Simulation_dataset: renaming

app/diffseldsparse_benchmark.ml

@@ -4,7 +4,7 @@ open Codepi
 let main ~n_h0 ~n_ha ~seed:i () =
   let open Simulation_dataset in
   let sim =
-    bppseqgen_mixed_simulation
+    bppseqgen_mixed
       ~tree:(NHX (Bistro.Workflow.input "example/trees_analyses/cyp_coding.Chrysithr_root.nhx"))
       ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
       ~n_h0 ~n_ha ~ne_s:4. ~seed:i ()

lib/simulation_dataset.ml

@@ -22,7 +22,7 @@ let tree_workflow = function
                 npairs } ->
     Simulator.pair_tree ~branch_length1 ~branch_length2 ~npairs
 
-module Convdet_simulation_param = struct
+module Mutsel_param = struct
   type t = {
     tree : tree ;
     branch_scale : float ;
@@ -52,7 +52,7 @@ module Convdet_simulation_param = struct
 end
 
 type t =
-  | Bppseqgen_simulation of {
+  | Bppseqgen of {
       hypothesis : Convergence_hypothesis.t ;
       tree : tree ;
       profiles : string ;
@@ -67,9 +67,9 @@ type t =
       n_ha : int ;
       ne_s : float ;
     }
-  | Convdet_simulation of Convdet_simulation_param.t
+  | Mutsel of Mutsel_param.t
 
-let bppseqgen_mixed_simulation ?(ne_s = 1.) ?(seed = 0) ~tree ~profiles ~n_h0 ~n_ha () =
+let bppseqgen_mixed ?(ne_s = 1.) ?(seed = 0) ~tree ~profiles ~n_h0 ~n_ha () =
   Bppseqgen_mixed {
     tree ;
     profiles ;
@@ -79,8 +79,8 @@ let bppseqgen_mixed_simulation ?(ne_s = 1.) ?(seed = 0) ~tree ~profiles ~n_h0 ~n
     ne_s ;
   }
 
-let bppseqgen_simulation ~hyp ~tree ~profiles ~nb_sites ~seed =
-  Bppseqgen_simulation {
+let bppseqgen ~hyp ~tree ~profiles ~nb_sites ~seed =
+  Bppseqgen {
     hypothesis = hyp ;
     tree ;
     profiles ;
@@ -88,21 +88,21 @@ let bppseqgen_simulation ~hyp ~tree ~profiles ~nb_sites ~seed =
     seed ;
   }
 
-let convdet_simulation ?branch_scale ?ne_s ?gBGC ?seed ~tree ~profiles ~n_h0 ~n_ha () =
-  Convdet_simulation (Convdet_simulation_param.make ?branch_scale ?ne_s ?gBGC ?seed ~tree ~profiles ~n_h0 ~n_ha ())
+let mutsel ?branch_scale ?ne_s ?gBGC ?seed ~tree ~profiles ~n_h0 ~n_ha () =
+  Mutsel (Mutsel_param.make ?branch_scale ?ne_s ?gBGC ?seed ~tree ~profiles ~n_h0 ~n_ha ())
 
-let convdet_simulation_of_param p = Convdet_simulation p
+let of_mutsel_param p = Mutsel p
 
 let tree ~branch_length_unit:_ = function
-  | Bppseqgen_simulation { tree ; _ }
+  | Bppseqgen { tree ; _ }
   | Bppseqgen_mixed { tree ; _ }
-  | Convdet_simulation { tree ; _ } ->
+  | Mutsel { tree ; _ } ->
     tree_workflow tree
 
 let seed = function
   | Bppseqgen_mixed s -> s.seed
-  | Bppseqgen_simulation s -> s.seed
-  | Convdet_simulation s -> s.seed
+  | Bppseqgen s -> s.seed
+  | Mutsel s -> s.seed
 
 let profile ~nb_sites ~profiles ~seed =
   Profile.profile_l_of_splitted_profile
@@ -111,7 +111,7 @@ let profile ~nb_sites ~profiles ~seed =
     profiles
     ~seed:(calc_fixed_seed ~str:profiles seed)
 
-let bppseqgen sim ~hypothesis ~nb_sites ~profiles =
+let bppseqgen_simulation sim ~hypothesis ~nb_sites ~profiles =
   let model_prefix = Convergence_hypothesis.string_of_model hypothesis in
   let descr = sprintf ".%s" model_prefix in
   let profile = profile ~nb_sites ~profiles ~seed:(seed sim) in
@@ -123,15 +123,15 @@ let bppseqgen sim ~hypothesis ~nb_sites ~profiles =
     ~hypothesis ~profile_f ~profile_c ~seed:(seed sim)
 
 let rec nucleotide_alignment = function
-  | Bppseqgen_simulation { hypothesis ; nb_sites ; profiles ; _ } as sim ->
-    bppseqgen sim ~hypothesis ~nb_sites ~profiles
+  | Bppseqgen { hypothesis ; nb_sites ; profiles ; _ } as sim ->
+    bppseqgen_simulation sim ~hypothesis ~nb_sites ~profiles
     |> Bppsuite.Bppseqgen.alignment
   | Bppseqgen_mixed { profiles ; seed ; n_h0 ; n_ha ; ne_s ; tree } ->
-    let h0 = nucleotide_alignment (Bppseqgen_simulation { hypothesis = H0 (Fixed ne_s) ; profiles ; seed ; nb_sites = n_h0 ; tree }) in
-    let ha = nucleotide_alignment (Bppseqgen_simulation { hypothesis = HaPC (Fixed ne_s) ; profiles ; seed ; nb_sites = n_ha ; tree }) in
+    let h0 = nucleotide_alignment (Bppseqgen { hypothesis = H0 (Fixed ne_s) ; profiles ; seed ; nb_sites = n_h0 ; tree }) in
+    let ha = nucleotide_alignment (Bppseqgen { hypothesis = HaPC (Fixed ne_s) ; profiles ; seed ; nb_sites = n_ha ; tree }) in
     Utils.fasta_cappend h0 ha
-  | Convdet_simulation param ->
-    Convdet_simulation_param.simulation param
+  | Mutsel param ->
+    Mutsel_param.simulation param
     |> Simulator.alignment_of_simulation
 
 include Detection_pipeline.Make(struct
@@ -150,13 +150,13 @@ let alignment_plot d =
 let oracle d =
   let n_h0, n_ha =
     match d with
-    | Bppseqgen_simulation { nb_sites ; hypothesis ; _ } -> (
+    | Bppseqgen { nb_sites ; hypothesis ; _ } -> (
         match hypothesis with
         | H0 _ -> nb_sites, 0
         | HaPC _ | HaPCOC _ -> 0, nb_sites
       )
     | Bppseqgen_mixed { n_h0 ; n_ha ; _ }
-    | Convdet_simulation { n_h0 ; n_ha ; _ } -> n_h0, n_ha
+    | Mutsel { n_h0 ; n_ha ; _ } -> n_h0, n_ha
   in
   Convergence_detection.oracle ~n_h0 ~n_ha
 
@@ -353,7 +353,7 @@ let explore_params ~(f: param_t -> _) =
 
 let simu_of_param ?n_h0:(n_h0=50) (p: param_t) =
   let bf, gbgc = p in
-  convdet_simulation
+  mutsel
     ~tree:(NHX (Workflow.input "example/trees_analyses/C4AmaranthaceaePolyroot.nhx"))
     ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
     ~branch_scale:bf

lib/simulation_dataset.mli

@@ -11,7 +11,7 @@ type tree =
 
 type t
 
-val bppseqgen_mixed_simulation :
+val bppseqgen_mixed :
   ?ne_s:float ->
   ?seed:int ->
   tree:tree ->
@@ -21,7 +21,7 @@ val bppseqgen_mixed_simulation :
   unit ->
   t
 
-val bppseqgen_simulation :
+val bppseqgen :
   hyp:Convergence_hypothesis.t ->
   tree:tree ->
   profiles:string ->
@@ -29,7 +29,7 @@ val bppseqgen_simulation :
   seed:int ->
   t
 
-module Convdet_simulation_param : sig
+module Mutsel_param : sig
   type t
   val make :
     ?branch_scale:float ->
@@ -47,7 +47,7 @@ module Convdet_simulation_param : sig
     Codepitk.Simulator.Site_independent_mutsel.simulation workflow
 end
 
-val convdet_simulation :
+val mutsel :
   ?branch_scale:float ->
   ?ne_s:float * float ->
   ?gBGC:float * float ->
@@ -59,7 +59,7 @@ val convdet_simulation :
   unit ->
   t
 
-val convdet_simulation_of_param : Convdet_simulation_param.t -> t
+val of_mutsel_param : Mutsel_param.t -> t
 
 include Detection_pipeline.Query with type t := t