
        current <- findPalindromes(x, min.armlength=2)
        checkIdentical(IRanges(), ranges(current))
    }

    x8 <- DNAString("ACCGNAAATTTNCGGT")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x8, class)
        current <- findPalindromes(x, min.armlength=2)
        checkIdentical(IRanges(c(6, 6, 7), c(10, 11, 11)), ranges(current))
        current <- findPalindromes(x, min.armlength=4)
        checkIdentical(IRanges(), ranges(current))
        current <- findPalindromes(x, min.armlength=3, max.looplength=8)
        checkIdentical(IRanges(c(6, 1), c(11, 16)), ranges(current))
    }
}

test_palindromeArmLength <- function()
{
    x2 <- DNAString("AATTT")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x2, class)
        checkIdentical(2L, palindromeArmLength(x))
        pals <- findPalindromes(x, min.armlength=2)
        checkIdentical(c(2L, 2L), palindromeArmLength(pals))
    }

    x3 <- DNAString("TTTAA")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x3, class)
        checkIdentical(2L, palindromeArmLength(x))
        pals <- findPalindromes(x, min.armlength=2)
        checkIdentical(c(2L, 2L), palindromeArmLength(pals))
    }

    x4 <- DNAString("AAATTT")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x4, class)
        checkIdentical(3L, palindromeArmLength(x))
        pals <- findPalindromes(x, min.armlength=2)
        checkIdentical(c(2L, 3L, 2L), palindromeArmLength(pals))
    }

    x5 <- DNAString("CTTGAAATTTGAAG")
    for (class in c("DNAString", "RNAString")) {
        x <- as(x5, class)
        checkIdentical(3L, palindromeArmLength(x))
        pals <- findPalindromes(x, min.armlength=2, max.looplength=8)
        checkIdentical(c(2L, 2L, 2L, 3L, 3L, 2L, 2L, 2L),
                       palindromeArmLength(pals))
    }
}