Module Primitives

module Primitives: sig .. end
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 Locality.annot;
   unary_rate : (alg_expr Locality.annot * 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 Locality.annot * 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 Mods.StringMap.t ->
elementary_rule -> Yojson.Basic.json
val rule_of_yojson : filenames:string array -> Yojson.Basic.json -> elementary_rule
type 'alg_expr print_expr = 
| Str_pexpr of string Locality.annot
| Alg_pexpr of 'alg_expr Locality.annot
val print_expr_to_yojson : filenames:int Mods.StringMap.t ->
('a -> Yojson.Basic.json) ->
('b -> Yojson.Basic.json) ->
('a, 'b) Alg_expr.e print_expr -> Yojson.Basic.json
val print_expr_of_yojson : filenames:string array ->
(Yojson.Basic.json -> 'a) ->
(Yojson.Basic.json -> 'b) ->
Yojson.Basic.json -> ('a, 'b) Alg_expr.e print_expr
type flux_kind = 
| ABSOLUTE
| RELATIVE
| PROBABILITY
val flux_kind_to_yojson : flux_kind -> Yojson.Basic.json
val flux_kind_of_yojson : Yojson.Basic.json -> flux_kind
val write_flux_kind : Bi_outbuf.t -> flux_kind -> unit
Output a JSON value of type Primitives.flux_kind.
val string_of_flux_kind : ?len:int -> flux_kind -> string
Serialize a value of type Primitives.flux_kind into a JSON string.
len : specifies the initial length of the buffer used internally. Default: 1024.
val read_flux_kind : Yojson.Safe.lexer_state -> Lexing.lexbuf -> flux_kind
Input JSON data of type Primitives.flux_kind.
val flux_kind_of_string : string -> flux_kind
Deserialize JSON data of type Primitives.flux_kind.
type modification = 
| ITER_RULE of alg_expr Locality.annot * elementary_rule
| UPDATE of int * alg_expr Locality.annot
| SNAPSHOT of 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
*)
| FLUX of flux_kind * alg_expr print_expr list
| FLUXOFF 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 : Nbr.t option;
   precondition : (Pattern.id array list, int) Alg_expr.bool Locality.annot;
   effect : modification list;
   repeat : (Pattern.id array list, int) Alg_expr.bool Locality.annot;
}
val perturbation_to_yojson : filenames:int Mods.StringMap.t ->
perturbation -> Yojson.Basic.json
val perturbation_of_yojson : filenames:string array -> Yojson.Basic.json -> 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 Locality.annot -> Pattern.id list
val map_expr_rule : (alg_expr Locality.annot -> alg_expr Locality.annot) ->
elementary_rule -> elementary_rule
val map_expr_perturbation : (alg_expr Locality.annot -> alg_expr Locality.annot) ->
((Pattern.id array list, int) Alg_expr.bool Locality.annot ->
(Pattern.id array list, int) Alg_expr.bool Locality.annot) ->
perturbation -> perturbation
val stops_of_perturbation : Operator.DepSet.t * Operator.DepSet.t * Operator.DepSet.t array *
Operator.DepSet.t array ->
perturbation -> (Nbr.t option * Nbr.t) list