Merge pull request #20 from nossleinad/fix_obs2partition!

Fix issue #19

src/models/discrete_models/codon_models.jl

@@ -341,17 +341,18 @@ function obs2partition!(dest::CodonPartition, seq::String; code = universal_code
         error("Sequence length does not match partition")
     end
 
-    for i = 1:Int(length(seq) / 3)
-        c = seq[3*(i-1)+1:3*(i-1)+3]
+    @views for j in axes(dest.state, 2)
+        c = seq[3*(j-1)+1:3*(j-1)+3]
         cod_ind = get(code.string2sense, c, -1)
         if cod_ind == -1
-            dest.state[:, i] = ones(eltype(dest.state), dest.states)
+            fill!(dest.state[:, j], 1.0)
             push!(problem_codons, c)
         else
-            dest.state[:, i] = zeros(eltype(dest.state), dest.states)
-            dest.state[cod_ind, i] = 1.0
+            fill!(dest.state[:, j], 0.0)
+            dest.state[cod_ind, j] = 1.0
         end
     end
+    fill!(dest.scaling, 0.0)
     return countmap(problem_codons)
 end
 

src/models/discrete_models/utils/seq_to_vec.jl

@@ -94,18 +94,20 @@ end
 
 
 
-#Creates new memory. This is currently required for the populate_tree function to do things automatically.
 function obs2partition!(dest::DiscretePartition, seq::String, dic::Dict)
-    #if length(seq) != dest.sites
-    #    @warn "obs2partition!() is changing the number of sites in a partition."
-    #end
-    dest.state = zeros(eltype(dest.state), dest.states, length(seq))
-    dest.sites = length(seq)
-    dest.scaling = zeros(length(seq))
-    unmatched = ones(eltype(dest.state), dest.states)
-    for (i, c) in enumerate(uppercase(seq))
-        dest.state[:, i] = get(dic, c, unmatched)
+    if length(seq) != dest.sites
+        error("Sequence length does not match partition")
     end
+
+    @views for j in axes(dest.state, 2)
+        value = get(dic, uppercase(seq[j]), -1)
+        if value == -1
+            fill!(dest.state[:, j], 1.0)
+        else
+            dest.state[:, j] .= value
+        end
+    end
+    fill!(dest.scaling, 0.0)
 end
 function obs2partition!(dest::NucleotidePartition, seq::String)
     obs2partition!(dest, seq, nuc_dict)