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 din_kind =

`\|`	`ABSOLUTE`
`\|`	`RELATIVE`
`\|`	`PROBABILITY`

val din_kind_to_yojson : din_kind -> Yojson.Basic.json

val din_kind_of_yojson : Yojson.Basic.json -> din_kind

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

Output a JSON value of type Primitives.din_kind.

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

Serialize a value of type Primitives.din_kind into a JSON string.

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 Primitives.din_kind.

val din_kind_of_string : string -> din_kind

Deserialize JSON data of type Primitives.din_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	`*)`
`\|`	`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 : 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;`
	`needs_backtrack : bool;`

}

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