millironx/SequenceVariation.jl
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fix: Remove excess type annotations from *Edit types

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This commit is contained in:
Thomas A. Christensen II 2024-10-01 11:09:32 -05:00
parent 8814882507
commit 43a2708a1e
Signed by: millironx
GPG key ID: B7044A3432851F64
1 changed files with 8 additions and 8 deletions
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16
src/Edit.jl
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@ -37,7 +37,7 @@ Gets the number of bases that `edit` adds to the reference sequence
""" """
_lendiff(edit::Edit) = error("_lendiff not implemented for type $(typeof(edit))") _lendiff(edit::Edit) = error("_lendiff not implemented for type $(typeof(edit))")
struct DeletionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} struct DeletionEdit{S,T} <: Edit{S,T}
position::UInt position::UInt
length::UInt length::UInt
@ -61,9 +61,9 @@ BioGenerics.leftposition(d::DeletionEdit) = d.position
BioGenerics.rightposition(d::DeletionEdit) = leftposition(d) + length(d) - 1 BioGenerics.rightposition(d::DeletionEdit) = leftposition(d) + length(d) - 1
_lendiff(d::DeletionEdit) = -1 * length(d) _lendiff(d::DeletionEdit) = -1 * length(d)
struct InsertionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} struct InsertionEdit{S<:BioSequence} <: Edit
position::UInt position::UInt
seq::S struct InsertionEdit{S,T} <: Edit{S,T} where {S<:BioSequence,T<:BioSymbol}
function InsertionEdit{S}(position::UInt, seq::S) where {S<:BioSequence} function InsertionEdit{S}(position::UInt, seq::S) where {S<:BioSequence}
iszero(position) && error("Insertion cannot be at a position outside the sequence") iszero(position) && error("Insertion cannot be at a position outside the sequence")
@ -78,9 +78,9 @@ BioGenerics.leftposition(i::InsertionEdit) = i.position
BioGenerics.rightposition(i::InsertionEdit) = leftposition(i) + 1 BioGenerics.rightposition(i::InsertionEdit) = leftposition(i) + 1
_lendiff(i::InsertionEdit) = length(i) _lendiff(i::InsertionEdit) = length(i)
struct SubstitutionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} struct SubstitutionEdit{T} <: Edit where {T<:BioSymbol}
position::UInt position::UInt
base::T struct SubstitutionEdit{S,T} <: Edit{S,T} where {S<:BioSequence,T<:BioSymbol}
function SubstitutionEdit{T}(position::UInt, base::T) where {T<:BioSymbol} function SubstitutionEdit{T}(position::UInt, base::T) where {T<:BioSymbol}
iszero(position) && iszero(position) &&
@ -111,15 +111,15 @@ function Base.parse(::Type{<:Edit{Se,Sy}}, s::Union{String,SubString{String}}) w
pos = parse(UInt, m[1]) pos = parse(UInt, m[1])
stop = parse(UInt, m[2]) stop = parse(UInt, m[2])
stop ≥ pos || throw(ArgumentError("Non-positive deletion length: \"" * s * "\"")) stop ≥ pos || throw(ArgumentError("Non-positive deletion length: \"" * s * "\""))
return DeletionEdit{Se,Sy}(pos, stop - pos + 1) return DeletionEdit(pos, stop - pos + 1)
elseif (m = match(r"^(\d+)([A-Za-z]+)$", s); m) !== nothing elseif (m = match(r"^(\d+)([A-Za-z]+)$", s); m) !== nothing
pos = parse(UInt, m[1]) pos = parse(UInt, m[1])
seq = Se(m[2]) seq = Se(m[2])
return InsertionEdit{Se,Sy}(pos, seq) return InsertionEdit{Se}(pos, seq)
elseif (m = match(r"^[A-Za-z](\d+)([A-Za-z])$", s); m) !== nothing elseif (m = match(r"^[A-Za-z](\d+)([A-Za-z])$", s); m) !== nothing
pos = parse(UInt, m[1]) pos = parse(UInt, m[1])
sym = Sy(first(m[2])) sym = Sy(first(m[2]))
return SubstitutionEdit{Se,Sy}(pos, sym) return SubstitutionEdit{Sy}(pos, sym)
else else
throw(ArgumentError("Failed to parse edit \"" * s * '"')) throw(ArgumentError("Failed to parse edit \"" * s * '"'))
end end