diff --git a/src/Edit.jl b/src/Edit.jl index df203f4..b95a667 100644 --- a/src/Edit.jl +++ b/src/Edit.jl @@ -30,6 +30,13 @@ function BioGenerics.rightposition(e::Edit) return error("rightposition not implemented for type $(typeof(e))") 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} position::UInt length::UInt @@ -52,6 +59,7 @@ end Base.hash(x::DeletionEdit, h::UInt) = hash(DeletionEdit, hash((x.position, x.length), h)) BioGenerics.leftposition(d::DeletionEdit) = d.position BioGenerics.rightposition(d::DeletionEdit) = leftposition(d) + length(d) - 1 +_lendiff(d::DeletionEdit) = -1 * length(d) struct InsertionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} 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)) BioGenerics.leftposition(i::InsertionEdit) = i.position BioGenerics.rightposition(i::InsertionEdit) = leftposition(i) + 1 +_lendiff(i::InsertionEdit) = length(i) struct SubstitutionEdit{S<:BioSequence,T<:BioSymbol} <: Edit{S,T} position::UInt @@ -90,6 +99,7 @@ function Base.hash(x::SubstitutionEdit, h::UInt) end BioGenerics.leftposition(s::SubstitutionEdit) = s.position 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} 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 * '"')) 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