public static void Main(string[] args)
{
Stopwatch watch = new Stopwatch();
watch.Start();
//TestSingle();
if (args != null && args.Length == 2)
{
bool useGSESAME = (args[0] == "GSESAME");
MicroRNASimHelper.Mode mode = (MicroRNASimHelper.Mode)Enum.Parse(typeof(MicroRNASimHelper.Mode), args[1]);
RunAllRNA(useGSESAME, mode);
}
Console.WriteLine("used seconds: " + watch.ElapsedMilliseconds / 1000.0);
}
public static void RunAllRNA(bool useGSESAME, MicroRNASimHelper.Mode mode, int start = 0, int end = 10000)
{
string simFileName = string.Format("sim_{0}_{1}", useGSESAME ? "GSESAME" : "Ours", mode.ToString());
Config.DAGPathPattern = @"DAG_new{0}.txt";
Config.MiRNAPath = "miranda";
Config.GeneralTablePath = "Go_annotated_times.txt";
Config.RNASimCacheFile = simFileName + "Cache.json";
RNASimCache.Read(Config.RNASimCacheFile);
var stateTimer = new Timer(obj => RNASimCache.Save(Config.RNASimCacheFile), null, 600000, 60000);
int maxConcurrency = Math.Min(20, Environment.ProcessorCount);
Console.WriteLine("Using {0} threads.", maxConcurrency);
var miRNAs = DAGLoader.LoadMicroRNA2(Config.MiRNAPath);
GOSimHelper.InitGOSimCache(miRNAs.SelectMany(m => m.Value.GOs).Distinct().ToArray());
List <MicroRNASimHelper> helpers = new List <MicroRNASimHelper>();
for (int i = 0; i < maxConcurrency; i++)
{
helpers.Add(new MicroRNASimHelper(miRNAs, useGSESAME, mode));
Console.WriteLine("Helper {0} initialized.", i);
}
var allRNAs = helpers.First().AllRNAs;
end = Math.Min(end, allRNAs.Length);
for (int i = start; i < end; i++)
{
for (int j = mode == MicroRNASimHelper.Mode.Euclidean ? start : i; j < allRNAs.Length; j++)
{
helpers[i % maxConcurrency].AddJob(allRNAs[i], allRNAs[j]);
}
}
var tasks = helpers.Select(h => h.CalcAllJobsAsync()).ToArray();
Task.WaitAll(tasks);
var sims = tasks.SelectMany(t => t.Result).ToList();
stateTimer.Dispose();
File.WriteAllText(simFileName + ".json", JsonConvert.SerializeObject(sims));
}
