Commit f3ec331f authored by Philippe Veber's avatar Philippe Veber
Browse files

tk/Tdg09: expose default implementation

parent 87b4f2e6
...@@ -417,10 +417,12 @@ module Make(Branch_info : Branch_info)(Leaf_info : Leaf_info)(Site : Site with t ...@@ -417,10 +417,12 @@ module Make(Branch_info : Branch_info)(Leaf_info : Leaf_info)(Site : Site with t
end end
end end
module Implementation_check = struct module Pack = struct
type leaf_info = int * Convergence_tree.condition
module Leaf_info = struct module Leaf_info = struct
type species = int type species = int
type t = species * Convergence_tree.condition type t = leaf_info
let condition = snd let condition = snd
let species = fst let species = fst
end end
...@@ -451,6 +453,10 @@ module Implementation_check = struct ...@@ -451,6 +453,10 @@ module Implementation_check = struct
|> branch branch_length1 `Ancestral |> branch branch_length1 `Ancestral
in in
Tree.node () (List1.init npairs ~f:make_pair) Tree.node () (List1.init npairs ~f:make_pair)
end
module Implementation_check = struct
open Pack
let likelihood_plot_demo (wag : Wag.t) = let likelihood_plot_demo (wag : Wag.t) =
let tree = pair_tree ~branch_length1:1. ~branch_length2:1. ~npairs:100 in let tree = pair_tree ~branch_length1:1. ~branch_length2:1. ~npairs:100 in
......
...@@ -124,13 +124,29 @@ module Make(Branch_info : Branch_info)(Leaf_info : Leaf_info)(Site : Site with t ...@@ -124,13 +124,29 @@ module Make(Branch_info : Branch_info)(Leaf_info : Leaf_info)(Site : Site with t
and type leaf_info := Leaf_info.t and type leaf_info := Leaf_info.t
and type branch_info := Branch_info.t and type branch_info := Branch_info.t
module Implementation_check : sig module Pack : sig
include S with type site := Amino_acid.t array type leaf_info = int * Convergence_tree.condition
and type leaf_info := int * Convergence_tree.condition
and type branch_info := Convergence_tree.Branch_info.t module Leaf_info : Leaf_info with type t = leaf_info
and type species = int
module Site : Site with type species = int
and type t = Amino_acid.t array
include module type of Make(Convergence_tree.Branch_info)(Leaf_info)(Site)
val simulate_profile : float -> Amino_acid.vector val simulate_profile : float -> Amino_acid.vector
val pair_tree :
branch_length1:float ->
branch_length2:float ->
npairs:int ->
(unit, leaf_info, Convergence_tree.branch_info) Tree.t
end
module Implementation_check : sig
open Pack
val likelihood_plot_demo : Wag.t -> unit val likelihood_plot_demo : Wag.t -> unit
val lrt_1_vs_2_null_simulation : val lrt_1_vs_2_null_simulation :
......
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