From ee92aad18fa969ecfad604a104ecc4b0c4b697f0 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Tue, 29 Aug 2023 11:15:00 +0200
Subject: [PATCH] Small fixes

* Remove the erroneous method Base.:*() with empty Varargs, and make sure
  that there is at least one `BioSequence`.
* Fixup inner constructor for the test type `SimpleSequence`
---
 src/biosequence/biosequence.jl   |  6 +++---
 test/biosequences/biosequence.jl | 10 +++++++---
 test/biosequences/indexing.jl    |  4 ++--
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/src/biosequence/biosequence.jl b/src/biosequence/biosequence.jl
index 94217364..f71ea95f 100644
--- a/src/biosequence/biosequence.jl
+++ b/src/biosequence/biosequence.jl
@@ -170,9 +170,9 @@ Base.repeat(chunk::BioSequence, n::Integer) = join(typeof(chunk), (chunk for i i
 Base.:^(x::BioSequence, n::Integer) = repeat(x, n)
 
 # Concatenation and Base.repeat operators
-function Base.:*(chunks::BioSequence...)
-    T = typeof(first(chunks))
-    join(T, chunks)
+function Base.:*(fst::BioSequence, rest::BioSequence...)
+    T = typeof(fst)
+    join(T, (fst, rest...))
 end
 
 """
diff --git a/test/biosequences/biosequence.jl b/test/biosequences/biosequence.jl
index 48d1dfd9..834c94d9 100644
--- a/test/biosequences/biosequence.jl
+++ b/test/biosequences/biosequence.jl
@@ -1,18 +1,22 @@
+struct Unsafe end
+
 # Create new biosequence for testing
 struct SimpleSeq <: BioSequence{RNAAlphabet{2}}
     x::Vector{UInt}
+    
+    SimpleSeq(::Unsafe, x::Vector{UInt}) = new(x)
 end
 
 function SimpleSeq(it)
-    SimpleSeq([BioSequences.encode(Alphabet(SimpleSeq), convert(RNA, i)) for i in it])
+    SimpleSeq(Unsafe(), [BioSequences.encode(Alphabet(SimpleSeq), convert(RNA, i)) for i in it])
 end
-Base.copy(x::SimpleSeq) = SimpleSeq(copy(x.x))
+Base.copy(x::SimpleSeq) = SimpleSeq(Unsafe(), copy(x.x))
 Base.length(x::SimpleSeq) = length(x.x)
 BioSequences.encoded_data_eltype(::Type{SimpleSeq}) = UInt
 BioSequences.extract_encoded_element(x::SimpleSeq, i::Integer) = x.x[i]
 
 BioSequences.encoded_setindex!(x::SimpleSeq, e::UInt, i::Integer) = x.x[i] = e
-SimpleSeq(::UndefInitializer, x::Integer) = SimpleSeq(zeros(UInt, x))
+SimpleSeq(::UndefInitializer, x::Integer) = SimpleSeq(Unsafe(), zeros(UInt, x))
 Base.resize!(x::SimpleSeq, len::Int) = (resize!(x.x, len); x)
 
 # Not part of the API, just used for testing purposes
diff --git a/test/biosequences/indexing.jl b/test/biosequences/indexing.jl
index c7d1470c..4cbbee4f 100644
--- a/test/biosequences/indexing.jl
+++ b/test/biosequences/indexing.jl
@@ -68,7 +68,7 @@
         @test_throws BoundsError seq[[5, 3, 13]]
 
         seq[[5, 2, 1]] == SimpleSeq([RNA_U, RNA_C, RNA_A])
-        seq[1:2:11] == SimpleSeq(seq.x[1:2:11])
+        seq[1:2:11] == SimpleSeq(collect(seq)[1:2:11])
     end
 end
 
@@ -99,7 +99,7 @@ end
             n = count(mask)
             seq2 = random_simple(n)
             cp = copy(s)
-            @test s[mask] == SimpleSeq(cp.x[mask])
+            @test s[mask] == SimpleSeq(collect(cp)[mask])
         end
 
         random_simple(len::Integer) = SimpleSeq(rand([RNA_A, RNA_C, RNA_G, RNA_U], len))