Detection_pipeline: added alignment_plot

lib/detection_pipeline.ml

@@ -79,6 +79,7 @@ module type S = sig
     query list ->
     Codepitk.Candidate_site.t list workflow
 
+  val alignment_plot : query -> svg file
 end
 
 module Make (Q : Query) = struct
@@ -343,4 +344,10 @@ module Make (Q : Query) = struct
     in
     Workflow.plugin ~descr:"detection_pipeline.ranking" f
 
+  let alignment_plot d =
+    Convergence_detection.plot_convergent_sites
+      ~tree:(Q.tree ~branch_length_unit:`Amino_acid d)
+      ~alignment:(amino_acid_alignment d)
+      ~detection_results:(multinomial_asymptotic_lrt d)
+      ()
 end

lib/detection_pipeline.mli

@@ -78,6 +78,8 @@ module type S = sig
     convergent_species:string list workflow ->
     query list ->
     Codepitk.Candidate_site.t list workflow
+
+  val alignment_plot : query -> svg file
 end
 
 module Make (Q : Query) : S with type query := Q.t

lib/simulation_pipeline.ml

@@ -62,13 +62,6 @@ let tree_workflow = function
 
 module Make(Q : Detection_pipeline.Query) = struct
   include Detection_pipeline.Make(Q)
-
-  let alignment_plot d =
-    Convergence_detection.plot_convergent_sites
-      ~tree:(Q.tree ~branch_length_unit:`Amino_acid d)
-      ~alignment:(amino_acid_alignment d)
-      ~detection_results:(multinomial_asymptotic_lrt d)
-      ()
 end
 
 module Mutsel_query = struct