void highlight(GraphSystem graphSystem)
{
List<int> highPlus = new List<int>();
List<int> highMinus = new List<int>();
foreach (ProteinNode node in Nodes)
{
if (node.Active) highPlus.Add(GetIdByName(node.Name));
else if (node.Blocked) highMinus.Add(GetIdByName(node.Name));
}
graphSystem.HighlightNodes(highPlus, HighlightNodesColorPos);
graphSystem.HighlightNodes(highMinus, HighlightNodesColorNeg);
}
void changeEdgeValues(IEnumerable<Tuple<List<int>, float>> edgeIds, GraphSystem gs)
{
var graph = gs.GetGraph();
foreach (var tuple in edgeIds)
{
foreach (int id in tuple.Item1)
{
graph.Edges[id].Value = tuple.Item2;
// to keep track of edge values without the need to get the graph from GraphSystem:
this.Edges[id].Value = tuple.Item2;
}
}
gs.UpdateGraph(graph);
}
void changeNodeStates(IEnumerable<int> blockNodes, IEnumerable<int> activateNodes, GraphSystem gs)
{
DeactivateAll();
UnblockAll();
foreach (var i in activateNodes)
{
GetProtein(i).Activate();
}
foreach (var i in blockNodes)
{
GetProtein(i).Deactivate();
GetProtein(i).Blocked = true;
}
}
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);
}
