public DCluster AddCluster(DCluster parent, string id)
{
if (parent == null)
{
Graph.LayoutAlgorithmSettings = new FastIncrementalLayoutSettings();
Graph.LayoutAlgorithmSettings.EdgeRoutingSettings.KeepOriginalSpline = true;
var settings = Graph.LayoutAlgorithmSettings as FastIncrementalLayoutSettings;
settings.AvoidOverlaps = true;
settings.NodeSeparation = 30;
settings.RouteEdges = true;
}
Subgraph cluster = new Subgraph(id == null ? GetNewNodeID() : id);
Cluster geometryCluster = new Cluster() { GeometryParent = parent == null ? Graph.GeometryGraph : (GeometryObject)parent.GeometryNode };
cluster.GeometryNode = geometryCluster;
geometryCluster.UserData = cluster;
DCluster ret = new DCluster((DObject)parent ?? this, cluster);
cluster.LabelText = null;
SetNodeBoundaryCurve(Graph, cluster);
if (parent == null)
m_RootCluster = ret;
else
parent.AddCluster(ret);
if (UpdateGraphBoundingBoxPreservingCenter())
Invalidate();
AddCluster(ret, false);
return ret;
}
public void AddNodeToCluster(DCluster owner, DNode node)
{
node.ParentObject = owner;
owner.AddNode(node);
owner.DrawingCluster.AddNode(node.DrawingNode);
owner.GeometryCluster.AddChild(node.GeometryNode);
}
private void RebuildFromDrawingGraph()
{
if (Graph.GeometryGraph == null)
{
// A geometry graph is required. Note that I have to set the node boundary curves myself (because they depend on the label size, which in turn depends on the rendering engine).
Graph.CreateGeometryGraph();
foreach (DrawingNode drawingNode in Graph.NodeMap.Values)
SetNodeBoundaryCurve(Graph, drawingNode);
}
// Create DNode instances
NodeMap.Clear();
foreach (DrawingNode drawingNode in Graph.NodeMap.Values)
NodeMap[drawingNode.Id] = new DNode(this, drawingNode);
// Create DCluster instances
if (Graph.RootSubgraph != null && Graph.RootSubgraph.GeometryNode != null)
{
m_RootCluster = new DCluster(this, Graph.RootSubgraph);
NodeMap[Graph.RootSubgraph.Id] = m_RootCluster;
PopulateDClusterFromDrawing(m_RootCluster, Graph.RootSubgraph);
}
// Create DEdge instances
Edges.Clear();
foreach (DrawingEdge drawingEdge in Graph.Edges)
Edges.Add(new DEdge(NodeMap[drawingEdge.SourceNode.Id], NodeMap[drawingEdge.TargetNode.Id], drawingEdge, ConnectionToGraph.Connected));
FirePropertyChanged("HasContent");
}
public DCluster AddCluster(DCluster parent)
{
return AddCluster(parent, null);
}
internal void AddCluster(DCluster cluster)
{
m_Clusters.Add(cluster);
}
private void PopulateDClusterFromDrawing(DCluster dc, Subgraph drawingc)
{
foreach (var drawingn in drawingc.Nodes)
dc.AddNode(NodeMap[drawingn.Id]);
foreach (var drawingc2 in drawingc.Subgraphs)
{
DCluster dc2 = new DCluster(dc, drawingc2);
dc.AddCluster(dc2);
NodeMap[drawingc2.Id] = dc2;
PopulateDClusterFromDrawing(dc2, drawingc2);
}
}
private void CreateGamete(DGraph graph, DCluster gamete)
{
var inNode = graph.AddNode("Gamete_in");
inNode.DrawingNode.Attr.Shape = MsaglShape.Circle;
inNode.DrawingNode.Attr.FillColor = MsaglColor.Red;
graph.AddNodeToCluster(gamete, inNode);
var splitter = graph.AddNode("Gamete_Splitter");
splitter.DrawingNode.Attr.Shape = MsaglShape.Circle;
splitter.DrawingNode.Attr.FillColor = MsaglColor.Blue;
graph.AddNodeToCluster(gamete, splitter);
var sperm = Clustering_Cell_AddNode(graph, gamete, "Sperm", "Sperm");
var oocyte = Clustering_Cell_AddNode(graph, gamete, "Oocyte", "Oocyte");
var matureOocyte = Clustering_Cell_AddNode(graph, gamete, "MatureOocyte", "Mature\nOocyte");
var zygote = Clustering_Cell_AddNode(graph, gamete, "Zygote", "Zygote");
Clustering_Cell_AddEdge(graph, inNode, splitter, null);
Clustering_Cell_AddEdge(graph, splitter, sperm, "Sperm_Effector_Act");
Clustering_Cell_AddEdge(graph, splitter, oocyte, "Oocyte_Effector_Act");
Clustering_Cell_AddEdge(graph, oocyte, matureOocyte, "Maturation");
Clustering_Cell_AddEdge(graph, matureOocyte, zygote, "Fertilization");//*/
}
private void CreateDifferentiation(DGraph graph, DCluster differentiation)
{
var inNode = graph.AddNode("Differentiation_in");
inNode.DrawingNode.Attr.Shape = MsaglShape.Circle;
inNode.DrawingNode.Attr.FillColor = MsaglColor.Red;
graph.AddNodeToCluster(differentiation, inNode);
var precursor = Clustering_Cell_AddNode(graph, differentiation, "Precursor", "Precursor");
var earlyMeiosis = Clustering_Cell_AddNode(graph, differentiation, "EarlyMeiosis", "Early Meiosis");
var meiosis = Clustering_Cell_AddNode(graph, differentiation, "Diff_Meiosis", "Meiosis");
var gamete = graph.AddCluster(differentiation, "Gamete");
Clustering_ApplyNodeAttributes(gamete);
CreateGamete(graph, gamete);
Clustering_Cell_AddEdge(graph, inNode, precursor, null);
Clustering_Cell_AddEdge(graph, precursor, earlyMeiosis, "GLD-1_Act\nOR\nGLD-2_Act");
Clustering_Cell_AddEdge(graph, earlyMeiosis, meiosis, "Pachytene");
Clustering_Cell_AddEdge(graph, meiosis, gamete, "MEK-2_Act\nAND\nMPK-1_Act");//*/
}
private void CreateProliferation(DGraph graph, DCluster proliferation)
{
var inNode = graph.AddNode("Proliferation_in");
inNode.DrawingNode.Attr.Shape = MsaglShape.Circle;
inNode.DrawingNode.Attr.FillColor = MsaglColor.Red;
graph.AddNodeToCluster(proliferation, inNode);
var splitter = graph.AddNode("Proliferation_Splitter");
splitter.DrawingNode.Attr.Shape = MsaglShape.Circle;
splitter.DrawingNode.Attr.FillColor = MsaglColor.Blue;
graph.AddNodeToCluster(proliferation, splitter);
var mitosis = graph.AddCluster(proliferation, "Mitosis");
Clustering_ApplyNodeAttributes(mitosis);
CreateMitosis(graph, mitosis);
var meiosis = graph.AddCluster(proliferation, "Meiosis");
Clustering_ApplyNodeAttributes(meiosis);
CreateMeiosis(graph, meiosis);
Clustering_Cell_AddEdge(graph, inNode, mitosis, null);
Clustering_Cell_AddEdge(graph, mitosis, splitter, "Early Meiosis");
Clustering_Cell_AddEdge(graph, splitter, graph.NodeMap["G0"], null);
Clustering_Cell_AddEdge(graph, splitter, graph.NodeMap["Inter"], null);//*/
}
private void CreateMeiosis(DGraph graph, DCluster meiosis)
{
var inter = Clustering_Cell_AddNode(graph, meiosis, "Inter", "Inter");
var rest = Clustering_Cell_AddNode(graph, meiosis, "Rest", "Rest");
var meiosis_cycle = graph.AddCluster(meiosis, "Meiosis_Cycle");
Clustering_ApplyNodeAttributes(meiosis_cycle);
var pro = Clustering_Cell_AddNode(graph, meiosis_cycle, "Pro", "Pro");
var meta = Clustering_Cell_AddNode(graph, meiosis_cycle, "Meta", "Meta");
var ana = Clustering_Cell_AddNode(graph, meiosis_cycle, "Ana", "Ana");
var telo = Clustering_Cell_AddNode(graph, meiosis_cycle, "Telo", "Telo");
Clustering_Cell_AddEdge(graph, inter, pro, null);
Clustering_Cell_AddEdge(graph, pro, meta, null);
Clustering_Cell_AddEdge(graph, meta, ana, null);
Clustering_Cell_AddEdge(graph, ana, telo, null);
Clustering_Cell_AddEdge(graph, meiosis_cycle, inter, "exit cell\ncycle");
Clustering_Cell_AddEdge(graph, meiosis_cycle, rest, null);//*/
}
private void CreateMitosis(DGraph graph, DCluster mitosis)
{
var inNode = graph.AddNode("Mitosis_In");
graph.AddNodeToCluster(mitosis, inNode);
inNode.DrawingNode.Attr.Shape = MsaglShape.Circle;
inNode.DrawingNode.Attr.FillColor = MsaglColor.Red;
var g0 = Clustering_Cell_AddNode(graph, mitosis, "G0", "G0");
var mitosis_cycle = graph.AddCluster(mitosis, "Mitosis_Cycle");
Clustering_ApplyNodeAttributes(mitosis_cycle);
var g1 = Clustering_Cell_AddNode(graph, mitosis_cycle, "G1", "G1");
var s = Clustering_Cell_AddNode(graph, mitosis_cycle, "S", "S");
var g2 = Clustering_Cell_AddNode(graph, mitosis_cycle, "G2", "G2");
var m = Clustering_Cell_AddNode(graph, mitosis_cycle, "M", "M");
Clustering_Cell_AddEdge(graph, inNode, g0, null);
Clustering_Cell_AddEdge(graph, g0, g1, null);
Clustering_Cell_AddEdge(graph, g1, s, null);
Clustering_Cell_AddEdge(graph, s, g2, null);
Clustering_Cell_AddEdge(graph, g2, m, null);
Clustering_Cell_AddEdge(graph, mitosis_cycle, g0, "exit cell\ncycle");//*/
}
private DNode Clustering_Cell_AddNode(DGraph graph, DCluster cluster, string id, string label)
{
var ret = graph.AddNode(id);
if (label != null)
ret.Label = new DTextLabel(ret, label);
graph.AddNodeToCluster(cluster, ret);
Clustering_ApplyNodeAttributes(ret);
return ret;
}
internal void AddCluster(DCluster cluster)
{
m_Clusters.Add(cluster);
}
