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