tk: moved pair_tree generation to Convergence_tree

lib/tk/convergence_tree.ml

@@ -237,3 +237,15 @@ let alignment_counts_map tree alignment f =
   let site i = f (counts seqs0 i) (counts seqs1 i) in
   let n = Alignment.ncols alignment in
   List.init n ~f:site
+
+let pair_tree ~node_info ~leaf_info ~branch_length1 ~branch_length2 ~npairs =
+  let leaf i cond = Tree.Leaf (leaf_info i cond) in
+  let branch length condition tip = Tree.branch { length ; condition } tip in
+  let tree = Tree.binary_node node_info in
+  let make_pair i =
+    tree
+      (branch branch_length2 `Ancestral (leaf (2 * i) `Ancestral))
+      (branch branch_length2 `Convergent (leaf (2 * i + 1) `Convergent))
+    |> branch branch_length1 `Ancestral
+  in
+  Tree.node node_info  (List1.init npairs ~f:make_pair)

lib/tk/convergence_tree.mli

@@ -41,3 +41,11 @@ val alignment_counts_map :
   Alignment.t ->
   (int Amino_acid.table -> int Amino_acid.table -> 'a) ->
   'a list
+
+val pair_tree :
+  node_info:'n ->
+  leaf_info:(int -> condition -> 'l) ->
+  branch_length1:float ->
+  branch_length2:float ->
+  npairs:int ->
+  ('n, 'l, branch_info) Phylogenetics.Tree.t

lib/tk/tdg09.ml

@@ -442,17 +442,10 @@ module Pack = struct
     Owl.Stats.dirichlet_rvs ~alpha:(Array.create ~len:Amino_acid.card alpha)
     |> Amino_acid.Vector.of_array_exn
 
-  let pair_tree ~branch_length1 ~branch_length2 ~npairs =
-    let leaf i cond = Tree.Leaf (i, cond) in
-    let branch length condition tip = Tree.branch { Convergence_tree.length ; condition } tip in
-    let tree = Tree.binary_node () in
-    let make_pair i =
-      tree
-        (branch branch_length2 `Ancestral (leaf (2 * i) `Ancestral))
-        (branch branch_length2 `Convergent (leaf (2 * i + 1) `Convergent))
-      |> branch branch_length1 `Ancestral
-    in
-    Tree.node ()  (List1.init npairs ~f:make_pair)
+  let pair_tree =
+    let leaf_info i cond = (i, cond) in
+    let node_info = () in
+    Convergence_tree.pair_tree ~leaf_info ~node_info
 end
 
 module Implementation_check = struct