State_interpreter (kappa-library.Kappa_runtime.State

type t

Abstract state

val empty : with_delta_activities:bool -> Counter.t -> Kappa_terms.Model.t -> t

empty ~with_delta_activities env

val initialize : 
  bind:('a -> ((bool * Rule_interpreter.t * t) -> 'a) -> 'a) ->
  return:((bool * Rule_interpreter.t * t) -> 'a) ->
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  (Kappa_terms.Primitives.alg_expr * Kappa_terms.Primitives.elementary_rule)
    list ->
  'a

initial env counter graph state builds up the initial state

val observables_values : 
  Kappa_terms.Model.t ->
  Rule_interpreter.t ->
  Counter.t ->
  Kappa_data_structures.Nbr.t array

Returns (the current biological time, an array of the current values of observables)

val do_modifications : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  Kappa_terms.Primitives.modification list ->
  bool * Rule_interpreter.t * t * bool

val a_loop : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  dumpIfDeadlocked:bool ->
  maxConsecutiveClash:int ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  bool * Rule_interpreter.t * t

One event loop

val end_of_simulation : 
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  unit

What to do after stopping simulation.