public List <int> DeactivateAll()
{
List <int> switched = new List <int>();
for (int i = 0; i < Nodes.Count; ++i)
{
ProteinNode prot = (ProteinNode)Nodes[i];
if (prot.Active)
{
switched.Add(i);
}
prot.Deactivate();
}
return(switched);
}
public List <int> UnblockAll()
{
List <int> switched = new List <int>();
for (int i = 0; i < Nodes.Count; ++i)
{
ProteinNode prot = (ProteinNode)Nodes[i];
if (prot.Blocked)
{
switched.Add(i);
}
prot.Blocked = false;
}
return(switched);
}
public void Propagate(GraphSystem graphSystem, float time)
{
List <Tuple <int, SignalType> > updatedSignals
= new List <Tuple <int, SignalType> >();
graphSystem.DehighlightNodes();
List <int> activateNodes = new List <int>();
List <int> blockNodes = new List <int>();
List <int> activateEdges = new List <int>();
List <int> blockEdges = new List <int>();
List <int> decoupleEdges = new List <int>();
List <int> coupleEdges = new List <int>();
// activate input proteins:
foreach (int i in inputs)
{
GetProtein(i).Activate();
}
highlight(graphSystem);
foreach (ProteinNode prot in Nodes)
{
if (prot.Active)
{
var outInteractions = GetOutcomingInteractions(prot.Name);
foreach (var tuple in outInteractions)
{
var outInteraction = tuple.Item1;
int outInteractionId = tuple.Item2;
ProteinNode nextProt = GetProtein(outInteraction.End2);
if (outInteraction.Type == "-")
{
// uncomment to add blocking sparks:
// graphSystem.AddSpark(outInteraction.End1, outInteraction.End2, time, HighlightNodesColorNeg);
blockNodes.Add(outInteraction.End2);
blockEdges.Add(outInteractionId);
}
else if (outInteraction.Type == "+")
{
graphSystem.AddSpark(outInteraction.End1, outInteraction.End2, time, HighlightNodesColorPos);
activateNodes.Add(outInteraction.End2);
foreach (var t in GetInteractions(prot.Name, nextProt.Name))
{
activateEdges.Add(t.Item2);
}
}
else if (outInteraction.Type == "b")
{
if (outInteraction.Value > decoupleStrength)
{
decoupleEdges.Add(outInteractionId);
}
else
{
coupleEdges.Add(outInteractionId);
}
}
}
}
}
// launch new sparks:
graphSystem.RefreshSparks();
// activate and block nodes:
changeNodeStates(blockNodes, activateNodes, graphSystem);
// couple and decouple nodes:
List <Tuple <List <int>, float> > edgeLists = new List <Tuple <List <int>, float> >();
edgeLists.Add(new Tuple <List <int>, float>(coupleEdges, coupleStrength));
edgeLists.Add(new Tuple <List <int>, float>(decoupleEdges, decoupleStrength));
changeEdgeValues(edgeLists, graphSystem);
// paint edges:
graphSystem.PaintAllEdges(EdgeNeutralColor);
graphSystem.PaintEdges(activateEdges, EdgePosColor);
graphSystem.PaintEdges(blockEdges, EdgeNegColor);
}
