Module Kappa_terms.Primitives

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_generic_toolset.Locality.annot;
unary_rate : (alg_expr Kappa_generic_toolset.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 Kappa_generic_toolset.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 Kappa_generic_toolset.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_generic_toolset.Locality.annot
| Alg_pexpr of 'alg_expr Kappa_generic_toolset.Locality.annot
val print_expr_to_yojson : filenames:int Kappa_generic_toolset.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 : Bi_outbuf.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_generic_toolset.Locality.annot * elementary_rule
| UPDATE of int * alg_expr Kappa_generic_toolset.Locality.annot
| 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_generic_toolset.Nbr.t option;
precondition : (Pattern.id array list, int) Alg_expr.bool Kappa_generic_toolset.Locality.annot;
effect : modification list;
repeat : (Pattern.id array list, int) Alg_expr.bool Kappa_generic_toolset.Locality.annot;
needs_backtrack : bool;
}
val perturbation_to_yojson : filenames:int Kappa_generic_toolset.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_generic_toolset.Locality.annot -> Pattern.id list
val map_expr_rule : (alg_expr Kappa_generic_toolset.Locality.annot -> alg_expr Kappa_generic_toolset.Locality.annot) -> elementary_rule -> elementary_rule
val map_expr_perturbation : (alg_expr Kappa_generic_toolset.Locality.annot -> alg_expr Kappa_generic_toolset.Locality.annot) -> ((Pattern.id array list, int) Alg_expr.bool Kappa_generic_toolset.Locality.annot -> (Pattern.id array list, int) Alg_expr.bool Kappa_generic_toolset.Locality.annot) -> perturbation -> perturbation
val fold_expr_rule : ('a -> alg_expr Kappa_generic_toolset.Locality.annot -> 'a) -> 'a -> elementary_rule -> 'a
val fold_expr_perturbation : ('a -> alg_expr Kappa_generic_toolset.Locality.annot -> 'a) -> ('a -> (Pattern.id array list, int) Alg_expr.bool Kappa_generic_toolset.Locality.annot -> 'a) -> 'a -> perturbation -> 'a