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fix: XString comparison operators #130

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fix: XString comparison operators #130

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764f01b
Updates comparison (==, !=, <=) to make XString objects compare again…
ahl27 Aug 18, 2025
5a4fdd6
adds testing for XString comparison operators
ahl27 Aug 18, 2025
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34 changes: 34 additions & 0 deletions R/XString-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -434,6 +434,13 @@ setMethod("==", signature(e1="BString", e2="character"),
setMethod("==", signature(e1="character", e2="BString"),
function(e1, e2) e2 == e1
)
setMethod("==", signature(e1="XString", e2="character"),
## Coerce to BString to handle things like RNAString("U") == "T"
function(e1, e2) as(e1, "BString") == e2
)
setMethod("==", signature(e1="character", e2="XString"),
function(e1, e2) e1 == as(e2, "BString")
)

setMethod("!=", signature(e1="XString", e2="XString"),
function(e1, e2) !(e1 == e2)
Expand All @@ -444,7 +451,34 @@ setMethod("!=", signature(e1="BString", e2="character"),
setMethod("!=", signature(e1="character", e2="BString"),
function(e1, e2) !(e1 == e2)
)
setMethod("!=", signature(e1="XString", e2="character"),
function(e1, e2) as(e1, "BString") != e2
)
setMethod("!=", signature(e1="character", e2="XString"),
function(e1, e2) e1 != as(e2, "BString")
)

### Comparisons are already implemented for XStringSet objects,
### so we can just dispatch to that code here.
setMethod("<=", signature(e1="XString", e2="XString"),
function(e1, e2)
{
if (!comparable_seqtypes(seqtype(e1), seqtype(e2))) {
class1 <- class(e1)
class2 <- class(e2)
stop("comparison between a \"", class1, "\" instance ",
"and a \"", class2, "\" instance ",
"is not supported")
}
as(e1, "XStringSet") <= as(e2, "XStringSet")
}
)
setMethod("<=", signature(e1="XString", e2="character"),
function(e1, e2) as(e1, "BStringSet") <= e2
)
setMethod("<=", signature(e1="character", e2="XString"),
function(e1, e2) e1 <= as(e2, "BStringSet")
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The "substr" and "substring" methods.
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58 changes: 54 additions & 4 deletions tests/testthat/test-XString-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -137,14 +137,64 @@ test_that("equality methods work as advertised", {
expect_true(AAString(aastr) != BString(bstr))
expect_true(bstr == BString(bstr))

## comparisons against character
expect_true(DNAString("AAA") == "AAA")
expect_true(DNAString("AAA") != "BBB")
expect_false(RNAString("UUU") == "TTT")
expect_true(AAString("UUU") == "UUU")
## these may seem redundant but need to ensure that order doesn't matter
expect_true("AAA" == DNAString("AAA"))
expect_true("BBB" != DNAString("AAA"))
expect_false("TTT" == RNAString("UUU"))
expect_true("UUU" == AAString("UUU"))

## invalid comparisons
expect_error(DNAString() == AAString(),
"comparison between a \"DNAString\" instance and a \"AAString\" instance is not supported")
expect_error(DNAString() == BString(),
"comparison between a \"DNAString\" instance and a \"BString\" instance is not supported")
expect_error(RNAString() == AAString(),
"comparison between a \"RNAString\" instance and a \"AAString\" instance is not supported")
expect_error(RNAString() == BString(),
"comparison between a \"RNAString\" instance and a \"BString\" instance is not supported")
})

test_that("inequality methods work as advertised", {
## Basic cases
expect_true(DNAString("AAA") <= DNAString("AAAA"))
expect_false(DNAString("AAA") > DNAString("AAAA"))
expect_true(DNAString("AAA") <= DNAString("AAA"))
expect_true(DNAString("A") <= DNAString("C"))
expect_false(DNAString("ATTT") > RNAString("AUUU"))
expect_true(AAString("AAA") <= AAString("BBB"))
expect_true(BString("Testing") <= BString("ZZZTesting"))

## have to check every combination for XString - character comparisons
## due to how dispatch works
expect_true(BString("ABCDEFG") <= "ABCDEFG")
expect_true(BString("ABCDEFG") < "ZYXWVUT")
expect_true(BString("ABCDEFG") >= "ABCDEFG")
expect_false(BString("ABCDEFG") > "ABCDEFG")

expect_true("ABCDEFG" <= BString("ABCDEFG"))
expect_false("ZYXWVUT" < BString("ABCDEFG"))
expect_true("ABCDEFG" >= BString("ABCDEFG"))
expect_false("ABCDEFG" > BString("ABCDEFG"))

## Cases with potentially invalid characters
expect_true(DNAString("AAA") < "BBB")
expect_true(DNAString("CCC") > "BBB")
expect_true(RNAString("UUU") >= "TTT")
expect_true(RNAString("UUU") >= "UUU")

## invalid comparisons
expect_error(DNAString(dnastr) == AAString(aastr),
expect_error(DNAString() <= AAString(),
"comparison between a \"DNAString\" instance and a \"AAString\" instance is not supported")
expect_error(DNAString(dnastr) == BString(bstr),
expect_error(DNAString() <= BString(),
"comparison between a \"DNAString\" instance and a \"BString\" instance is not supported")
expect_error(RNAString(rnastr) == AAString(aastr),
expect_error(RNAString() <= AAString(),
"comparison between a \"RNAString\" instance and a \"AAString\" instance is not supported")
expect_error(RNAString(rnastr) == BString(bstr),
expect_error(RNAString() <= BString(),
"comparison between a \"RNAString\" instance and a \"BString\" instance is not supported")
})

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