Switch to inner constructors and explicit for subtypes

Author: nossleinad

src/models/discrete_models/codon_models.jl

@@ -325,6 +325,10 @@ mutable struct CodonPartition <: DiscretePartition
             zeros(sites),
         )
     end
+    function CodonPartition(state, states, sites, scaling; code = universal_code)
+        @assert size(state) == (states, sites) && states == length(code.sense_codons)
+        new(state, states, sites, scaling)
+    end
 end
 
 #Make this handle IUPAC ambigs sensible. Any codon compatible with the ambig should get a 1.0

src/models/discrete_models/discrete_partitions.jl

@@ -12,7 +12,7 @@ end
 
 #Overloading the copy_partition to avoid deepcopy.
 function copy_partition(src::T) where {T<:DiscretePartition}
-    return T(ntuple(i -> copy(getfield(src, i)), fieldcount(T))...)
+    return T(copy(src.state), src.states, src.sites, copy(src.scaling))
 end
 
 #I should add a constructor that constructs a DiscretePartition from an existing array.
@@ -21,79 +21,98 @@ mutable struct CustomDiscretePartition <: DiscretePartition
     states::Int
     sites::Int
     scaling::Array{Float64,1}
-end
-
-CustomDiscretePartition(states, sites) =
-    CustomDiscretePartition(zeros(states, sites), states, sites, zeros(sites))
-
-function CustomDiscretePartition(freq_vec::Vector{Float64}, sites::Int64) #Add this constructor to all partition types
-    state_arr = zeros(length(freq_vec), sites)
-    state_arr .= freq_vec
-    return CustomDiscretePartition(state_arr, length(freq_vec), sites, zeros(sites))
+    function CustomDiscretePartition(states, sites)
+        new(zeros(states, sites), states, sites, zeros(sites))
+    end
+    function CustomDiscretePartition(freq_vec::Vector{Float64}, sites::Int64) #Add this constructor to all partition types
+        state_arr = zeros(length(freq_vec), sites)
+        state_arr .= freq_vec
+        new(state_arr, length(freq_vec), sites, zeros(sites))
+    end
+    function CustomDiscretePartition(state, states, sites, scaling)
+        @assert size(state) == (states, sites)
+        new(state, states, sites, scaling)
+    end
 end
 
 mutable struct NucleotidePartition <: DiscretePartition
     state::Array{Float64,2}
     states::Int
     sites::Int
     scaling::Array{Float64,1}
-end
-
-NucleotidePartition(sites) = NucleotidePartition(zeros(4, sites), 4, sites, zeros(sites))
-
-function NucleotidePartition(freq_vec::Vector{Float64}, sites::Int64)
-    @assert length(freq_vec) == 4
-    state_arr = zeros(4, sites)
-    state_arr .= freq_vec
-    return NucleotidePartition(state_arr, 4, sites, zeros(sites))
+    function NucleotidePartition(sites)
+        new(zeros(4, sites), 4, sites, zeros(sites))
+    end
+    function NucleotidePartition(freq_vec::Vector{Float64}, sites::Int64)
+        @assert length(freq_vec) == 4
+        state_arr = zeros(4, sites)
+        state_arr .= freq_vec
+        new(state_arr, 4, sites, zeros(sites))
+    end
+    function NucleotidePartition(state, states, sites, scaling)
+        @assert size(state) == (states, sites) && states == 4
+        new(state, states, sites, scaling)
+    end
 end
 
 mutable struct GappyNucleotidePartition <: DiscretePartition
     state::Array{Float64,2}
     states::Int
     sites::Int
     scaling::Array{Float64,1}
-end
-
-GappyNucleotidePartition(sites) = GappyNucleotidePartition(zeros(5, sites), 5, sites, zeros(sites))
-
-function GappyNucleotidePartition(freq_vec::Vector{Float64}, sites::Int64)
-    @assert length(freq_vec) == 5
-    state_arr = zeros(5, sites)
-    state_arr .= freq_vec
-    return GappyNucleotidePartition(state_arr, 5, sites, zeros(sites))
+    function GappyNucleotidePartition(sites)
+        new(zeros(5, sites), 5, sites, zeros(sites))
+    end
+    function GappyNucleotidePartition(freq_vec::Vector{Float64}, sites::Int64)
+        @assert length(freq_vec) == 5
+        state_arr = zeros(5, sites)
+        state_arr .= freq_vec
+        new(state_arr, 5, sites, zeros(sites))
+    end
+    function GappyNucleotidePartitionPartition(state, states, sites, scaling)
+        @assert size(state) == (states, sites) && states == 5
+        new(state, states, sites, scaling)
+    end
 end
 
 mutable struct AminoAcidPartition <: DiscretePartition
     state::Array{Float64,2}
     states::Int
     sites::Int
     scaling::Array{Float64,1}
-end
-
-AminoAcidPartition(sites) = AminoAcidPartition(zeros(20, sites), 20, sites, zeros(sites))
-
-function AminoAcidPartition(freq_vec::Vector{Float64}, sites::Int64)
-    @assert length(freq_vec) == 20
-    state_arr = zeros(20, sites)
-    state_arr .= freq_vec
-    return AminoAcidPartition(state_arr, 20, sites, zeros(sites))
+    function AminoAcidPartition(sites)
+        new(zeros(20, sites), 20, sites, zeros(sites))
+    end
+    function AminoAcidPartition(freq_vec::Vector{Float64}, sites::Int64)
+        @assert length(freq_vec) == 20
+        state_arr = zeros(20, sites)
+        state_arr .= freq_vec
+        new(state_arr, 20, sites, zeros(sites))
+    end
+    function AminoAcidPartition(state, states, sites, scaling)
+        @assert size(state) == (states, sites) && states == 20
+        new(state, states, sites, scaling)
+    end
 end
 
 mutable struct GappyAminoAcidPartition <: DiscretePartition
     state::Array{Float64,2}
     states::Int
     sites::Int
     scaling::Array{Float64,1}
-end
-
-GappyAminoAcidPartition(sites) = GappyAminoAcidPartition(zeros(21, sites), 21, sites, zeros(sites))
-
-function GappyAminoAcidPartition(freq_vec::Vector{Float64}, sites::Int64)
-    @assert length(freq_vec) == 21
-    state_arr = zeros(21, sites)
-    state_arr .= freq_vec
-    return GappyAminoAcidPartition(state_arr, 21, sites, zeros(sites))
+    function GappyAminoAcidPartition(sites)
+        new(zeros(21, sites), 21, sites, zeros(sites))
+    end
+    function GappyAminoAcidPartition(freq_vec::Vector{Float64}, sites::Int64)
+        @assert length(freq_vec) == 21
+        state_arr = zeros(21, sites)
+        state_arr .= freq_vec
+        new(state_arr, 21, sites, zeros(sites))
+    end
+    function GappyAminoAcidPartition(state, states, sites, scaling)
+        @assert size(state) == (states, sites) && states == 21
+        new(state, states, sites, scaling)
+    end
 end
 
 """