Module `Generic_rule_interpreter.Make`Source

Parameters

module Instances : Instances_sig.S

Signature

Sourcetype t

Abstract graph

Sourcetype instance

Sourcetype result =

| Clash
| Corrected
| Blocked
| Success of t
(*
Clash means rectangular approximation failure Corrected means molecular ambiguity failure
*)

Initialisation

Source

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

algebraic expression computation

get_alg is by default Model.get_alg but it is not hard wired because perturbations can redefined alg_expr.

Source

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

Source

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

Sourceval activity : t -> float

Sourceval get_edges : t -> Kappa_site_graphs.Edges.t

Core

Source

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

Returns the graph obtained by applying the rule. rule_id is mandatory if the rule has an unary rate.

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

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

Source

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

apply_rule ~outputs ~maxConsecutiveClash ?is_blocked model counter st Returns (corresponding_syntactic_rule, is_final_step, new_state). is_final_step is determined by the counter. corresponding_syntactic_rule is equal to None if and only if a null event occured

Source

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

Apply the rule for sure if it is possible. Try apply_rule but in case of null_event, it computes the exact injections of the left hand side to do apply the rule and returns the remaining exact injections.

Source

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

Source

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

Source

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

Resynchronize the state after a rule application.

It takes the function to store the new activities as an argument whose signature is store rule_id syntactic_rule_id new_activity.

As long as you don't use any algebraic variable (that include don't pick a rule randomly), you can apply several rules in row before resynchronizing. (This is what initial state does.)

takes the list of perturbations to be tried and returns it updated

Source

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

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

Sourceval get_random_state : t -> Random.State.t

Source

val update_edges_from_actions : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_site_graphs.Signature.s ->
  Counter.t ->
  Kappa_terms.Pattern.Env.t ->
  t ->
  (Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.action list
   * Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.site list) ->
  t

Sourceval send_instances_message : Instances.message -> t -> t

Blocking events

Source

type event_predicate =
  int option ->
  Kappa_terms.Matching.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.test list ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.action list ->
  bool

Sourceval set_events_to_block : event_predicate option -> t -> t

Stories

Source

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

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

Species

Source

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

Sourceval remove_tracked_species : string -> t -> t

Debugging

Sourcetype stats = {

mixture_stats : Kappa_site_graphs.Edges.stats;

}

Sourceval stats : t -> stats

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

Sourceval debug_print : Format.formatter -> t -> unit

Source

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

Internals

Source

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_terms.Instantiation.concrete 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_terms.Instantiation.concrete Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t)
  * Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t

Source

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

Source

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_site_graphs.Agent.t) list
  * Kappa_data_structures.Operator.DepSet.t

obs_from_transformations domain state transformations

returns
(obs, deps)

Source

val add_outdated_dependencies : 
  Kappa_data_structures.Operator.DepSet.t ->
  t ->
  t

Sourceval debug_print_instances : Format.formatter -> t -> unit

package kappa-library

Module Generic_rule_interpreter.MakeSource

Parameters

Signature

Initialisation

algebraic expression computation

Core

Blocking events

Stories

Species

Debugging

Module `Generic_rule_interpreter.Make`Source