millironx/SequenceVariation.jl
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Add rightposition functions

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This commit is contained in:
Thomas A. Christensen II 2022-06-22 12:06:27 -05:00
parent 538b612faf
commit 89cad0120f
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 14 additions and 1 deletions
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15
src/SequenceVariation.jl
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@ -21,7 +21,7 @@ TODO now:
""" """
using BioAlignments: BioAlignments, PairwiseAlignment using BioAlignments: BioAlignments, PairwiseAlignment
using BioGenerics: BioGenerics, leftposition using BioGenerics: BioGenerics, leftposition, rightposition
using BioSequences: BioSequences, BioSequence, NucleotideSeq, AminoAcidSeq, LongSequence, isgap using BioSequences: BioSequences, BioSequence, NucleotideSeq, AminoAcidSeq, LongSequence, isgap
using BioSymbols: BioSymbol using BioSymbols: BioSymbol
@ -109,6 +109,7 @@ struct Edit{S <: BioSequence, T <: BioSymbol}
end end
Base.:(==)(e1::Edit, e2::Edit) = e1.pos == e2.pos && e1.x == e2.x Base.:(==)(e1::Edit, e2::Edit) = e1.pos == e2.pos && e1.x == e2.x
Base.hash(x::Edit, h::UInt) = hash(Edit, hash((x.x, x.pos), h)) Base.hash(x::Edit, h::UInt) = hash(Edit, hash((x.x, x.pos), h))
Base.length(e::Edit) = e isa Substitution ? 1 : length(mutation(e))
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}
parse(T, String(s)) parse(T, String(s))
@ -136,6 +137,17 @@ end
mutation(e::Edit) = e.x mutation(e::Edit) = e.x
BioGenerics.leftposition(e::Edit) = e.pos BioGenerics.leftposition(e::Edit) = e.pos
function BioGenerics.rightposition(e::Edit)
if mutation(e) isa Substitution
return leftposition(e)
elseif mutation(e) isa Insertion
return leftposition(e) + 1
elseif mutation(e) isa Deletion
return leftposition(e) + length(e) - 1
else
error("Unknown mutation type $(typeof(mutation(e)))")
end
end
#= #=
@noinline throw_parse_error(T, p::Integer) = error("Failed to parse $T at byte $p") @noinline throw_parse_error(T, p::Integer) = error("Failed to parse $T at byte $p")
@ -356,6 +368,7 @@ reference(v::Variation) = v.reference
edit(v::Variation) = v.edit edit(v::Variation) = v.edit
mutation(v::Variation) = mutation(edit(v)) mutation(v::Variation) = mutation(edit(v))
BioGenerics.leftposition(v::Variation) = leftposition(edit(v)) BioGenerics.leftposition(v::Variation) = leftposition(edit(v))
BioGenerics.rightposition(v::Variation) = rightposition(edit(v))
Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit
Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h)) Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h))