Biocaml 0.4-dev : Biocaml_mzData.Precursor

struct

 type t = {

  mslevel: int;

(** 1: MS, 2: MS/MS,... *)



  mz: float;

(** MassToChargeRatio *)



  z: float;

(** ChargeState *)



  int: float;

(** Intensity *)



 }



 (* Commission of atomic weights and isotopic abondance *)

 let mass_proton = 1.00727646677 (* Dalton *)



 let mass p = (p.mz -. mass_proton) *. p.z



 (* Get <ionSelection> content. FIXME: the spec does not define which

   param. should be present. *)

 let rec get_ionSelection xml p depth =

  match Xmlm.input xml with

  | `El_start((_, "cvParam"), attr) ->

   let depth = depth + 1 in (* for </cvParam> *)

   let name = attribute_exn "name" attr in

   let value = attribute_exn "value" attr in

   if name = "MassToChargeRatio" then

    get_ionSelection xml { p with mz = Float.of_string value } depth

   else if name = "ChargeState" then

    get_ionSelection xml { p with z = Float.of_string value } depth

   else if name = "Intensity" then

    get_ionSelection xml { p with int = Float.of_string value } depth

   else

    get_ionSelection xml p depth

  | `El_start _ -> get_ionSelection xml p (depth + 1)

  | `El_end -> if depth = 0 then p (* </ionSelection> *)

        else get_ionSelection xml p (depth - 1)

  | `Data _ | `Dtd _ -> get_ionSelection xml p depth (* skip *)



 let rec get_precursor xml p =

  match Xmlm.input xml with

  | `El_start((_, "ionSelection"), _) -> get_ionSelection xml p 0

  | `El_start _ -> skip_tag xml; get_precursor xml p (* <activation> *)

  | `El_end -> p (* </precursor> *)

  | `Data _ | `Dtd _ -> get_precursor xml p



 (* Knowing that <precursorList> was just read, parse the [xml] to

   get the list of precursors. *)

 let rec add_list xml pl =

  match Xmlm.input xml with

  | `El_start((_, "precursor"), attr) ->

   let mslevel = int_of_string(attribute_exn "msLevel" attr) in

   let p = get_precursor xml { mslevel; mz = Float.nan; z = Float.nan; int = Float.nan } in

   add_list xml (p :: pl)

  | `El_start _ -> skip_tag xml; add_list xml pl

  | `El_end -> pl           (* </precursorList> *)

  | `Data _ | `Dtd _ -> add_list xml pl



 let list xml = add_list xml []

end