Source file newick.ml
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open Core
include Newick_ast
module I = Newick_parser.MenhirInterpreter
let message_of_env env =
try
match I.top env with
| Some (I.Element (s, _, _, _)) ->
I.number s
|> Newick_parser_errors.message
|> Option.return
| None -> None
with Stdlib.Not_found -> None
let fail lexbuf (checkpoint : t I.checkpoint) =
match checkpoint with
| I.HandlingError env ->
let msg =
match message_of_env env with
| Some msg -> msg
| None -> "Syntax error"
in
Error (mkerror lexbuf msg)
| _ -> assert false
let loop lexbuf result =
let supplier = I.lexer_lexbuf_to_supplier Newick_lexer.token lexbuf in
I.loop_handle Result.return (fail lexbuf) supplier result
let parse lexbuf =
try loop lexbuf (Newick_parser.Incremental.start lexbuf.lex_curr_p)
with
| Newick_lexer.Error (`Newick_parser_error e) ->
Error (`Newick_parser_error e)
let from_file fn =
In_channel.with_file fn ~f:(fun ic ->
parse (Lexing.from_channel ic)
)
let from_file_exn fn =
from_file fn
|> Result.map_error ~f:string_of_error
|> Result.ok_or_failwith
let from_string s =
parse (Lexing.from_string s)
let from_string_exn s =
from_string s
|> Result.map_error ~f:string_of_error
|> Result.ok_or_failwith
let rec unparse ({ name ; children ; tags ; parent_branch } : t) =
let name = Option.value ~default:"" name
and tags = match tags with
| [] -> ""
| xs -> List.map xs ~f:unparse_tag
|> String.concat
|> sprintf "[&&NHX%s]"
in
let children = match children with
| [] -> ""
| xs ->
List.map xs ~f:unparse
|> String.concat ~sep:","
|> sprintf "(%s)"
in
let parent_branch = Option.value_map parent_branch ~default:""
~f:(fun length ->
Float.to_string_hum length ~decimals:12 ~strip_zero:true
|> sprintf ":%s")
in
children ^ name ^ parent_branch ^ tags
and unparse_tag (k, v) = sprintf ":%s=%s" k v
let to_string t = unparse t ^ ";"
let to_file t fn =
Out_channel.write_all fn ~data:(to_string t)
let of_tree
?(node_id = Fn.const None) ?(node_tags = Fn.const [])
?(leaf_id = Fn.const None) ?(leaf_tags = Fn.const [])
?(branch_length = Fn.const None)
?parent_branch tree : t =
let rec node ?parent_branch = function
| Tree.Node { data ; branches } -> {
name = node_id data ; tags = node_tags data ; parent_branch ;
children = List1.map branches ~f:branch |> List1.to_list
}
| Tree.Leaf l ->
{ name = leaf_id l ; tags = leaf_tags l ; parent_branch ; children = [] }
and branch (Branch b) = node ?parent_branch:(branch_length b.data) b.tip
in
node ?parent_branch tree
let test_string_equal x y =
let b = String.(x = y) in
if not b then fprintf stderr "expected: %s\ngot %s\n" x y ;
b
let%test "parse . unparse is identity" =
let data = "(Chrysithr:3.1[&&NHX:Condition=0],((((((((((((((((((Ele.bald:9[&&NHX:Condition=1],Ele.bal2:6[&&NHX:Condition=1]):1[&&NHX:Condition=1],Ele.bal4:6[&&NHX:Condition=1]):1[&&NHX:Condition=1],(Ele.vivi:8[&&NHX:Condition=1],Ele.vivA:6[&&NHX:Condition=1]):3[&&NHX:Condition=1]):50[&&NHX:Condition=1:Transition=1],Ele.bal3:14[&&NHX:Condition=0]):3[&&NHX:Condition=0],Ele.viv2:9[&&NHX:Condition=0]):27[&&NHX:Condition=0],Ele.fici:17[&&NHX:Condition=0]):1[&&NHX:Condition=0],(Ele.grac:3[&&NHX:Condition=0],Ele.lim2:6[&&NHX:Condition=0]):13[&&NHX:Condition=0]):3[&&NHX:Condition=0],(Ele.rost:22[&&NHX:Condition=0],((Ele.limo:4[&&NHX:Condition=0],Ele.pal2:2[&&NHX:Condition=0]):11[&&NHX:Condition=0],(Ele.acut:10[&&NHX:Condition=0],(Ele.palu:6[&&NHX:Condition=0],(Ele.gra2:3[&&NHX:Condition=0],Ele.lim3:2[&&NHX:Condition=0]):0[&&NHX:Condition=0]):4[&&NHX:Condition=0]):5[&&NHX:Condition=0]):8[&&NHX:Condition=0]):2[&&NHX:Condition=0]):2[&&NHX:Condition=0],Ele.geni:27[&&NHX:Condition=0]):10[&&NHX:Condition=0],Ele.quan:33[&&NHX:Condition=0]):32[&&NHX:Condition=0],((Abildgaar:24[&&NHX:Condition=0],Bulbostyl:0.103[&&NHX:Condition=1:Transition=1]):4[&&NHX:Condition=0],(Actinosch:15[&&NHX:Condition=0],(Fimb.lit:16[&&NHX:Condition=0],((Fimb.dic:11[&&NHX:Condition=0],Fimb.fe2:4[&&NHX:Condition=0]):6[&&NHX:Condition=0],(Fimb.li2:46[&&NHX:Condition=1],(Fimb.di2:9[&&NHX:Condition=1],Fimb.fer:4[&&NHX:Condition=1]):17[&&NHX:Condition=1]):66[&&NHX:Condition=1:Transition=1]):2[&&NHX:Condition=0]):34[&&NHX:Condition=0]):19[&&NHX:Condition=0]):28[&&NHX:Condition=0]):10[&&NHX:Condition=0],(Bolboscho:49[&&NHX:Condition=0],((Fuir.abn:19[&&NHX:Condition=0],Fuir.umb:36[&&NHX:Condition=0]):10[&&NHX:Condition=0],(((Scho.lac:4[&&NHX:Condition=0],Scho.val:1[&&NHX:Condition=0]):43[&&NHX:Condition=0],Scho.muc:42[&&NHX:Condition=0]):11[&&NHX:Condition=0],((((Hellmut1:14[&&NHX:Condition=0],Isolepis:25[&&NHX:Condition=0]):9[&&NHX:Condition=0],Hellmut2:31[&&NHX:Condition=0]):7[&&NHX:Condition=0],Scirpoid:29[&&NHX:Condition=0]):4[&&NHX:Condition=0],(Cyp.spha:45[&&NHX:Condition=0],(Cyp.alt3:30[&&NHX:Condition=0],(Cyp.era6:35[&&NHX:Condition=0],((Cyp.era1:19[&&NHX:Condition=0],Cyp.fusc:20[&&NHX:Condition=0]):11[&&NHX:Condition=0],(Cyp.pulc:22[&&NHX:Condition=0],(Cyp.capi:10[&&NHX:Condition=1],(Volkiell:62[&&NHX:Condition=1],(Cyp.ust2:7[&&NHX:Condition=1],(Remirea:13[&&NHX:Condition=1],(Cyp.iria:11[&&NHX:Condition=1],((Killinga:0.217[&&NHX:Condition=1],Pycreus:29[&&NHX:Condition=1]):43[&&NHX:Condition=1],((Cyp.long:4[&&NHX:Condition=1],Cyp.rotu:5[&&NHX:Condition=1]):9[&&NHX:Condition=1],(Cyp.papy:13[&&NHX:Condition=1],Cyp.ustu:8[&&NHX:Condition=1]):4[&&NHX:Condition=1]):1[&&NHX:Condition=1]):4[&&NHX:Condition=1]):31[&&NHX:Condition=1]):2[&&NHX:Condition=1]):5[&&NHX:Condition=1]):1[&&NHX:Condition=1]):48[&&NHX:Condition=1:Transition=1]):4[&&NHX:Condition=0]):1[&&NHX:Condition=0]):5[&&NHX:Condition=0]):5[&&NHX:Condition=0]):12[&&NHX:Condition=0]):29[&&NHX:Condition=0]):4[&&NHX:Condition=0]):3[&&NHX:Condition=0]):9[&&NHX:Condition=0]):4[&&NHX:Condition=0],(Blysmus:31[&&NHX:Condition=0],((Eriophor:5[&&NHX:Condition=0],Scirpus:9[&&NHX:Condition=0]):14[&&NHX:Condition=0],(((Schoenox:22[&&NHX:Condition=0],Uncin.un:18[&&NHX:Condition=0]):15[&&NHX:Condition=0],Uncin.ph:25[&&NHX:Condition=0]):11[&&NHX:Condition=0],(Carex.com:4[&&NHX:Condition=0],(Carex.hal:10[&&NHX:Condition=0],(Carex.ber:8[&&NHX:Condition=0],Carex.pen:3[&&NHX:Condition=0]):3[&&NHX:Condition=0]):1[&&NHX:Condition=0]):20[&&NHX:Condition=0]):37[&&NHX:Condition=0]):15[&&NHX:Condition=0]):21[&&NHX:Condition=0]):5[&&NHX:Condition=0],((Rhy.alba:26[&&NHX:Condition=0],Rhy.grac:45[&&NHX:Condition=0]):21[&&NHX:Condition=0],(Rhy.albi:11[&&NHX:Condition=0],(Rhy.rubr:8[&&NHX:Condition=1],(Rhy.glob:32[&&NHX:Condition=1],Rhy.glo2:19[&&NHX:Condition=1]):11[&&NHX:Condition=1]):31[&&NHX:Condition=1:Transition=1]):59[&&NHX:Condition=0]):17[&&NHX:Condition=0]):20[&&NHX:Condition=0],Carpha:79[&&NHX:Condition=0]):8[&&NHX:Condition=0],(Schoenus:64[&&NHX:Condition=0],(Baumea:18[&&NHX:Condition=0],Machaeri:5[&&NHX:Condition=0]):43[&&NHX:Condition=0]):32[&&NHX:Condition=0]):16[&&NHX:Condition=0],Cladium:78[&&NHX:Condition=0]):13[&&NHX:Condition=0],(Coleochlo:111[&&NHX:Condition=0],Microdra:57[&&NHX:Condition=0]):80[&&NHX:Condition=0]):38[&&NHX:Condition=0])[&&NHX:Condition=0];" in
test_string_equal data (to_string (from_string_exn data))
module Tree_repr = struct
type ast = t
type node_info = {
name : string option ;
tags : tag list ;
}
type tree = (node_info, node_info, float option) Tree.t
type branch = (node_info, node_info, float option) Tree.branch
type t =
| Tree of tree
| Branch of branch
let of_ast newick =
let rec node ({name ; tags ; children ; _} : ast) =
match children with
| [] ->
Tree.leaf { name ; tags }
| children ->
let branches = List.map children ~f:branch in
Tree.node { name ; tags } (List1.of_list_exn branches)
and branch ({ parent_branch ; _ } as tree : ast) =
let tip = node tree in
Tree.branch parent_branch tip
in
match newick.parent_branch with
| None -> Tree (node newick)
| Some _ -> Branch (branch newick)
let ast_of_tree ?parent_branch (tree_repr : tree) =
of_tree tree_repr
?parent_branch
~node_id:(fun { name ; _} -> name)
~node_tags:(fun { tags ; _ } -> tags)
~leaf_id:(fun { name ; _} -> name)
~leaf_tags:(fun { tags ; _ } -> tags)
~branch_length:(Fn.id)
let to_ast = function
| Tree t -> ast_of_tree t
| Branch (Tree.Branch b) -> ast_of_tree ?parent_branch:b.data b.tip
let map_inner_tree tree ~f =
match tree with
| Tree t -> Tree (f t)
| Branch (Branch { tip ; data }) ->
Branch (Tree.branch data (f tip))
let with_inner_tree tree ~f =
match tree with
| Tree t
| Branch (Branch { tip = t ; _ }) -> f t
end