public MicroRNASimHelper(IReadOnlyDictionary <string, MiRNA> miRNAs = null, bool useGSESAME = false, Mode mode = Mode.Count)
{
_miRNAs = miRNAs ?? DAGLoader.LoadMicroRNA2(Config.MiRNAPath);
_miRNASimCache = new Dictionary <string, Dictionary <string, double> >();
_goSimHelpers = Enumerable.Range(1, Config.DAGCount).Select(i => new GOSimHelper(i)).ToArray();
_jobs = new List <MiRNASim>();
_useGSESAME = useGSESAME;
_mode = mode;
}
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));
}
public static void TestSingle()
{
Config.DAGPathPattern = @"DAG_new{0}.txt";
Config.MiRNAPath = "miranda";
var miRNAs = DAGLoader.LoadMicroRNA2(Config.MiRNAPath);
GOSimHelper.InitGOSimCache(miRNAs.SelectMany(m => m.Value.GOs).Distinct().ToArray());
MicroRNASimHelper rnaSim = new MicroRNASimHelper(miRNAs, false, MicroRNASimHelper.Mode.Euclidean);
Stopwatch watch = new Stopwatch();
watch.Start();
//hsa-let-7c,hsa-let-7d-star
Console.WriteLine(string.Join(", ", rnaSim.CalcSim("hsa-let-7c", "hsa-let-7d-star")));
Console.WriteLine("used seconds: " + watch.ElapsedMilliseconds / 1000.0);
Console.ReadKey();
}
public GOSimHelper(int dagId)
{
string dagFileName = string.Format(Config.DAGPathPattern, dagId);
var dag = DAGLoader.LoadPreprocessedDAG(dagFileName);
_totalGenes = dag.TotalGenes;
_base = Math.Log(dag.TotalAnotedTimes);
_allGO = dag.nodes.Keys.ToArray();
_dag = new DAGNode[dag.nodes.Keys.Max() + 1];
_aliasMapping = dag.AliasMapping;
if (GOSimCache == null)
{
InitGOSimCache(_allGO);
}
foreach (var p in _aliasMapping)
{
var truncatedGO = p.Value.TruncateGO();
if (GOSimCache[p.Value.TruncateGO()] == null)
{
GOSimCache[truncatedGO] = new float[MaxGOTruncated + 1];//new Dictionary<int, double>();
Array.Clear(GOSimCache[truncatedGO], 0, MaxGOTruncated + 1);
}
}
foreach (var p in dag.nodes)
{
_dag[p.Key] = p.Value;
}
if (_aliasMapping != null)
{
foreach (var pair in _aliasMapping)
{
_dag[pair.Key] = _dag[pair.Value];
}
}
//_goSimCache = new Dictionary<int, Dictionary<int, double>>();
_bitmap = new byte[_allGO.Max() + 1];
Array.Clear(_bitmap, 0, _bitmap.Length);
}