kappa-library 4.1.3 (latest)

Compiled kappa model unit

module Transformation : sig ... end

Elementary rule transformations

type alg_expr = (Pattern.id array list, int) Alg_expr.e

type elementary_rule = {

rate : alg_expr Kappa_data_structures.Loc.annoted;
unary_rate : (alg_expr Kappa_data_structures.Loc.annoted * alg_expr option) option;
connected_components : Pattern.id array;
removed : Instantiation.abstract Transformation.t list;
inserted : Instantiation.abstract Transformation.t list;
delta_tokens : (alg_expr Kappa_data_structures.Loc.annoted * int) list;
syntactic_rule : int;
(*
0 means generated for perturbation.
*)
instantiations : Instantiation.abstract Instantiation.event;
(*
In the reverse order on purpose so that we rev_map when we concretize
*)

}

If unary_rate is Some _, rate means binary rate. Else rate is the rate independently of the connectivity

val extract_cc_ids : elementary_rule -> Pattern.id array

val extract_abstract_event : 
  elementary_rule ->
  Instantiation.abstract Instantiation.event

val rule_to_yojson : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  elementary_rule ->
  Yojson.Basic.t

val rule_of_yojson : 
  filenames:string array ->
  Yojson.Basic.t ->
  elementary_rule

val fully_specified_pattern_to_positive_transformations : 
  Pattern.cc ->
  Instantiation.concrete Transformation.t list

type 'alg_expr print_expr =

| Str_pexpr of string Kappa_data_structures.Loc.annoted
| Alg_pexpr of 'alg_expr Kappa_data_structures.Loc.annoted

val print_expr_to_yojson : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  ('a -> Yojson.Basic.t) ->
  ('b -> Yojson.Basic.t) ->
  ('a, 'b) Alg_expr.e print_expr ->
  Yojson.Basic.t

val print_expr_of_yojson : 
  filenames:string array ->
  (Yojson.Basic.t -> 'a) ->
  (Yojson.Basic.t -> 'b) ->
  Yojson.Basic.t ->
  ('a, 'b) Alg_expr.e print_expr

type din_kind =

| ABSOLUTE
| RELATIVE
| PROBABILITY

val din_kind_to_yojson : din_kind -> Yojson.Basic.t

val din_kind_of_yojson : Yojson.Basic.t -> din_kind

val write_din_kind : Buffer.t -> din_kind -> unit

Output a JSON value of type din_kind.

val string_of_din_kind : ?len:int -> din_kind -> string

Serialize a value of type din_kind into a JSON string.

parameter len
specifies the initial length of the buffer used internally. Default: 1024.

val read_din_kind : Yojson.Safe.lexer_state -> Lexing.lexbuf -> din_kind

Input JSON data of type din_kind.

val din_kind_of_string : string -> din_kind

Deserialize JSON data of type din_kind.

type modification =

| ITER_RULE of alg_expr Kappa_data_structures.Loc.annoted * elementary_rule
| UPDATE of int * alg_expr Kappa_data_structures.Loc.annoted
| SNAPSHOT of bool * alg_expr print_expr list
| STOP of alg_expr print_expr list
| CFLOW of string option * Pattern.id array * Instantiation.abstract Instantiation.test list list
(*
First string is the named used by the user
*)
| DIN of din_kind * alg_expr print_expr list
| DINOFF of alg_expr print_expr list
| CFLOWOFF of string option * Pattern.id array
| PLOTENTRY
| PRINT of alg_expr print_expr list * alg_expr print_expr list
| SPECIES of alg_expr print_expr list * Pattern.id array * Instantiation.abstract Instantiation.test list list
| SPECIES_OFF of alg_expr print_expr list

type perturbation = {

alarm : Kappa_data_structures.Nbr.t option;
precondition : (Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted;
effect : modification list;
repeat : (Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted;
needs_backtrack : bool;

}

val perturbation_to_yojson : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  perturbation ->
  Yojson.Basic.t

val perturbation_of_yojson : 
  filenames:string array ->
  Yojson.Basic.t ->
  perturbation

val exists_modification : (modification -> bool) -> perturbation array -> bool

val extract_connected_components_modifications : 
  modification list ->
  Pattern.id list

val extract_connected_components_bool : 
  (Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted ->
  Pattern.id list

val map_expr_rule : 
  (alg_expr Kappa_data_structures.Loc.annoted ->
    alg_expr Kappa_data_structures.Loc.annoted) ->
  elementary_rule ->
  elementary_rule

val map_expr_perturbation : 
  (alg_expr Kappa_data_structures.Loc.annoted ->
    alg_expr Kappa_data_structures.Loc.annoted) ->
  ((Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted ->
    (Pattern.id array list, int) Alg_expr.bool
      Kappa_data_structures.Loc.annoted) ->
  perturbation ->
  perturbation

val fold_expr_rule : 
  ('a -> alg_expr Kappa_data_structures.Loc.annoted -> 'a) ->
  'a ->
  elementary_rule ->
  'a

val fold_expr_perturbation : 
  ('a -> alg_expr Kappa_data_structures.Loc.annoted -> 'a) ->
  ('a ->
    (Pattern.id array list, int) Alg_expr.bool
      Kappa_data_structures.Loc.annoted ->
    'a) ->
  'a ->
  perturbation ->
  'a

package kappa-library