gistfile1.clj

(defprotocol AKappaExpression
  "Kappa expression"
  (agents [e] "get all agents in this expression")
  (complexes [e] "get all complexes in this expression")
  (subexpr [e ids] "get a subexpression for the given agent ids")
  (merge [e1 e2] "merge two expressions")
  (count-automorphisms [e] "count the number of automorphisms")
  (expression? [e] "predicate for AKappaExpression")
  (match [e1 e2] "returns a map from agent ids in e1 to their matching agent ids in e2")
  ;; should this methods be part of AKappaAgent?
  (complex [e id] "get the complex to which agent id belongs")
  (new-id [e id] "give a new id to agent id"))

(deftype Expression [as cs]
  AKappaExpression
  (agents [_] as)
  (complexes [_] cs)
  (subexpr [e ids] (zipmap ids (map e ids)))
  (merge [e1 e2] (...))
  (count-automorphisms [e] ...)
  (expression? [_] true)
  (match [e1 e2] (match-expr e1 e2)))