open Bistro
open File_formats

type result = [
  | `Pcoc of [`pcoc] directory
  | `Pcoc_gamma of [`pcoc] directory
  | `Pcoc_C60 of [`pcoc] directory
  | `Diffsel of [`diffsel] directory
  | `Identical_LG of [`identical] directory
  | `Identical_WAG of [`identical] directory
  | `Topological_LG of [`topological] directory
  | `Topological_WAG of [`topological] directory
  | `Tdg09 of [`tdg09] directory
  | `Multinomial of cpt file
  | `Msd of [`msd] directory * float
]

val meth_string_of_result : result -> string

type dataset_res = {
  model_prefix : string ;
  tree_prefix : string ;
  dataset : Dataset.t ;
  res_by_tools: result list ;
  merged_results : cpt file ;
  plot_merged_results : svg file
}

val merge_results :
  ?fna_infos:text file ->
  res_by_tools : result list ->
  unit ->
  cpt file

val merge_result_tables :
  ?fna_infos:text file ->
  ?oracle:cpt file ->
  ?multinomial:cpt file ->
  ?tdg09:cpt file ->
  ?identical:cpt file ->
  ?topological:cpt file ->
  ?pcoc:cpt file ->
  ?pcoc_v2:cpt file ->
  ?pcoc_pcp:cpt file ->
  ?diffsel:cpt file ->
  ?diffseldsparse:cpt file ->
  unit ->
  cpt file

val plot_merge_results :
  ? t_choices : text file ->
  plot_all_sites: bool ->
  res_by_tools : result list ->
  tree:nhx file ->
  faa:aminoacid_fasta file ->
  tsv:cpt file ->
  unit ->
  svg file

val plot_convergent_sites :
  ?plot_all_sites:bool ->
  alignment:aminoacid_fasta file ->
  detection_results:cpt file ->
  tree:nhx file ->
  unit ->
  svg file

val recall_precision_curve :
  cpt file ->
  svg file

val oracle :
  n_h0:int ->
  n_ha:int ->
  cpt file

val recall_precision_auc_table :
  cpt file ->
  (string * float) list workflow