LKappa (kappa-library.Kappa

type ('a, 'annoted) link =

| ANY_FREE
| LNK_VALUE of int * 'annoted
| LNK_FREE
| LNK_ANY
| LNK_SOME
| LNK_TYPE of 'a * 'a
(*
port * agent_type
*)

type switching =

| Linked of int
| Freed
| Maintained
| Erased

type rule_internal =

| I_ANY
| I_ANY_CHANGED of int
| I_ANY_ERASED
| I_VAL_CHANGED of int * int
| I_VAL_ERASED of int

type rule_agent = {

ra_type : int;
ra_erased : bool;
ra_ports : ((int, int * int) link Kappa_data_structures.Loc.annoted * switching) array;
ra_ints : rule_internal array;
ra_syntax : (((int, int * int) link Kappa_data_structures.Loc.annoted * switching) array * rule_internal array) option;

}

A representation of 'left-hand-side' agent that stores how everything is transformed. In an observable (a mixture in an alg_expr), everything is Maintained (represented by I_VAL_CHANGED (i,i) for internal states).

The field ra_syntax represents how the user describe the agent before compilation. Therefore, compil_of_ast in this module generates rule_agent where ra_syntax is Some (Array.copy ra_ports, Array.copy ra_ints).

type rule_mixture = rule_agent list

rule_mixture is the mixture description from the initial state of a rule

type rule = {

r_mix : rule_mixture;
(*
Initial mixture state
*)
r_created : Raw_mixture.t;
(*
Mixture state after rule is applied
*)
r_delta_tokens : ((rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted * int) list;
r_rate : (rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted;
r_un_rate : ((rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted * (rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted option) option;
r_edit_style : bool;
(*
If rule was written in edit style, else it's rewrite style
*)

}

val agent_to_erased : Kappa_site_graphs.Signature.s -> rule_agent -> rule_agent

val to_erased : Kappa_site_graphs.Signature.s -> rule_mixture -> rule_mixture

val to_maintained : rule_mixture -> rule_mixture

val to_raw_mixture : 
  Kappa_site_graphs.Signature.s ->
  rule_mixture ->
  Raw_mixture.t

val copy_rule_agent : rule_agent -> rule_agent

val max_link_id : rule_mixture -> int

val raise_if_modification : Kappa_data_structures.Loc.t -> 'a option -> unit

val raise_several_internal_states : Kappa_data_structures.Loc.t -> 'a

val raise_not_enough_specified : 
  status:string ->
  side:string ->
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val raise_several_occurence_of_site : 
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val raise_counter_misused : 
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val raise_link_only_one_occurence : int -> Kappa_data_structures.Loc.t -> 'a

val raise_link_should_be_removed : 
  int ->
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val print_rule_mixture : 
  noCounters:bool ->
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  ltypes:bool ->
  Raw_mixture.t ->
  Stdlib.Format.formatter ->
  rule_mixture ->
  unit

val print_link : 
  ('a -> Stdlib.Format.formatter -> 'a -> unit) ->
  (Stdlib.Format.formatter -> 'a -> unit) ->
  (Stdlib.Format.formatter -> 'b -> unit) ->
  Stdlib.Format.formatter ->
  ('a, 'b) link ->
  unit

val link_to_json : 
  ('a -> 'a -> Yojson.Basic.t) ->
  ('a -> Yojson.Basic.t) ->
  ('b -> Yojson.Basic.t list) ->
  ('a, 'b) link ->
  Yojson.Basic.t

Fragile: the list MUST NOT be a singleton

val link_of_json : 
  ('a -> Yojson.Basic.t -> 'a) ->
  (Yojson.Basic.t -> 'a) ->
  (Yojson.Basic.t list -> 'b) ->
  Yojson.Basic.t ->
  ('a, 'b) link

val print_rates : 
  noCounters:bool ->
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  (Stdlib.Format.formatter -> int -> unit) ->
  (Stdlib.Format.formatter -> int -> unit) ->
  Stdlib.Format.formatter ->
  rule ->
  unit

val print_rule : 
  noCounters:bool ->
  full:bool ->
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  (Stdlib.Format.formatter -> int -> unit) ->
  (Stdlib.Format.formatter -> int -> unit) ->
  Stdlib.Format.formatter ->
  rule ->
  unit

val rule_to_json : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  rule ->
  Yojson.Basic.t

val rule_of_json : filenames:string array -> Yojson.Basic.t -> rule