305 lines
13 KiB
Racket
305 lines
13 KiB
Racket
#lang racket
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;;; dds/rs
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;;; Definitions for working with reaction systems.
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(require graph "utils.rkt" "generic.rkt")
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(provide
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;; Structures
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(struct-out reaction)
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(struct-out state)
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(struct-out dynamics)
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;; Functions
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(contract-out [enabled? (-> reaction? (set/c symbol?) boolean?)]
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[list-enabled (-> reaction-system/c (set/c species?) (listof symbol?))]
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[union-products (-> reaction-system/c (listof symbol?) (set/c species?))]
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[apply-rs (-> reaction-system/c (set/c species?) (set/c species?))]
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[ht-str-triples->rs (-> (hash/c symbol? (list/c string? string? string?)) reaction-system/c)]
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[read-org-rs (-> string? reaction-system/c)]
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[read-context-sequence (-> string? (listof (set/c species?)))]
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[rs->ht-str-triples (-> reaction-system/c (hash/c symbol? (list/c string? string? string?)))]
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[dds-step-one (-> dynamics? state? (set/c state?))]
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[dds-step-one-annotated (-> dynamics? state? (set/c (cons/c (set/c symbol?) state?)))]
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[dds-step (-> dynamics? (set/c state? #:kind 'dont-care) (set/c state?))]
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[dds-build-state-graph (-> dynamics? (set/c state? #:kind 'dont-care) graph?)]
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[dds-build-n-step-state-graph (-> dynamics? (set/c state? #:kind 'dont-care) number? graph?)]
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[dds-build-state-graph-annotated (-> dynamics? (set/c state? #:kind 'dont-care) graph?)]
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[dds-build-n-step-state-graph-annotated (-> dynamics? (set/c state? #:kind 'dont-care) number? graph?)]
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[build-interactive-process-graph (-> reaction-system/c (listof (set/c species?)) graph?)]
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[build-interactive-process (-> reaction-system/c (listof (set/c species?)) (listof (list/c (set/c species?) (set/c species?))))]
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[pretty-print-state-graph (-> graph? graph?)])
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;; Predicates
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(contract-out [species? (-> any/c boolean?)])
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;; Contracts
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(contract-out [reaction-system/c contract?]))
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(module+ test
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(require rackunit))
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;;; =================
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;;; Basic definitions
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;;; =================
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;;; A species is a symbol.
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(define species? symbol?)
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;;; A reaction is a triple of sets, giving the reactants, the
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;;; inhibitors, and the products, respectively.
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(struct reaction (reactants inhibitors products) #:transparent)
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;;; A reaction is enabled on a set if all of its reactants are in the
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;;; set and none of its inhibitors are.
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(define/match (enabled? r s)
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[((reaction r i p) s)
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(and (subset? r s) (set-empty? (set-intersect i s)))])
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;;; A reaction system is a dictionary mapping reaction names to
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;;; reactions.
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(define reaction-system/c (hash/c symbol? reaction?))
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;;; Returns the list of reaction names enabled on a given set.
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(define (list-enabled rs s)
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(for/list ([(name reaction) (in-hash rs)]
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#:when (enabled? reaction s))
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name))
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;;; Returns the union of the product sets of the given reactions in a
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;;; reaction system. If no reactions are supplied, returns the empty
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;;; set.
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;;;
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;;; This function can be seen as producing the result of the
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;;; application of the given reactions to a set. Clearly, it does not
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;;; check whether the reactions are actually enabled.
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(define (union-products rs as)
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(if (empty? as)
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(set)
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(apply set-union
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(for/list ([a as])
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(reaction-products (hash-ref rs a))))))
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;;; Applies a reaction system to a set.
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(define (apply-rs rs s)
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(let ([as (list-enabled rs s)])
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(union-products rs as)))
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(module+ test
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(test-case "Basic definitions"
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(define r1 (reaction (set 'x) (set 'y) (set 'z)))
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(define r2 (reaction (set 'x) (set) (set 'y)))
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(define rs (make-immutable-hash (list (cons 'a r1) (cons 'b r2))))
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(define s1 (set 'x 'z))
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(define s2 (set 'x 'y))
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(check-true (enabled? r1 s1))
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(check-false (enabled? r1 s2))
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(check-equal? (list-enabled rs s1) '(a b))
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(check-equal? (list-enabled rs s2) '(b))
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(check-equal? (union-products rs '(a b)) (set 'y 'z))
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(check-equal? (apply-rs rs s1) (set 'y 'z))
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(check-equal? (apply-rs rs s2) (set 'y))))
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;;; ====================
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;;; Org-mode interaction
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;;; ====================
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;;; This section contains some useful primitives for Org-mode
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;;; interoperability.
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;;; Converts a triple of strings to a reaction.
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(define/match (str-triple->reaction lst)
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[((list str-reactants str-inhibitors str-products))
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(reaction (list->set (read-symbol-list str-reactants))
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(list->set (read-symbol-list str-inhibitors))
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(list->set (read-symbol-list str-products)))])
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;;; Converts a hash table mapping reaction names to triples of strings
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;;; to a reaction system.
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(define (ht-str-triples->rs ht)
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(for/hash ([(a triple) (in-hash ht)])
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(values a (str-triple->reaction triple))))
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(module+ test
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(test-case "ht-str-triples->rs"
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(check-equal?
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(ht-str-triples->rs #hash((a . ("x t" "y" "z"))))
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(make-immutable-hash (list (cons 'a (reaction (set 'x 't) (set 'y) (set 'z))))))))
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;;; Reads a reaction system from an Org-mode style string.
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(define read-org-rs (compose ht-str-triples->rs read-org-variable-mapping))
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(module+ test
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(test-case "read-org-rs"
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(check-equal? (read-org-rs "((\"a\" \"x t\" \"y\" \"z\") (\"b\" \"x\" \"q\" \"z\"))")
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(hash
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'a
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(reaction (set 'x 't) (set 'y) (set 'z))
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'b
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(reaction (set 'x) (set 'q) (set 'z))))))
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;;; Reads a context sequence from an Org sexp corresponding to a list.
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(define (read-context-sequence str)
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(map (compose list->set read-symbol-list) (flatten (string->any str))))
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(module+ test
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(test-case "read-context-sequence"
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(check-equal? (read-context-sequence "((\"x y\") (\"z\") (\"\") (\"t\"))")
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(list (set 'x 'y) (set 'z) (set) (set 't)))))
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;;; Converts a reaction to a triple of strings.
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(define/match (reaction->str-triple r)
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[((reaction r i p))
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(map (compose drop-first-last any->string set->list)
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(list r i p))])
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;;; Converts a reaction system to a hash table mapping reaction names
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;;; to triples of strings.
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(define (rs->ht-str-triples rs)
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(for/hash ([(a r) (in-hash rs)])
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(values a (reaction->str-triple r))))
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(module+ test
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(test-case "rs->ht-str-triples"
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(check-equal?
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(rs->ht-str-triples (make-immutable-hash (list (cons 'a (reaction (set 'x 't) (set 'y) (set 'z))))))
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#hash((a . ("t x" "y" "z"))))))
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;;; ============================
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;;; Dynamics of reaction systems
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;;; ============================
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;;; An interactive process of a reaction system is a sequence of
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;;; states driven by a sequence of contexts in the following way. The
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;;; reaction system starts with the initial context. Then, at every
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;;; step, the result of applying the reaction system is merged with
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;;; the next element of the context sequence, and the reaction system
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;;; is then applied to the result of the union.
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;;; A state of a reaction system is a set of species representing the
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;;; result of the application of the reactions from the previous
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;;; steps, plus the rest of the context sequence. When the context
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;;; sequence is empty, nothing is added to the current state.
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(struct state (result rest-contexts) #:transparent)
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;;; The dynamics of the reaction system only stores the reaction
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;;; system itself.
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(struct dynamics (rs) #:transparent
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#:methods gen:dds
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[;; Since reaction systems are deterministic, a singleton set is
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;; always produced. It is annotated by the list of rules which
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;; were enabled in the current step.
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(define (dds-step-one-annotated dyn st)
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(let* ([rs (dynamics-rs dyn)]
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[apply-rs-annotate
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(λ (s rest-ctx)
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(let ([en (list-enabled rs s)])
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(set (cons (list->set en)
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(state (union-products rs en) rest-ctx)))))])
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(match st
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[(state res (cons ctx rest-ctx))
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(apply-rs-annotate (set-union res ctx) rest-ctx)]
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[(state res '())
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(apply-rs-annotate res '())])))])
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;;; Builds the state graph of a reaction system driven by a given
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;;; context sequence. When the context sequence is exhausted, keeps
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;;; running the system without contexts. In other words, the context
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;;; sequence is padded with empty contexts at the end.
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(define (build-interactive-process-graph rs contexts)
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(dds-build-state-graph-annotated (dynamics rs)
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(set (state (set) contexts))))
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;;; Builds the interactive process driven by the given context
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;;; sequence. The output is a list of pairs of lists in which the
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;;; first element is the current context and the second element is the
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;;; result of the application of reactions to the previous state. The
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;;; interactive process stops one step after the end of the context
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;;; sequence, to show the effect of the last context.
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(define (build-interactive-process rs contexts)
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(let ([dyn (dynamics rs)]
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[padded-contexts (append contexts (list (set)))])
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(for/fold ([proc '()]
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[st (state (set) padded-contexts)]
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#:result (reverse proc))
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([c padded-contexts])
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(values
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(cons (match st
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[(state res ctx)
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(list (if (empty? ctx) (set) (car ctx)) res)])
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proc)
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(set-first (dds-step-one dyn st))))))
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;;; Pretty-prints the context sequence and the current result of a
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;;; state of the reaction system. Note that we need to keep the full
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;;; context sequence in the name of each state to avoid confusion
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;;; between the states at different steps of the evolution.
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(define/match (pretty-print-state st)
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[((state res ctx))
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(format "C:~a\nD:{~a}" (pretty-print-set-sets ctx) (pretty-print-set res))])
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;;; Pretty prints the state graph of a reaction system.
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(define (pretty-print-state-graph sgr)
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(update-graph sgr #:v-func pretty-print-state #:e-func pretty-print-set-sets))
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(module+ test
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(test-case "Dynamics of reaction systems"
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(define r1 (reaction (set 'x) (set 'y) (set 'z)))
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(define r2 (reaction (set 'x) (set) (set 'y)))
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(define rs (make-immutable-hash (list (cons 'a r1) (cons 'b r2))))
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(define dyn (dynamics rs))
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(define state1 (state (set) (list (set 'x) (set 'y) (set 'z) (set) (set 'z))))
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(define sgr (dds-build-state-graph-annotated dyn (set state1)))
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(define ip (build-interactive-process-graph rs (list (set 'x) (set 'y) (set 'z) (set) (set 'z))))
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(check-equal? (dds-step-one-annotated dyn state1)
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(set (cons
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(set 'a 'b)
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(state (set 'y 'z) (list (set 'y) (set 'z) (set) (set 'z))))))
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(check-equal? (dds-step-one dyn state1)
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(set (state (set 'y 'z) (list (set 'y) (set 'z) (set) (set 'z)))))
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(check-true (has-vertex? sgr (state (set 'y 'z) (list (set 'y) (set 'z) (set) (set 'z)))))
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(check-true (has-vertex? sgr (state (set) (list (set 'z) (set) (set 'z)))))
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(check-true (has-vertex? sgr (state (set) (list (set) (set 'z)))))
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(check-true (has-vertex? sgr (state (set) (list (set 'z)))))
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(check-true (has-vertex? sgr (state (set) (list (set 'x) (set 'y) (set 'z) (set) (set 'z)))))
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(check-true (has-vertex? sgr (state (set) '())))
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(check-equal? (edge-weight sgr
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(state (set) '())
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(state (set) '()))
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(set (set)))
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(check-equal? (edge-weight sgr
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(state (set 'y 'z) (list (set 'y) (set 'z) (set) (set 'z)))
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(state (set) (list (set 'z) (set) (set 'z))))
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(set (set)))
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(check-equal? (edge-weight sgr
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(state (set) (list (set 'z) (set) (set 'z)))
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(state (set) (list (set) (set 'z))))
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(set (set)))
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(check-equal? (edge-weight sgr
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(state (set) (list (set) (set 'z)))
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(state (set) (list (set 'z))))
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(set (set)))
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(check-equal? (edge-weight sgr
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(state (set) (list (set 'z)))
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(state (set) '()))
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(set (set)))
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(check-equal? (edge-weight sgr
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(state (set) (list (set 'x) (set 'y) (set 'z) (set) (set 'z)))
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(state (set 'y 'z) (list (set 'y) (set 'z) (set) (set 'z))))
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(set (set 'a 'b)))
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(check-equal? sgr ip)
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(check-equal? (build-interactive-process rs (list (set 'x) (set 'y) (set 'z) (set) (set 'z)))
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(list
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(list (set 'x) (set))
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(list (set 'y) (set 'y 'z))
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(list (set 'z) (set))
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(list (set) (set))
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(list (set 'z) (set))
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(list (set) (set))))))
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