File_format: nhx special case of newick

lib/file_formats.ml

@@ -5,16 +5,16 @@ class type bimbam = object
   method format : [`bimbam]
 end
 
-class type nhx = object
-  inherit text
-  method format : [`nhx]
-end
-
 class type newick = object
   inherit text
   method format : [`newick]
 end
 
+class type nhx = object
+  inherit newick
+  method newick_variant : [`nhx]
+end
+
 class type phylip = object
   inherit text
   method format : [`phylip]

lib/orthomam.ml

@@ -3,7 +3,7 @@ open Bistro
 open File_formats
 open Codepitk
 
-let ensembl_tree : nhx file =
+let ensembl_tree : newick file =
   Bistro_unix.wget "ftp://ftp.ensembl.org/pub/release-99/compara/species_trees/vertebrates_species-tree_Ensembl.nh"
 
 type alignment = Alignment of Orthomam_db.t * Orthomam_db.alignment
@@ -460,7 +460,7 @@ let%pworkflow convergence_species_tree_pdf ~convergent_species db =
   |> Biotk_croquis.Croquis.Layout.simple
   |> Fn.flip Biotk_croquis.Croquis.Layout.render_pdf [%dest]
 
-let%workflow ranking_of_results ~alignment_ids ~convergent_species (alignments : aminoacid_fasta file list) (trees : newick file list) result_files ~column_label =
+let%workflow ranking_of_results ~alignment_ids ~convergent_species (alignments : aminoacid_fasta file list) (trees : #newick file list) result_files ~column_label =
   let ranking_size = 1_000 in
   let column_label = [%param column_label] in
   let alignment_ids = Array.of_list [%param alignment_ids] in

lib/orthomam.mli

@@ -36,11 +36,11 @@ val species_with_echolocation : string list
 
 val prestin : Orthomam_db.t -> query
 
-val ensembl_tree : nhx file
+val ensembl_tree : newick file
 
 val compare_tree_branch_lengths :
-  newick file ->
-  newick file ->
+  nhx file ->
+  nhx file ->
   pdf file
 
 val number_of_missing_sequences_repartition :