diff --git a/src/biosequence/biosequence.jl b/src/biosequence/biosequence.jl index 5254794d..1af1e87a 100644 --- a/src/biosequence/biosequence.jl +++ b/src/biosequence/biosequence.jl @@ -157,3 +157,4 @@ include("printing.jl") include("transformations.jl") include("counting.jl") include("copying.jl") +include("seqbroadcast.jl") \ No newline at end of file diff --git a/src/biosequence/seqbroadcast.jl b/src/biosequence/seqbroadcast.jl new file mode 100644 index 00000000..4ad71b67 --- /dev/null +++ b/src/biosequence/seqbroadcast.jl @@ -0,0 +1,155 @@ +#= + +Let's have a look at the example of broadcasting addition with a vector. + +@less broadcast(+, [1,2,3], 1) +=== +broadcast(f::Tf, As...) where {Tf} = materialize(broadcasted(f, As...)) + + +@less Base.broadcasted(+, [1,2,3], 1) +=== +@inline function broadcasted(f, arg1, arg2, args...) + arg1′ = broadcastable(arg1) + arg2′ = broadcastable(arg2) + args′ = map(broadcastable, args) + broadcasted(combine_styles(arg1′, arg2′, args′...), f, arg1′, arg2′, args′...) +end +@inline broadcasted(::S, f, args...) where S<:BroadcastStyle = Broadcasted{S}(f, args) + +bc = Base.broadcasted(Base.Broadcast.combine_styles(arg1, arg2), +, arg1, arg2) +Base.Broadcast.Broadcasted(+, ([1, 2, 3], 1)) + +typeof(bc) +Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, typeof(+), Tuple{Vector{Int64}, Int64}} + + +@less Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}}(+, (arg1, arg2)) +=== +function Broadcasted{Style}(f::F, args::Args, axes=nothing) where {Style, F, Args<:Tuple} + # using Core.Typeof rather than F preserves inferrability when f is a type + Broadcasted{Style, typeof(axes), Core.Typeof(f), Args}(f, args, axes) +end + + +@less materialize(bc) +=== +@inline materialize(bc::Broadcasted) = copy(instantiate(bc)) +materialize(x) = x + + +@less Base.Broadcast.instantiate(bc) +=== +@inline function instantiate(bc::Broadcasted{Style}) where {Style} + if bc.axes isa Nothing # Not done via dispatch to make it easier to extend instantiate(::Broadcasted{Style}) + axes = combine_axes(bc.args...) + else + axes = bc.axes + check_broadcast_axes(axes, bc.args...) + end + return Broadcasted{Style}(bc.f, bc.args, axes) +end + + +@less Base.Broadcast.combine_axes(bc.args...) +=== +@inline combine_axes(A, B...) = broadcast_shape(axes(A), combine_axes(B...)) +@inline combine_axes(A, B) = broadcast_shape(axes(A), axes(B)) + + +@less @less Base.Broadcast.broadcast_shape(axes([1,2,3]), axes(1)) +=== +broadcast_shape(shape::Tuple) = shape +broadcast_shape(shape::Tuple, shape1::Tuple, shapes::Tuple...) = broadcast_shape(_bcs(shape, shape1), shapes...) + + +@less Base.Broadcast._bcs(axes([1,2,3]), axes(1)) +=== +_bcs(shape::Tuple, ::Tuple{}) = (shape[1], _bcs(tail(shape), ())...) + +_bcs consolidates two shapes into a single output shape + +shape = axes([1,2,3]) +@less Base.Broadcast._bcs(Base.tail(shape), ()) +=== +_bcs(::Tuple{}, ::Tuple{}) = () +() + +(shape[1], _bcs(tail(shape), ())...) + + +@less copy(Base.Broadcast.instantiate(bc)) +=== +@inline function copy(bc::Broadcasted{Style}) where {Style} + ElType = combine_eltypes(bc.f, bc.args) + if Base.isconcretetype(ElType) + # We can trust it and defer to the simpler `copyto!` + return copyto!(similar(bc, ElType), bc) + end + # When ElType is not concrete, use narrowing. Use the first output + # value to determine the starting output eltype; copyto_nonleaf! + # will widen `dest` as needed to accommodate later values. + bc′ = preprocess(nothing, bc) + iter = eachindex(bc′) + y = iterate(iter) + if y === nothing + # if empty, take the ElType at face value + return similar(bc′, ElType) + end + # Initialize using the first value + I, state = y + @inbounds val = bc′[I] + dest = similar(bc′, typeof(val)) + @inbounds dest[I] = val + # Now handle the remaining values + # The typeassert gives inference a helping hand on the element type and dimensionality + # (work-around for #28382) + ElType′ = ElType === Union{} ? Any : ElType <: Type ? Type : ElType + RT = dest isa AbstractArray ? AbstractArray{<:ElType′, ndims(dest)} : Any + return copyto_nonleaf!(dest, bc′, iter, state, 1)::RT +end + + +@less Base.Broadcast.combine_eltypes(bc.f, bc.args) +=== +combine_eltypes(f, args::Tuple) = promote_typejoin_union(Base._return_type(f, eltypes(args))) + +@less Base.Broadcast.eltypes(bc.args) + +@less Base._return_type(+, Base.Broadcast.eltypes(bc.args)) + +@less Base.Broadcast.promote_typejoin_union(Base._return_type(+, Base.Broadcast.eltypes(bc.args))) +=== +function promote_typejoin_union(::Type{T}) where T + if T === Union{} + return Union{} + elseif T isa UnionAll + return Any # TODO: compute more precise bounds + elseif T isa Union + return promote_typejoin(promote_typejoin_union(T.a), promote_typejoin_union(T.b)) + elseif T <: Tuple + return typejoin_union_tuple(T) + else + return T + end +end + + +@less similar(bc, Base.Broadcast.combine_eltypes(bc.f, bc.args)) +=== +Base.similar(bc::Broadcasted, ::Type{T}) where {T} = similar(bc, T, axes(bc)) +Base.similar(::Broadcasted{DefaultArrayStyle{N}}, ::Type{ElType}, dims) where {N,ElType} = similar(Array{ElType}, dims) +Base.similar(::Broadcasted{DefaultArrayStyle{N}}, ::Type{Bool}, dims) where N = similar(BitArray, dims) + +@less copyto!(similar(bc, Base.Broadcast.combine_eltypes(bc.f, bc.args)), bc) + + + +=# + +Base.broadcastable(x::BioSequence) = x + + + + +