Instantiation (kappa-library.Kappa

All names refers to the one from the signature

type agent_name = int

type site_name = int

type internal_state = int

type binding_type = agent_name * site_name

type abstract = Matching.Agent.t

in a rule

type concrete = Kappa_site_graphs.Agent.t

in a simulation state

type 'a site = 'a * site_name

type 'a test =

| Is_Here of 'a
| Has_Internal of 'a site * internal_state
| Is_Free of 'a site
| Is_Bound of 'a site
| Has_Binding_type of 'a site * binding_type
| Is_Bound_to of 'a site * 'a site

type 'a action =

| Create of 'a * (site_name * internal_state option) list
| Mod_internal of 'a site * internal_state
| Bind of 'a site * 'a site
| Bind_to of 'a site * 'a site
| Free of 'a site
| Remove of 'a

val sort_concrete_action_list : concrete action list -> concrete action list

val sort_concrete_action_list_reverse : 
  concrete action list ->
  concrete action list

val sort_abstract_action_list : concrete action list -> concrete action list

val sort_abstract_action_list_reverse : 
  concrete action list ->
  concrete action list

type 'a binding_state =

| ANY
| FREE
| BOUND
| BOUND_TYPE of binding_type
| BOUND_to of 'a site

type 'a event = {

tests : 'a test list list;
(*
The tests written in the rule (pattern by pattern)
*)
actions : 'a action list;
(*
The modifications written in the rule
*)
side_effects_src : ('a site * 'a binding_state) list;
(*
the site of the agents mentioned in the rule where there is a side effects
*)
side_effects_dst : 'a site list;
(*
the site of agents not mentionned in the rule that have been freed by side effect
*)
connectivity_tests : 'a test list;
(*
witness that patterns where connected (unary instances only of course)
*)

}

val empty_event : 'a event

val rename_abstract_test : 
  debug_mode:bool ->
  int ->
  Kappa_data_structures.Renaming.t ->
  abstract test ->
  abstract test

val rename_abstract_action : 
  debug_mode:bool ->
  int ->
  Kappa_data_structures.Renaming.t ->
  abstract action ->
  abstract action

val rename_abstract_event : 
  debug_mode:bool ->
  int ->
  Kappa_data_structures.Renaming.t ->
  abstract event ->
  abstract event

val rename_abstract_side_effect : 
  debug_mode:bool ->
  int ->
  Kappa_data_structures.Renaming.t ->
  ((Matching.Agent.t * 'a) * Matching.Agent.t binding_state) ->
  (Matching.Agent.t * 'a) * Matching.Agent.t binding_state

val concretize_test : 
  debug_mode:bool ->
  (Matching.t * int Kappa_data_structures.Mods.IntMap.t) ->
  abstract test ->
  concrete test

val concretize_action : 
  debug_mode:bool ->
  (Matching.t * int Kappa_data_structures.Mods.IntMap.t) ->
  abstract action ->
  concrete action

val try_concretize_action : 
  debug_mode:bool ->
  (Matching.t * int Kappa_data_structures.Mods.IntMap.t) ->
  abstract action ->
  concrete action option

Same than concretize_action, except that it returns None if the provided injection's domain does not contain a fresh agent that is involved in the action that is being concretized.

val concretize_event : 
  debug_mode:bool ->
  (Matching.t * int Kappa_data_structures.Mods.IntMap.t) ->
  abstract event ->
  concrete event

val matching_abstract_concrete : 
  debug_mode:bool ->
  abstract event ->
  concrete event ->
  Kappa_data_structures.Renaming.t option

val subst_map_agent_in_concrete_test : 
  (int -> int) ->
  concrete test ->
  concrete test

val subst_agent_in_concrete_test : int -> int -> concrete test -> concrete test

val subst_map_agent_in_concrete_action : 
  (int -> int) ->
  concrete action ->
  concrete action

val subst_agent_in_concrete_action : 
  int ->
  int ->
  concrete action ->
  concrete action

val subst_map_agent_in_concrete_side_effect : 
  (int -> int) ->
  (concrete site * concrete binding_state) ->
  concrete site * concrete binding_state

val subst_agent_in_concrete_side_effect : 
  int ->
  int ->
  (concrete site * concrete binding_state) ->
  concrete site * concrete binding_state

val subst_map_agent_in_concrete_event : 
  (int -> int) ->
  concrete event ->
  concrete event

val subst_map2_agent_in_concrete_event : 
  (int -> int) ->
  (int -> int) ->
  concrete event ->
  concrete event

val subst_agent_in_concrete_event : 
  int ->
  int ->
  concrete event ->
  concrete event

val print_concrete_test : 
  ?sigs:Kappa_site_graphs.Signature.s ->
  Stdlib.Format.formatter ->
  concrete test ->
  unit

val print_concrete_action : 
  ?sigs:Kappa_site_graphs.Signature.s ->
  Stdlib.Format.formatter ->
  concrete action ->
  unit

val print_concrete_binding_state : 
  ?sigs:Kappa_site_graphs.Signature.s ->
  Stdlib.Format.formatter ->
  concrete binding_state ->
  unit

val json_dictionnary : string

val test_to_json : ('a -> Yojson.Basic.t) -> 'a test -> Yojson.Basic.t

val test_of_json : (Yojson.Basic.t -> 'a) -> Yojson.Basic.t -> 'a test

val write_test : 
  (Stdlib.Buffer.t -> 'a -> unit) ->
  Stdlib.Buffer.t ->
  'a test ->
  unit

val read_test : 
  (Yojson.Basic.lexer_state -> Stdlib.Lexing.lexbuf -> 'a) ->
  Yojson.Basic.lexer_state ->
  Stdlib.Lexing.lexbuf ->
  'a test

val action_to_json : ('a -> Yojson.Basic.t) -> 'a action -> Yojson.Basic.t

val action_of_json : (Yojson.Basic.t -> 'a) -> Yojson.Basic.t -> 'a action

val write_action : 
  (Stdlib.Buffer.t -> 'a -> unit) ->
  Stdlib.Buffer.t ->
  'a action ->
  unit

val read_action : 
  (Yojson.Basic.lexer_state -> Stdlib.Lexing.lexbuf -> 'a) ->
  Yojson.Basic.lexer_state ->
  Stdlib.Lexing.lexbuf ->
  'a action

val event_to_json : ('a -> Yojson.Basic.t) -> 'a event -> Yojson.Basic.t

val event_of_json : (Yojson.Basic.t -> 'a) -> Yojson.Basic.t -> 'a event

val write_event : 
  (Stdlib.Buffer.t -> 'a -> unit) ->
  Stdlib.Buffer.t ->
  'a event ->
  unit

val read_event : 
  (Yojson.Basic.lexer_state -> Stdlib.Lexing.lexbuf -> 'a) ->
  Yojson.Basic.lexer_state ->
  Stdlib.Lexing.lexbuf ->
  'a event