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

(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

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

import qualified Data.Map as Map

type Mol = String
type Mixture = Map.Map Mol Integer
type Rxn = (Mixture, (Mixture -> Mixture), Double)

getActivities :: [Rxn] -> Mixture -> [Double]
getActivities rxns mixture =
  let f acc mol sc = if sc == 1 -- sc is stoichiometric coefficient
                       then fromIntegral $ mixture Map.! mol

rhz

import qualified Data.Map as Map
import qualified Data.Set as Set
import Data.Maybe
import Data.List
import Random (randomRIO)
import qualified Data.Enumerator as E
import qualified Data.Enumerator.List as EL

type Mol = String
type Mixture = Map.Map Mol Integer

rhz

import qualified Data.Map as Map
import qualified Data.Set as Set

type IntMap = Map.Map Int Int
type IntSet = Set.Set Int

extend :: IntMap -> IntSet -> IntMap -> Maybe (IntMap, IntSet)
extend inj codom map = Map.foldrWithKey f (Just (inj, codom)) map
  where f :: Int -> Int -> Maybe (IntMap, IntSet) -> Maybe (IntMap, IntSet)
        f i j (Just (inj, codom)) = if Set.member j codom

rhz

JOB "Main 1.kappa 10000 0 500 +RTS -hc -T"
DATE "Fri Mar 16 08:01 2012"
SAMPLE_UNIT "seconds"
VALUE_UNIT "bytes"
BEGIN_SAMPLE 0.00
END_SAMPLE 0.00
BEGIN_SAMPLE 0.09
(898)CAF:nodeOfId	16
(2523)findNewInjs.ccIdInjs/...	48
(1943)infinity/add.(...)/ad...	16

rhz

JOB "Main 1.kappa 10000 0 500 +RTS -hc -T"
DATE "Fri Mar 16 08:13 2012"
SAMPLE_UNIT "seconds"
VALUE_UNIT "bytes"
BEGIN_SAMPLE 0.00
END_SAMPLE 0.00
BEGIN_SAMPLE 0.09
(2524)create/findNewInjs.cc...	104
(1740)evalMixture/evalObs.a...	192
(2308)diff.addModifications...	64

rhz

module Main where

import System.Process
import System.Environment (getArgs)
import Data.List (intercalate)

data Gender = Male
            | Female

data Var = FirstValue

rhz

diff --git main/main.ml main/main.ml
index fa98968..86c90ff 100644
--- main/main.ml
+++ main/main.ml
@@ -37,6 +37,7 @@ let main =
 		("-load-sim", Arg.String (fun file -> Parameter.marshalizedInFile := file) , "load simulation package instead of kappa files") ; 
 		("-make-sim", Arg.String (fun file -> Parameter.marshalizedOutFile := file) , "save kappa files as a simulation package") ; 
 		("--implicit-signature", Arg.Unit (fun () -> Parameter.implicitSignature := true), "Program will guess agent signatures automatically") ;
+		("--float-precision", Arg.Int (fun p -> Parameter.floatPrecision := Some p), "Use given precision to print floating point numbers (e.g. time)") ;
 		("-seed", Arg.Int (fun i -> Parameter.seedValue := Some i), "Seed for the random number generator") ;