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Update ispalindromic #304

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merged 2 commits into from
Mar 22, 2024
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Update ispalindromic #304

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8993aba
Update `ispalindromic`
jakobnissen Mar 22, 2024
8ebf461
Fixup: Performance
jakobnissen Mar 22, 2024
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30 changes: 23 additions & 7 deletions src/biosequence/predicates.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -59,20 +59,36 @@ end


"""
ispalindromic(seq::BioSequence)
ispalindromic(seq::NucSeq) -> Bool

Check if `seq` is palindromic. A palindromic sequence is identical to its
reverse-complement, so this should be equivalent to checking if
`seq == reverse_complement(seq)`.

# Examples
```jldoctest
julia> ispalindromic(dna"TGCA")
true

julia> ispalindromic(dna"TCCT")
false

julia> ispalindromic(rna"ACGGU")
false
```

Return `true` if `seq` is a palindromic sequence; otherwise return `false`.
"""
function ispalindromic(seq::BioSequence{<:NucleicAcidAlphabet})
for i in 1:cld(length(seq), 2)
if seq[i] != complement(seq[end - i + 1])
return false
end
end
_ispalindromic(seq)
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Did you mean to insert 4-spaces instead of a TAB-character here?

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Whoops yes!

end

return true
# For two-bit alphabets, all odd-length sequences are not palindromic.
function ispalindromic(seq::BioSequence{<:Union{DNAAlphabet{2}, RNAAlphabet{2}}})
isodd(length(seq)) ? false : _ispalindromic(seq)
end

@inline _ispalindromic(seq) = all(seq[i] == complement(seq[end - i + 1]) for i in 1:cld(length(seq), 2))

"""
hasambiguity(seq::BioSequence)
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