millironx/SequenceVariation.jl
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refactor: Use types to power _lendiff function

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This commit is contained in:
Thomas A. Christensen II 2024-10-01 11:07:46 -05:00
parent be731665bc
commit 8814882507
Signed by: millironx
GPG key ID: B7044A3432851F64
1 changed files with 10 additions and 12 deletions
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22
src/Edit.jl
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@ -30,6 +30,13 @@ function BioGenerics.rightposition(e::Edit)
return error("rightposition not implemented for type $(typeof(e))") return error("rightposition not implemented for type $(typeof(e))")
end end
"""
_lendiff(edit::Edit)
Gets the number of bases that `edit` adds to the reference sequence
"""
_lendiff(edit::Edit) = error("_lendiff not implemented for type $(typeof(edit))")
struct DeletionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} struct DeletionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T}
position::UInt position::UInt
length::UInt length::UInt
@ -52,6 +59,7 @@ end
Base.hash(x::DeletionEdit, h::UInt) = hash(DeletionEdit, hash((x.position, x.length), h)) Base.hash(x::DeletionEdit, h::UInt) = hash(DeletionEdit, hash((x.position, x.length), h))
BioGenerics.leftposition(d::DeletionEdit) = d.position 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)
struct InsertionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} struct InsertionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T}
position::UInt position::UInt
@ -68,6 +76,7 @@ Base.:(==)(x::InsertionEdit, y::InsertionEdit) = x.position == y.position && x.s
Base.hash(x::InsertionEdit, h::UInt) = hash(InsertionEdit, hash((x.position, x.seq), h)) Base.hash(x::InsertionEdit, h::UInt) = hash(InsertionEdit, hash((x.position, x.seq), h))
BioGenerics.leftposition(i::InsertionEdit) = i.position 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)
struct SubstitutionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} struct SubstitutionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T}
position::UInt position::UInt
@ -90,6 +99,7 @@ function Base.hash(x::SubstitutionEdit, h::UInt)
end end
BioGenerics.leftposition(s::SubstitutionEdit) = s.position BioGenerics.leftposition(s::SubstitutionEdit) = s.position
BioGenerics.rightposition(s::SubstitutionEdit) = leftposition(s) BioGenerics.rightposition(s::SubstitutionEdit) = leftposition(s)
_lendiff(s::SubstitutionEdit) = 0
function Base.parse(::Type{T}, s::AbstractString) where {T<:Edit{Se,Sy}} where {Se,Sy} function Base.parse(::Type{T}, s::AbstractString) where {T<:Edit{Se,Sy}} where {Se,Sy}
return parse(T, String(s)) return parse(T, String(s))
@ -114,15 +124,3 @@ function Base.parse(::Type{<:Edit{Se,Sy}}, s::Union{String,SubString{String}}) w
throw(ArgumentError("Failed to parse edit \"" * s * '"')) throw(ArgumentError("Failed to parse edit \"" * s * '"'))
end end
end end
"""
_lendiff(edit::Edit)
Gets the number of bases that `edit` adds to the reference sequence
"""
function _lendiff(edit::Edit)
x = _mutation(edit)
# Each edit type has logic for its length, we just need to know what direction to go
multiplier = x isa Substitution ? 0 : (x isa Deletion ? -1 : 1)
return length(x) * multiplier
end