rhz

import qualified Data.Map as Map
import Random (randomRIO)

type Mol = String
type Mixture = Map.Map Mol Integer
type Rxn = (Mixture, (Mixture -> Mixture)) -- (Lhs, Action)
type State = (Double, Integer, Mixture) -- (Time, NumSteps, Mixture)

getActivities :: [Rxn] -> Mixture -> [Integer]
getActivities rxns mixture = []

rhz

(defn get-molecule [state mol]
  (get-in state [:mixture mol] 0))

(defn get-activities [state] ;; FIXME this fn takes upto 80% of the time
  (into {} (for [{:keys [lhs rate] :as r} (:rxns state)]
             [r (apply * rate (for [[mol freq] lhs]
                                (* (get-molecule state mol) freq)))])))

rhz

(ns mca.gillespie
  (:require [clojure.contrib.generic.math-functions :as math]))

(defn choice [m]
  (let [r (rand (apply + (vals m)))]
    (loop [[[k w] & kws] (seq m)
           sum 0]
      (if (or (nil? kws) (< r (+ sum w))) k
          (recur kws (+ sum w))))))

rhz

(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?

rhz

(require '[clojure.string :as s]
         '[incanter.stats :as stats]
         '[clojure.contrib.generic.math-functions :as m]
         '[clojure.contrib.combinatorics :as c])

;;;; Conversion

(defn get-rows [s]
  (let [[sep & ss] (.split s "\n")]
    (take-nth 2 (partition-by #{sep} ss))))

rhz

(defn prob-n [pred tol in n] ;; in is a csv's filename
  (let [as (for [[_ _ p m] (map #(.split % ";") (rest (.split (slurp in) "\n"))) :when p]
             (if (empty? m) [p] [p m])) ;; take the third and fourth (if possible) column of each row
        conteo (for [as (c/combinations as n)]
                 (if (apply pred tol as) 1 0))]
    (/ (reduce + conteo) (count conteo))))

(defn ningun-apellido-en-comun [tol & as]
  (let [distinct-as (distinct (apply concat as))
        conteo (for [a distinct-as]

rhz

diff --git a/src/main/clojure/clojure/data/finger_tree.clj b/src/main/clojure/clojure/data/finger_tree.clj
index bc00343..557aaaf 100644
--- a/src/main/clojure/clojure/data/finger_tree.clj
+++ b/src/main/clojure/clojure/data/finger_tree.clj
@@ -537,13 +537,17 @@
     (count [_] (:len (measured tree)))
   IPersistentSet
     (disjoin [this k]
-      (let [[l x r] (split-tree tree #(>= 0 (cmpr k (:right %))))]
-        (if (= x k)

rhz

diff --git a/main.lisp b/main.lisp
index 0dfaf15..ec5730e 100644
--- a/main.lisp
+++ b/main.lisp
@@ -270,6 +270,17 @@ Returns T upon successful installation, NIL otherwise."
                (get-pkgbuild pkg-name)
                (quit)))))))))
 
+(defun search-packages (query)
+  (maybe-refresh-cache)

rhz

No message.
  [Thrown class java.lang.IndexOutOfBoundsException]

Restarts:
 0: [QUIT] Quit to the SLIME top level
 1: [ABORT] ABORT to SLIME level 0

Backtrace:
  0: clojure.lang.PersistentVector.arrayFor(PersistentVector.java:106)
  1: clojure.lang.PersistentVector.nth(PersistentVector.java:110)

rhz

(defn get-complexes
  "Returns a seq with the ids of the complexes in expr (which is a
  map from id (Integer) to Kappa agent)."
  [expr]
  (if (:complexes (meta expr)) (:complexes (meta expr))
      (let [get-complex (partial complex expr)]
        (loop [remaining expr
               last-complex #{}
               groups (transient [])]
          (let [remaining (remove (comp last-complex key) remaining)]