kappa-library 4.1.3 · OCaml Package

Compiled representation of a full Kappa model

type t

val init : 
  filenames:string list ->
  Pattern.Env.t ->
  unit Kappa_data_structures.NamedDecls.t ->
  Primitives.alg_expr Kappa_data_structures.Loc.annoted
    Kappa_data_structures.NamedDecls.t ->
  (Kappa_data_structures.Operator.DepSet.t
   * Kappa_data_structures.Operator.DepSet.t
   * Kappa_data_structures.Operator.DepSet.t array
   * Kappa_data_structures.Operator.DepSet.t array) ->
  ((string Kappa_data_structures.Loc.annoted option
    * LKappa.rule Kappa_data_structures.Loc.annoted)
     array
   * Primitives.elementary_rule array) ->
  Primitives.alg_expr Kappa_data_structures.Loc.annoted array ->
  Primitives.perturbation array ->
  Contact_map.t ->
  Kappa_site_graphs.Counters_info.counter_sig option array array ->
  t

init sigs tokens algs dependencies (ast_rules,rules) obs perts

val deconstruct : 
  t ->
  string list
  * Pattern.Env.t
  * unit Kappa_data_structures.NamedDecls.t
  * Primitives.alg_expr Kappa_data_structures.Loc.annoted
      Kappa_data_structures.NamedDecls.t
  * (Kappa_data_structures.Operator.DepSet.t
     * Kappa_data_structures.Operator.DepSet.t
     * Kappa_data_structures.Operator.DepSet.t array
     * Kappa_data_structures.Operator.DepSet.t array)
  * ((string Kappa_data_structures.Loc.annoted option
      * LKappa.rule Kappa_data_structures.Loc.annoted)
       array
     * Primitives.elementary_rule array)
  * Primitives.alg_expr Kappa_data_structures.Loc.annoted array
  * Primitives.perturbation array
  * Contact_map.t
  * Kappa_site_graphs.Counters_info.counter_sig option array array

val nb_tokens : t -> int

val nb_algs : t -> int

val nb_rules : t -> int

val nb_syntactic_rules : t -> int

val nb_perturbations : t -> int

val domain : t -> Pattern.Env.t

val get_obs : t -> Primitives.alg_expr Kappa_data_structures.Loc.annoted array

val get_rules : t -> Primitives.elementary_rule array

val new_domain : Pattern.Env.t -> t -> t

val signatures : t -> Kappa_site_graphs.Signature.s

val tokens_finder : t -> int Kappa_data_structures.Mods.StringMap.t

val algs_finder : t -> int Kappa_data_structures.Mods.StringMap.t

val contact_map : t -> Contact_map.t

val counters_info : t -> Kappa_site_graphs.Counters_info.t

val counter_info : 
  t ->
  int ->
  int ->
  Kappa_site_graphs.Counters_info.counter_sig option

val get_alg : t -> int -> Primitives.alg_expr

val get_algs : 
  t ->
  (string * Primitives.alg_expr Kappa_data_structures.Loc.annoted) array

val get_perturbation : t -> int -> Primitives.perturbation

val get_rule : t -> int -> Primitives.elementary_rule

val get_ast_rule : t -> int -> LKappa.rule

val get_ast_rule_with_label : 
  t ->
  int ->
  string Kappa_data_structures.Loc.annoted option
  * LKappa.rule Kappa_data_structures.Loc.annoted

val get_ast_rule_rate_pos : 
  unary:bool ->
  t ->
  int ->
  Kappa_data_structures.Loc.t

val map_observables : (Primitives.alg_expr -> 'a) -> t -> 'a array

val fold_rules : 
  (int -> 'a -> Primitives.elementary_rule -> 'a) ->
  'a ->
  t ->
  'a

val fold_ast_rules : (int -> 'a -> LKappa.rule -> 'a) -> 'a -> t -> 'a

val fold_perturbations : 
  (int -> 'a -> Primitives.perturbation -> 'a) ->
  'a ->
  t ->
  'a

val get_alg_reverse_dependencies : 
  t ->
  int ->
  Kappa_data_structures.Operator.DepSet.t

val get_token_reverse_dependencies : 
  t ->
  int ->
  Kappa_data_structures.Operator.DepSet.t

val all_dependencies : 
  t ->
  Kappa_data_structures.Operator.DepSet.t
  * Kappa_data_structures.Operator.DepSet.t
  * Kappa_data_structures.Operator.DepSet.t array
  * Kappa_data_structures.Operator.DepSet.t array

val num_of_agent : string Kappa_data_structures.Loc.annoted -> t -> int

val num_of_alg : string Kappa_data_structures.Loc.annoted -> t -> int

val num_of_token : string Kappa_data_structures.Loc.annoted -> t -> int

val nums_of_rule : string -> t -> int list

val print_ast_rule : 
  noCounters:bool ->
  ?env:t ->
  Format.formatter ->
  int ->
  unit

The int is the ast_rule_id

val print_rule : noCounters:bool -> ?env:t -> Format.formatter -> int -> unit

Same as above but the int is this time the rule_id

val print_agent : ?env:t -> Format.formatter -> int -> unit

val print_alg : ?env:t -> Format.formatter -> int -> unit

val print_token : ?env:t -> Format.formatter -> int -> unit

val print : 
  noCounters:bool ->
  (t -> Format.formatter -> Primitives.alg_expr -> unit) ->
  (t -> Format.formatter -> Primitives.elementary_rule -> unit) ->
  (t -> Format.formatter -> Primitives.perturbation -> unit) ->
  Format.formatter ->
  t ->
  unit

val print_kappa : 
  noCounters:bool ->
  (t -> Format.formatter -> Primitives.alg_expr -> unit) ->
  ?pr_rule:(t -> Format.formatter -> Primitives.elementary_rule -> unit) ->
  (t -> Format.formatter -> Primitives.perturbation -> unit) ->
  Format.formatter ->
  t ->
  unit

val to_yojson : t -> Yojson.Basic.t

val of_yojson : Yojson.Basic.t -> t

val check_if_counter_is_filled_enough : t -> unit

val overwrite_vars : (int * Primitives.alg_expr) list -> t -> t

val propagate_constant : 
  warning:
    (pos:Kappa_data_structures.Loc.t -> (Format.formatter -> unit) -> unit) ->
  ?max_time:float ->
  ?max_events:int ->
  updated_vars:int list ->
  alg_overwrite:(int * Primitives.alg_expr) list ->
  t ->
  t

propagate_constant updated_vars overwrite_vars env

val fold_mixture_in_expr : ('a -> Pattern.id array list -> 'a) -> 'a -> t -> 'a

val unary_patterns : t -> Pattern.Set.t

package kappa-library