From 8993aba545dfa296db8a4484ff5cae25a0eda1a4 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Fri, 22 Mar 2024 14:22:28 +0100
Subject: [PATCH 1/2] Update `ispalindromic`

Expand the documentation to explain that it is palindromic with respect to the
reverse-complement. Also implement a fast-path for 2-bit nucleotides.
---
 src/biosequence/predicates.jl | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/biosequence/predicates.jl b/src/biosequence/predicates.jl
index 37c2e9d9..e75b9161 100644
--- a/src/biosequence/predicates.jl
+++ b/src/biosequence/predicates.jl
@@ -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)
+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)

From 8ebf46109e6615af2e305d3c5b08d67b0ad13156 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Fri, 22 Mar 2024 14:34:47 +0100
Subject: [PATCH 2/2] Fixup: Performance

---
 src/biosequence/predicates.jl | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/biosequence/predicates.jl b/src/biosequence/predicates.jl
index e75b9161..c8b3cfea 100644
--- a/src/biosequence/predicates.jl
+++ b/src/biosequence/predicates.jl
@@ -80,15 +80,21 @@ false
 Return `true` if `seq` is a palindromic sequence; otherwise return `false`.
 """
 function ispalindromic(seq::BioSequence{<:NucleicAcidAlphabet})
-	_ispalindromic(seq)
+    _ispalindromic(seq)
 end
 
 # 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)
+    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))
+@inline function _ispalindromic(seq)
+    L = lastindex(seq)
+    for i in 1:cld(length(seq), 2)
+        seq[i] == complement(seq[L - i + 1]) || return false
+    end
+    true
+end
 
 """
     hasambiguity(seq::BioSequence)