{
 "cells": [
  {
   "cell_type": "code",
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   "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  2.841473 seconds (29.15 M allocations: 760.187 MiB, 13.26% gc time, 23.18% compilation time)\n",
      "861.983010 seconds (3.91 G allocations: 351.983 GiB, 7.58% gc time, 1.66% compilation time)\n",
      "The answer is correct.\n",
      "The answer is correct.\n"
     ]
    }
   ],
   "source": [
    "# importing the example model and the sparseQFCA module\n",
    "using sparseQFCA, JSON, SparseArrays, DelimitedFiles\n",
    "@time open(\"iMM1415.json\") do f\n",
    "    dict = JSON.parse(f);\n",
    "    data = dict[\"reactions\"];\n",
    "    global name = [(data[i])[\"name\"] for i in 1:length(data)];\n",
    "    global lower_bound = [(data[i])[\"lower_bound\"] for i in 1:length(data)];\n",
    "    global upper_bound = [(data[i])[\"upper_bound\"] for i in 1:length(data)];\n",
    "    global gene_reaction_rule = [(data[i])[\"gene_reaction_rule\"] for i in 1:length(data)];\n",
    "    metabolites = [(data[i])[\"metabolites\"] for i in 1:length(data)];\n",
    "    id = [((dict[\"metabolites\"])[i])[\"id\"] for i in 1:length(dict[\"metabolites\"])];\n",
    "    S = Matrix{Float64}(undef, length(id), length(metabolites));\n",
    "    for i in 1:length(metabolites)\n",
    "        for j in 1:length(id)\n",
    "            S[j, i] = get(metabolites[i], id[j], 0)\n",
    "        end\n",
    "    end\n",
    "    global S = sparse(S);\n",
    "end\n",
    "@assert typeof(S) == SparseMatrixCSC{Float64,Int64}\n",
    "rev = readdlm(\"rev.csv\", header = false)[:, 1] .== 1\n",
    "@assert typeof(rev) == BitArray{1}\n",
    "# finding all the flux coupling relations among the reactions\n",
    "certificates, blocked, fctable = @time QFCA(S, rev)\n",
    "println(\"The answer is $(all((readdlm(\"blocked.csv\", header = false) .== 1) .== blocked) ? \"correct\" : \"wrong\").\")\n",
    "println(\"The answer is $(all(readdlm(\"fctable.csv\", header = false) .== fctable) ? \"correct\" : \"wrong\").\")\n",
    "open(\"certificates.txt\", \"w\") do io\n",
    "    writedlm(io, certificates)\n",
    "end"
   ]
  }
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