kappa-library 4.1.3 · OCaml Package

type t

type instance

type result =

| Clash
| Corrected
| Blocked
| Success of t

val value_alg : 
  Counter.t ->
  t ->
  Kappa_terms.Primitives.alg_expr ->
  Kappa_data_structures.Nbr.t

val empty : 
  outputs:(Data.t -> unit) ->
  with_trace:bool ->
  Random.State.t ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t

val force_rule : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  Trace.event_kind ->
  ?rule_id:int ->
  Kappa_terms.Primitives.elementary_rule ->
  t option

val update_outdated_activities : 
  debug_mode:bool ->
  (int -> float -> float -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  int list ->
  t * int list

val overwrite_var : 
  int ->
  Counter.t ->
  t ->
  Kappa_terms.Primitives.alg_expr ->
  t

val snapshot : 
  debug_mode:bool ->
  raw:bool ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  Data.snapshot

val add_tracked : 
  outputs:(Data.t -> unit) ->
  Kappa_terms.Pattern.id array ->
  string ->
  Kappa_terms.Instantiation.abstract Kappa_terms.Instantiation.test list list ->
  t ->
  t

val remove_tracked : Kappa_terms.Pattern.id array -> string option -> t -> t

val add_tracked_species : 
  Kappa_terms.Pattern.id array ->
  string ->
  Kappa_terms.Instantiation.abstract Kappa_terms.Instantiation.test list list ->
  t ->
  t

val remove_tracked_species : string -> t -> t

val value_bool : 
  Counter.t ->
  t ->
  (Kappa_terms.Pattern.id array list, int) Kappa_terms.Alg_expr.bool ->
  bool

val apply_given_rule : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  ?rule_id:int ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  Trace.event_kind ->
  Kappa_terms.Primitives.elementary_rule ->
  result

val incorporate_extra_pattern : 
  debug_mode:bool ->
  Kappa_terms.Pattern.Env.t ->
  t ->
  Kappa_terms.Pattern.id ->
  t

val activity : t -> float

val apply_instance : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  ?maxConsecutiveBlocked:int ->
  maxConsecutiveClash:int ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  instance ->
  int option * bool * t

val apply_concrete_positive_transformation : 
  Kappa_site_graphs.Signature.s ->
  ?mod_connectivity_store:Roots.mod_ccs_cache ->
  Instances.t ->
  Kappa_site_graphs.Edges.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t ->
  Kappa_site_graphs.Edges.t

val print : Kappa_terms.Model.t -> Format.formatter -> t -> unit

val pick_an_instance : debug_mode:bool -> Kappa_terms.Model.t -> t -> instance

val is_correct_instance : Kappa_terms.Model.t -> t -> instance -> bool

val get_random_state : t -> Random.State.t

val obs_from_transformations : 
  debug_mode:bool ->
  Kappa_terms.Pattern.Env.t ->
  Kappa_site_graphs.Edges.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t
    list ->
  (Kappa_terms.Pattern.id * Kappa_terms.Instantiation.concrete) list
  * Kappa_data_structures.Operator.DepSet.t

val print_stats : Format.formatter -> t -> unit

val apply_negative_transformation : 
  ?mod_connectivity_store:Roots.mod_ccs_cache ->
  Instances.t ->
  (Kappa_site_graphs.Agent.t Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t) ->
  Kappa_site_graphs.Agent.t Kappa_terms.Primitives.Transformation.t ->
  Kappa_site_graphs.Agent.t Kappa_terms.Instantiation.site list
  * Kappa_site_graphs.Edges.t

val apply_positive_transformation : 
  debug_mode:bool ->
  Kappa_site_graphs.Signature.s ->
  ?mod_connectivity_store:Roots.mod_ccs_cache ->
  Instances.t ->
  ((Kappa_terms.Matching.t * int Kappa_data_structures.Mods.IntMap.t)
   * Kappa_site_graphs.Agent.t Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t) ->
  Kappa_terms.Instantiation.abstract Kappa_terms.Primitives.Transformation.t ->
  ((Kappa_terms.Matching.t * int Kappa_data_structures.Mods.IntMap.t)
   * Kappa_site_graphs.Agent.t Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t)
  * Kappa_site_graphs.Agent.t Kappa_terms.Primitives.Transformation.t

package kappa-library