protected void Init(SimulatorInitArgs args, bool registerLogger)
{
var selfMPs = GetSelfPatterns();
// get simulation initial events from application
var pairs = GetInitialEvents();
Init(selfMPs, pairs, args, registerLogger);
}
protected void Init(Stream selfStream, SimulatorInitArgs args, bool registerLogger)
{
var bSelfformatter = new BinaryFormatter();
var selfPatterns = (List <MolecularPattern>)bSelfformatter.Deserialize(selfStream);
// get simulation initial events from application
var initEvents = GetInitialEvents();
Init(selfPatterns, initEvents, args, registerLogger);
}
protected void Init(Stream selfStream, Stream runInitStream, SimulatorInitArgs args, bool registerLogger)
{
var bSelfformatter = new BinaryFormatter();
var selfPatterns = (List <MolecularPattern>)bSelfformatter.Deserialize(selfStream);
var bInitformatter = new BinaryFormatter();
var initEvents = (List <SimulatorInitEvent>)bInitformatter.Deserialize(runInitStream);
Init(selfPatterns, initEvents, args, registerLogger);
}
private void Init(List <MolecularPattern> selfPatterns,
List <SimulatorInitEvent> initEvents, SimulatorInitArgs args, bool registerLogger)
{
// create and start local agents
// number of local tissue must be equal to the number of NS nodes
LocalTissues = new List <LocalTissue>(new LocalTissue[args.NumLocals]);
for (int i = 0; i < args.NumLocals; i++)
{
var lt = new LocalTissue();
LocalTissues[i] = lt;
lt.Start();
}
// create, train and start thymus agents
Thymuses = new List <Thymus>(new Thymus[args.NumThymuses]);
for (int i = 0; i < args.NumThymuses; i++)
{
var thymus = new Thymus(args.NumTCells, args.PeptideLen);
thymus.Train(selfPatterns); // train the thymus by self patterns
Thymuses[i] = thymus;
thymus.Start();
}
// create and start bone marrow agents
BoneMarrows = new List <BoneMarrow <T> >(new BoneMarrow <T> [args.NumBoneMarrows]);
for (int i = 0; i < args.NumBoneMarrows; i++)
{
var bm = new BoneMarrow <T>(args.NumAPCs, OnProcessSpamp, OnProcessSdamp, OnProcessAntigen);
BoneMarrows[i] = bm;
bm.Start();
}
// create and start lymph node agents
LymphNodes = new List <LymphNode>(new LymphNode[args.NumLymphNodes]);
for (int i = 0; i < args.NumLymphNodes; i++)
{
var ln = new LymphNode();
LymphNodes[i] = ln;
ln.Start();
}
if (registerLogger)
{
// register logger event
foreach (var tissue in Tissues)
{
tissue.LogEvent += new EventHandler <LogEventArgs>(OnLog);
}
}
// schedule all initial events
foreach (var pair in initEvents.Where(e => e.LocalNodeId < LocalTissues.Count))
{
if (pair.Signal == null)
{
throw new Exception("Event signal cannot be null.");
}
if (pair.LocalNodeId > args.NumLocals)
{
throw new Exception("Event refers to an invalid local node ID. Check number of local nodes and localNodeId of event.");
}
Scheduler.Schedule(LocalTissues[pair.LocalNodeId].HandleSignal, pair.Time, pair.Signal);
}
Initialized = true;
}