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ChrisRackauckasChrisRackauckas
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fix int64->int
1 parent 30d0fc0 commit 471602e

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-32
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6 files changed

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‎README.md‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ cells contain proteins whose concentrations are modeled as simply a vector
2424
of numbers (it can be anything linearly indexable).
2525

2626
```julia
27-
immutable Cell{B} <: MultiScaleArrayLeaf{B}
27+
immutable Cell{B} <: AbstractMultiScaleArrayLeaf{B}
2828
x::Vector{B}
2929
end
3030
immutable Population{T<:AbstractMultiScaleArray,B<:Number} <: AbstractMultiScaleArray{B}
@@ -37,7 +37,7 @@ immutable Tissue{T<:AbstractMultiScaleArray,B<:Number} <: AbstractMultiScaleArra
3737
y::Vector{B}
3838
end_idxs::Vector{Int}
3939
end
40-
immutable Embryo{T<:AbstractMultiScaleArray,B<:Number} <: MultiScaleArrayHead{B}
40+
immutable Embryo{T<:AbstractMultiScaleArray,B<:Number} <: AbstractMultiScaleArrayHead{B}
4141
x::Vector{T}
4242
y::Vector{B}
4343
end_idxs::Vector{Int}
@@ -143,7 +143,7 @@ techniques for each new model.
143143

144144
## Defining A MultiScaleModel: The Interface
145145

146-
The required interface is as follows. Leaf types must extend MultiScaleArrayLeaf, the
146+
The required interface is as follows. Leaf types must extend AbstractMultiScaleArrayLeaf, the
147147
highest level of the model or the head extends MultiScaleModelHead, and all
148148
intermediate types extend AbstractMultiScaleArray. The leaf has an array `x::Vector{B}`.
149149
Each type above then contains three fields:
@@ -186,7 +186,7 @@ extended as one pleases. For example, we can change the definition of the cell
186186
to have:
187187

188188
```julia
189-
immutable Cell{B} <: MultiScaleArrayLeaf{B}
189+
immutable Cell{B} <: AbstractMultiScaleArrayLeaf{B}
190190
x::Vector{B}
191191
celltype::Symbol
192192
end

‎src/MultiScaleArrays.jl‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,8 @@ import Base: length, push!, deleteat!,getindex, setindex!, eachindex,
66
import RecursiveArrayTools: recursivecopy!
77
using Iterators
88
abstract AbstractMultiScaleArray{B} <: AbstractArray{B,1}
9-
abstract MultiScaleArrayLeaf{B} <: AbstractMultiScaleArray{B}
10-
abstract MultiScaleArrayHead{B} <: AbstractMultiScaleArray{B}
9+
abstract AbstractMultiScaleArrayLeaf{B} <: AbstractMultiScaleArray{B}
10+
abstract AbstractMultiScaleArrayHead{B} <: AbstractMultiScaleArray{B}
1111

1212
Base.show(io::IO, x::AbstractMultiScaleArray) = invoke(show, Tuple{IO, Any}, io, x)
1313
Base.show(io::IO, ::MIME"text/plain", x::AbstractMultiScaleArray) = show(io, x)
@@ -19,7 +19,7 @@ include("math.jl")
1919
include("level_iterations.jl")
2020

2121
# Types
22-
export AbstractMultiScaleArray, MultiScaleArrayLeaf, MultiScaleArrayHead
22+
export AbstractMultiScaleArray, AbstractMultiScaleArrayLeaf, AbstractMultiScaleArrayHead
2323

2424
# Constructors
2525
export construct, similar, deepcopy, recursivecopy!

‎src/addition_deletion.jl‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
function add_daughter!(m::MultiScaleArrayHead,x::AbstractMultiScaleArray)
1+
function add_daughter!(m::AbstractMultiScaleArrayHead,x::AbstractMultiScaleArray)
22
push!(m.x,x)
33
if !isempty(m.y)
44
m.end_idxs[end] = m.end_idxs[end-1]+length(x)
@@ -31,11 +31,11 @@ function __add_daughter!(m::AbstractMultiScaleArray,x::AbstractMultiScaleArray)
3131
nothing
3232
end
3333

34-
function __add_daughter!(m::AbstractMultiScaleArray,x::AbstractMultiScaleArray,i::Tuple{Int64})
34+
function __add_daughter!(m::AbstractMultiScaleArray,x::AbstractMultiScaleArray,i::Tuple{Int})
3535
__add_daughter!(m,x,i[1])
3636
end
3737

38-
function __add_daughter!(m::AbstractMultiScaleArray,x::AbstractMultiScaleArray,i::Int64)
38+
function __add_daughter!(m::AbstractMultiScaleArray,x::AbstractMultiScaleArray,i::Int)
3939
__add_daughter!(m.x[i],x)
4040
for j = i:num_daughters(m)
4141
m.end_idxs[j] += length(x)
@@ -46,7 +46,7 @@ function __add_daughter!(m::AbstractMultiScaleArray,x::AbstractMultiScaleArray,i
4646
nothing
4747
end
4848

49-
function add_daughter!(m::MultiScaleArrayHead,x::AbstractMultiScaleArray,i::Int)
49+
function add_daughter!(m::AbstractMultiScaleArrayHead,x::AbstractMultiScaleArray,i::Int)
5050
__add_daughter!(m.x[i],x)
5151
for j = i:num_daughters(m)
5252
m.end_idxs[j] += length(x)
@@ -57,7 +57,7 @@ function add_daughter!(m::MultiScaleArrayHead,x::AbstractMultiScaleArray,i::Int)
5757
nothing
5858
end
5959

60-
function add_daughter!(m::MultiScaleArrayHead,x::AbstractMultiScaleArray,i::Int...)
60+
function add_daughter!(m::AbstractMultiScaleArrayHead,x::AbstractMultiScaleArray,i::Int...)
6161
__add_daughter!(m.x[i[1]],x,i[2:end])
6262
for j = i[1]:num_daughters(m)
6363
m.end_idxs[j] += length(x)
@@ -80,7 +80,7 @@ function __remove_daughter!(m::AbstractMultiScaleArray,i::Int)
8080
del_length
8181
end
8282

83-
function remove_daughter!(m::MultiScaleArrayHead,i::Int)
83+
function remove_daughter!(m::AbstractMultiScaleArrayHead,i::Int)
8484
del_length = length(m.x[i])
8585
deleteat!(m.x,i); deleteat!(m.end_idxs,i)
8686
for j = i:num_daughters(m)
@@ -92,16 +92,16 @@ function remove_daughter!(m::MultiScaleArrayHead,i::Int)
9292
nothing
9393
end
9494

95-
function __remove_daughter!(m::MultiScaleArrayLeaf,i::Int)
95+
function __remove_daughter!(m::AbstractMultiScaleArrayLeaf,i::Int)
9696
deleteat!(m.x,i)
9797
1
9898
end
9999

100-
function __remove_daughter!(m::AbstractMultiScaleArray,i::Tuple{Int64})
100+
function __remove_daughter!(m::AbstractMultiScaleArray,i::Tuple{Int})
101101
__remove_daughter!(m,i[1])
102102
end
103103

104-
function remove_daughter!(m::MultiScaleArrayHead,i::Int...)
104+
function remove_daughter!(m::AbstractMultiScaleArrayHead,i::Int...)
105105
del_length = __remove_daughter!(m.x[i[1]],i[2:end])
106106
for j = i[1]:num_daughters(m)
107107
m.end_idxs[j] -= del_length

‎src/indexing.jl‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -42,11 +42,11 @@ end
4242
end
4343
end
4444

45-
@inline function getindex(m::MultiScaleArrayLeaf,i::Int)
45+
@inline function getindex(m::AbstractMultiScaleArrayLeaf,i::Int)
4646
m.x[i]
4747
end
4848

49-
@inline function getindex(m::MultiScaleArrayLeaf,i::Int...)
49+
@inline function getindex(m::AbstractMultiScaleArrayLeaf,i::Int...)
5050
m.x[i[1]]
5151
end
5252

@@ -58,19 +58,19 @@ end
5858
end
5959
end
6060

61-
@inline function getindex(m::MultiScaleArrayLeaf,i...)
61+
@inline function getindex(m::AbstractMultiScaleArrayLeaf,i...)
6262
m.x[i[1]]
6363
end
6464

65-
@inline function getindex(m::MultiScaleArrayLeaf,i::CartesianIndex{1})
65+
@inline function getindex(m::AbstractMultiScaleArrayLeaf,i::CartesianIndex{1})
6666
m.x[i[1]]
6767
end
6868

69-
@inline function setindex!(m::MultiScaleArrayLeaf,x,i::Int)
69+
@inline function setindex!(m::AbstractMultiScaleArrayLeaf,x,i::Int)
7070
m.x[i] = x
7171
end
7272

73-
@inline function setindex!(m::MultiScaleArrayLeaf,x,i::Int...)
73+
@inline function setindex!(m::AbstractMultiScaleArrayLeaf,x,i::Int...)
7474
m.x[i[1]] = x
7575
end
7676

@@ -86,7 +86,7 @@ end
8686
[m[i] for i in 1:length(m)]
8787
end
8888

89-
@inline function getindex(m::MultiScaleArrayLeaf,::Colon)
89+
@inline function getindex(m::AbstractMultiScaleArrayLeaf,::Colon)
9090
m.x
9191
end
9292

@@ -98,6 +98,6 @@ eachindex(m::AbstractMultiScaleArray) = 1:length(m)
9898
endof(m::AbstractMultiScaleArray) = length(m)
9999

100100
Base.eltype{B}(S::AbstractMultiScaleArray{B}) = B
101-
#broadcast_getindex(m::MultiScaleArrayLeaf,i::Int) = (println("here");m[i])
101+
#broadcast_getindex(m::AbstractMultiScaleArrayLeaf,i::Int) = (println("here");m[i])
102102
#broadcast_getindex(m::AbstractMultiScaleArray,i::Int) = (println("here");m[i])
103103
#broadcast_getindex(m::AbstractMultiScaleArray,i::Int...) = m[i]

‎src/shape_construction.jl‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
1-
length(m::MultiScaleArrayLeaf) = length(m.x)
1+
length(m::AbstractMultiScaleArrayLeaf) = length(m.x)
22
length(m::AbstractMultiScaleArray) = m.end_idxs[end]
3-
num_daughters(m::MultiScaleArrayLeaf) = 0
3+
num_daughters(m::AbstractMultiScaleArrayLeaf) = 0
44
num_daughters(m::AbstractMultiScaleArray) = size(m.x)[1]
55
ndims(m::AbstractMultiScaleArray) = 1
66
size(m::AbstractMultiScaleArray,i::Int) = Int((i==1))*length(m)
@@ -15,15 +15,15 @@ function similar(m::AbstractMultiScaleArray)
1515
m_new
1616
end
1717

18-
similar(m::MultiScaleArrayLeaf) = construct(typeof(m),similar(m.x))
18+
similar(m::AbstractMultiScaleArrayLeaf) = construct(typeof(m),similar(m.x))
1919

2020
#=
2121
function print_matrix(IO,m::AbstractMultiScaleArray,str1,str2,str3)
2222
print_matrix(IO,m.x,str1,str2,str3)
2323
end
2424
=#
2525

26-
function construct{T<:MultiScaleArrayLeaf,T2}(::Type{T},x::Vector{T2})
26+
function construct{T<:AbstractMultiScaleArrayLeaf,T2}(::Type{T},x::Vector{T2})
2727
T(x)
2828
end
2929

@@ -51,7 +51,7 @@ function ==(m1::AbstractMultiScaleArray,m2::AbstractMultiScaleArray)
5151
m1 === m2
5252
end
5353

54-
function recursivecopy!(b::MultiScaleArrayLeaf,a::MultiScaleArrayLeaf)
54+
function recursivecopy!(b::AbstractMultiScaleArrayLeaf,a::AbstractMultiScaleArrayLeaf)
5555
@inbounds copy!(b,a)
5656
end
5757

‎test/runtests.jl‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ using Base.Test
55
macro define_hierarchy(BottomType,names)
66
quote
77
name = $(esc(names))[1]
8-
immutable $(esc(name)){$(esc(BottomType))} <: MultiScaleArrayLeaf{$(esc(BottomType))}
8+
immutable $(esc(name)){$(esc(BottomType))} <: AbstractMultiScaleArrayLeaf{$(esc(BottomType))}
99
x::Vector{$(esc(BottomType))}
1010
end
1111
@@ -27,7 +27,7 @@ end
2727

2828
### Setup a hierarchy
2929

30-
immutable Cell{B} <: MultiScaleArrayLeaf{B}
30+
immutable Cell{B} <: AbstractMultiScaleArrayLeaf{B}
3131
x::Vector{B}
3232
end
3333
immutable Population{T<:AbstractMultiScaleArray,B<:Number} <: AbstractMultiScaleArray{B}
@@ -40,7 +40,7 @@ immutable Tissue{T<:AbstractMultiScaleArray,B<:Number} <: AbstractMultiScaleArra
4040
y::Vector{B}
4141
end_idxs::Vector{Int}
4242
end
43-
immutable Embryo{T<:AbstractMultiScaleArray,B<:Number} <: MultiScaleArrayHead{B}
43+
immutable Embryo{T<:AbstractMultiScaleArray,B<:Number} <: AbstractMultiScaleArrayHead{B}
4444
x::Vector{T}
4545
y::Vector{B}
4646
end_idxs::Vector{Int}

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