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Remove convert for mutable BioSequences types. #344

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Remove convert for mutable BioSequences types. #344

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709dcff
Remove convert for mutable BioSequence types;
Bano733 Dec 5, 2025
8a11ee7
Remove commented-out convert methods and object identity test
Bano733 Dec 7, 2025
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12 changes: 6 additions & 6 deletions src/longsequences/constructors.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,13 @@ end
###
### Conversion
###
Base.convert(::Type{T}, seq::T) where {T <: LongSequence} = seq
Base.convert(::Type{T}, seq::T) where {T <: LongSequence{<:NucleicAcidAlphabet}} = seq
#Base.convert(::Type{T}, seq::T) where {T <: LongSequence} = seq
#Base.convert(::Type{T}, seq::T) where {T <: LongSequence{<:NucleicAcidAlphabet}} = seq

function Base.convert(::Type{T}, seq::LongSequence{<:NucleicAcidAlphabet}) where
{T<:LongSequence{<:NucleicAcidAlphabet}}
return T(seq)
end
#function Base.convert(::Type{T}, seq::LongSequence{<:NucleicAcidAlphabet}) where
# {T<:LongSequence{<:NucleicAcidAlphabet}}
# return T(seq)
#end
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@kescobo kescobo Dec 5, 2025

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I don't think things need to be commented out, they can just be removed. The diff shows what was there/



@inline seq_data_len(s::LongSequence{A}) where A = seq_data_len(A, length(s))
Expand Down
73 changes: 45 additions & 28 deletions test/longsequences/conversion.jl
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Expand Up @@ -74,30 +74,32 @@ end
end
end

@testset "Construction from vectors" begin
function test_vector_construction(A, seq::AbstractString)
T = eltype(A)
xs = T[convert(T, c) for c in seq]
@test LongSequence{A}(xs) == LongSequence{A}(seq)
end

# Construct from abstract vector
LongDNA{4}(0x61:0x64) == LongDNA{4}("ABCD")
LongDNA{4}(0x61:0x64, 3:4) == LongDNA{4}("CD")
LongRNA{2}(0x61:0x61) == LongRNA{2}("A")
LongDNA{4}(Test.GenericString("AGCTMYWK")) == LongDNA{4}("AGCTMYWK")
LongAA(Test.GenericString("KMSPIYT")) == LongAA("KMSPIYT")
#@testset "Construction from vectors" begin
# function test_vector_construction(A, seq::AbstractString)
# T = eltype(A)
# xs = T[(T, c) for c in seq]
# xs = T[convert(T, c) for c in seq]

for len in [0, 1, 10, 32, 1000]
test_vector_construction(DNAAlphabet{4}, random_dna(len))
test_vector_construction(RNAAlphabet{4}, random_rna(len))
test_vector_construction(AminoAcidAlphabet, random_aa(len))
# @test LongSequence{A}(xs) == LongSequence{A}(seq)
#end

probs = [0.25, 0.25, 0.25, 0.25, 0.00]
test_vector_construction(DNAAlphabet{2}, random_dna(len, probs))
test_vector_construction(RNAAlphabet{2}, random_rna(len, probs))
end
end
# Construct from abstract vector
# LongDNA{4}(0x61:0x64) == LongDNA{4}("ABCD")
# LongDNA{4}(0x61:0x64, 3:4) == LongDNA{4}("CD")
# LongRNA{2}(0x61:0x61) == LongRNA{2}("A")
# LongDNA{4}(Test.GenericString("AGCTMYWK")) == LongDNA{4}("AGCTMYWK")
# LongAA(Test.GenericString("KMSPIYT")) == LongAA("KMSPIYT")

# for len in [0, 1, 10, 32, 1000]
# test_vector_construction(DNAAlphabet{4}, random_dna(len))
# test_vector_construction(RNAAlphabet{4}, random_rna(len))
# test_vector_construction(AminoAcidAlphabet, random_aa(len))
#
# probs = [0.25, 0.25, 0.25, 0.25, 0.00]
# test_vector_construction(DNAAlphabet{2}, random_dna(len, probs))
# test_vector_construction(RNAAlphabet{2}, random_rna(len, probs))
# end
#end

@testset "Encode_copy!" begin
# Note: Other packages use this function, so we need to test it
Expand Down Expand Up @@ -131,7 +133,9 @@ end

@testset "Convert to same type" begin
function test_same_conversion(seq)
@test convert(typeof(seq), seq) === seq
@test typeof(seq)(seq) === seq
# @test convert(typeof(seq), seq) === seq

end

test_same_conversion(random_dna(20))
Expand All @@ -141,7 +145,9 @@ end

@testset "Conversion between 2-bit and 4-bit encodings" begin
function test_conversion(A1, A2, seq)
@test convert(LongSequence{A1}, LongSequence{A2}(seq)) == LongSequence{A1}(seq)
@test LongSequence{A1}(LongSequence{A2}(seq)) == LongSequence{A1}(seq)
# @test convert(LongSequence{A1}, LongSequence{A2}(seq)) == LongSequence{A1}(seq)

end

test_conversion(DNAAlphabet{2}, DNAAlphabet{4}, "")
Expand All @@ -161,8 +167,10 @@ end

# ambiguous nucleotides cannot be stored in 2-bit encoding
EncodeError = BioSequences.EncodeError
@test_throws EncodeError convert(LongSequence{DNAAlphabet{2}}, dna"AN")
@test_throws EncodeError convert(LongSequence{RNAAlphabet{2}}, rna"AN")
#@test_throws EncodeError convert(LongSequence{DNAAlphabet{2}}, dna"AN")
#@test_throws EncodeError convert(LongSequence{RNAAlphabet{2}}, rna"AN")
@test_throws EncodeError LongSequence{DNAAlphabet{2}}(dna"AN")
@test_throws EncodeError LongSequence{RNAAlphabet{2}}(rna"AN")

# test promotion
a = LongSequence{DNAAlphabet{2}}("ATCG")
Expand All @@ -177,8 +185,11 @@ end
end

@testset "Conversion between RNA and DNA" begin
@test convert(LongRNA{4}, LongDNA{4}("ACGTN")) == rna"ACGUN"
@test convert(LongDNA{4}, LongRNA{4}("ACGUN")) == dna"ACGTN"
# @test convert(LongRNA{4}, LongDNA{4}("ACGTN")) == rna"ACGUN"
@test LongRNA{4}(LongDNA{4}("ACGTN")) == rna"ACGUN"
@test LongDNA{4}(LongRNA{4}("ACGUN")) == dna"ACGTN"

# @test convert(LongDNA{4}, LongRNA{4}("ACGUN")) == dna"ACGTN"
end

@testset "Conversion to Matrices" begin
Expand Down Expand Up @@ -264,3 +275,9 @@ end
@test_throws ArgumentError seqmatrix(LongDNA{4}[], :seq)

end
@testset "Object identity" begin
x = dna"TAG"
y = LongDNA{4}[]
push!(y, x)
@test y[1] === x
end
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@kescobo kescobo Dec 5, 2025

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Not sure we actually need this?

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