Genetic

src/Genetics.jl

@@ -1,68 +1,68 @@
-# using Diversity
-# using Diversity.API
+using Diversity
+using Diversity.API
 
-# using PopGen
-# using StringDistances
-# using LinearAlgebra
+using PopGen
+using StringDistances
+using LinearAlgebra
 
-# using FASTX
+using FASTX
 
-# abstract type AbstractGeneticTypes{PopData} <: 
-#     Diversity.API.AbstractTypes
-# end
+abstract type AbstractGeneticTypes{PopData} <: 
+    Diversity.API.AbstractTypes
+end
 
-# struct GeneticType{PopData} <: AbstractGeneticTypes{PopData}
-#     dat::PopData
-#     ntypes::Int64
-#     Zmatrix::Matrix{Float64}
-# end
+struct GeneticType{PopData} <: AbstractGeneticTypes{PopData}
+    dat::PopData
+    ntypes::Int64
+    Zmatrix::Matrix{Float64}
+end
 
-# function _hammingDistance(geno1, geno2)
-#     ismissing(geno1) || ismissing(geno2) && return missing
-#     if length(geno1) > 2
-#         @warn "hamming_distance may not work correctly for ploidy > 2"
-#     end
-#     #TODO Fix ploidy > 2 - e.g. (1, 1, 1, 2) ≠ (1, 2, 2, 2)
+function _hammingDistance(geno1, geno2)
+    ismissing(geno1) || ismissing(geno2) && return missing
+    if length(geno1) > 2
+        @warn "hamming_distance may not work correctly for ploidy > 2"
+    end
+    #TODO Fix ploidy > 2 - e.g. (1, 1, 1, 2) ≠ (1, 2, 2, 2)
 
-#     max(sum(geno1 .∉ Ref(geno2)), sum(geno2 .∉ Ref(geno1)))
-# end
+    max(sum(geno1 .∉ Ref(geno2)), sum(geno2 .∉ Ref(geno1)))
+end
 
-# function GeneticType(dat::PopData) 
-#     # Initialise objects
-#     matrix_obj = PopGen.loci_matrix(dat)
-#     ntypes = size(matrix_obj, 1)
-#     output = zeros(Float64, ntypes, ntypes)
-#     indices = PopGen.pairwise_pairs(1:ntypes)
+function GeneticType(dat::PopData) 
+    # Initialise objects
+    matrix_obj = PopGen.loci_matrix(dat)
+    ntypes = size(matrix_obj, 1)
+    output = zeros(Float64, ntypes, ntypes)
+    indices = PopGen.pairwise_pairs(1:ntypes)
 
-#     # Calculate distance matrix
-#     for (a, b) in indices
-#         output[a, b] = sum(_hammingDistance.((@view matrix_obj[a, :]),
-#                                              (@view matrix_obj[b, :])))
-#     end
-#     dist = Symmetric(output)
-#     dist /= maximum(dist)
+    # Calculate distance matrix
+    for (a, b) in indices
+        output[a, b] = sum(_hammingDistance.((@view matrix_obj[a, :]),
+                                             (@view matrix_obj[b, :])))
+    end
+    dist = Symmetric(output)
+    dist /= maximum(dist)
 
-#     # Calculate similarity matrix
-#     Zmatrix = 1 .- dist
+    # Calculate similarity matrix
+    Zmatrix = 1 .- dist
 
-#     return GeneticType{PopData}(dat, ntypes, Zmatrix)
-# end
+    return GeneticType{PopData}(dat, ntypes, Zmatrix)
+end
 
-# function GeneticType(dat::Vector) # Vector{BioSequences.AminoAcidSequence}
-#     # Initialise objects
-#     ntypes = length(dat)
-#     output = zeros(Int64, ntypes, ntypes)
-#     indices = PopGen.pairwise_pairs(1:ntypes)
+function GeneticType(dat::Vector) # Vector{BioSequences.AminoAcidSequence}
+    # Initialise objects
+    ntypes = length(dat)
+    output = zeros(Int64, ntypes, ntypes)
+    indices = PopGen.pairwise_pairs(1:ntypes)
 
-#     # Calculate distance matrix
-#     for (a, b) in indices
-#         output[a, b] = evaluate(Hamming(), dat[a], dat[b])
-#     end
-#     dist = Symmetric(output)
-#     dist /= maximum(dist)
+    # Calculate distance matrix
+    for (a, b) in indices
+        output[a, b] = evaluate(Hamming(), dat[a], dat[b])
+    end
+    dist = Symmetric(output)
+    dist /= maximum(dist)
 
-#     # Calculate similarity matrix
-#     Zmatrix = 1 .- dist
+    # Calculate similarity matrix
+    Zmatrix = 1 .- dist
 
-#     return GeneticType{BioSequences.AminoAcidSequence}(dat, ntypes, Zmatrix)
-# end
+    return GeneticType{BioSequences.AminoAcidSequence}(dat, ntypes, Zmatrix)
+end