moved pair_tree workflow definition to simulation dataset

lib/mutsel_simulator.ml

@@ -61,27 +61,3 @@ let fitness_histogram sim =
     OCamlR_grDevices.dev_off ()
   in
   Workflow.path_plugin ~descr:"simulator.fitness_histogram" f
-
-let pair_tree ~branch_length1 ~branch_length2 ~npairs =
-  let f = fun%workflow dest ->
-    let open Phylogenetics in
-    let branch_length1, branch_length2, npairs = [%param branch_length1, branch_length2, npairs] in
-    let leaf name = Tree.leaf { Newick_ast.name = Some name } in
-    let branch ~length ~condition tip =
-      let tags = match condition with
-        | `Ancestral -> ["Condition", "0"]
-        | `Convergent -> ["Condition", "1" ; "Transition", "1"]
-      in
-      Tree.branch { Newick_ast.length = Some length ; tags } tip in
-    let make_pair i =
-      Tree.binary_node { Newick_ast.name = None }
-        (branch ~length:branch_length2 ~condition:`Ancestral (leaf (sprintf "A%d" i)))
-        (branch ~length:branch_length2 ~condition:`Convergent (leaf (sprintf "C%d" i)))
-      |> branch ~length:branch_length1 ~condition:`Ancestral
-    in
-    let tree =
-      Newick.Tree (Tree.node { Newick_ast.name = None } (List1.init npairs ~f:make_pair))
-    in
-    Newick.to_file tree dest
-  in
-  Workflow.path_plugin ~descr:"simulator.pair_tree" f

lib/mutsel_simulator.mli

@@ -21,8 +21,3 @@ val alignment_of_simulation :
 val fitness_histogram :
   Mutsel_simulator.Site_independent.simulation workflow ->
   pdf file
-
-val pair_tree :
-  branch_length1:float ->
-  branch_length2:float ->
-  npairs:int -> nhx file

lib/simulation_pipeline.ml

@@ -9,11 +9,7 @@ let calc_fixed_seed ~(str:string) (seed:int) : int =
 
 type tree =
   | NHX of nhx file
-  | Pair_tree of {
-      npairs : int ;
-      branch_length1 : float ;
-      branch_length2 : float ;
-    }
+  | Convergence_tree of Codepitk.Convergence_tree.t workflow
 
 let nhx_of_convergence_tree tree =
   let f = fun%workflow dest ->
@@ -36,6 +32,19 @@ let nhx_of_convergence_tree tree =
   in
   Workflow.path_plugin ~descr:"nhx_of_convergence_tree" f
 
+let pair_tree ~branch_length1 ~branch_length2 ~npairs =
+  let leaf_info i c =
+    sprintf "%c%d"
+      (match c with `Convergent -> 'C' | `Ancestral -> 'A')
+      i
+  in
+  Convergence_tree (
+    Codepitk.Convergence_tree.pair_tree
+      ~leaf_info ~node_info:()
+      ~branch_length1 ~branch_length2 ~npairs
+    |> Workflow.data
+  )
+
 module type S = sig
   type query
 
@@ -47,10 +56,8 @@ end
 
 let tree_workflow = function
   | NHX w -> w
-  | Pair_tree { branch_length1 ;
-                branch_length2 ;
-                npairs } ->
-    Mutsel_simulator.pair_tree ~branch_length1 ~branch_length2 ~npairs
+  | Convergence_tree w ->
+    nhx_of_convergence_tree w
 
 module Make(Q : Detection_pipeline.Query) = struct
   include Detection_pipeline.Make(Q)

lib/simulation_pipeline.mli

@@ -3,16 +3,17 @@ open File_formats
 
 type tree =
   | NHX of nhx file
-  | Pair_tree of {
-      npairs : int;
-      branch_length1 : float;
-      branch_length2 : float;
-    }
+  | Convergence_tree of Codepitk.Convergence_tree.t workflow
 
 val nhx_of_convergence_tree :
   Codepitk.Convergence_tree.t workflow ->
   nhx file
 
+val pair_tree :
+  branch_length1:float ->
+  branch_length2:float ->
+  npairs:int -> tree
+
 module type S = sig
   type query