public static uint CalculateConnectionWeight(DeBruijnNode FirstNode, DeBruijnNode SecondNode)
{
//First verify that they share
if (!FirstNode.GetExtensionNodes().Contains(SecondNode))
{
throw new Exception("Can't calculate non-overlapping extensions");
}
return(SecondNode.KmerCount);
}
/// <summary>
/// Removes nodes in link from the graph.
/// Parallelization Note: Locks required here. We are modifying graph structure here.
/// </summary>
/// <param name="nodes">List of nodes to remove.</param>
/// <param name="lastNodes">Set of all nodes occurring at end of dangling links.</param>
private static void RemoveLinkNodes(DeBruijnPath nodes, HashSet <DeBruijnNode> lastNodes)
{
// Nodes in the list are part of a single dangling link.
// Only the last element of link can have left or right extensions that are valid parts of graph.
DeBruijnNode linkStartNode = nodes.PathNodes.Last();
// Update adjacency of nodes connected to the last node.
// Read lock not required as linkStartNode's dictionary will not get updated
// Locks used during removal of extensions.
foreach (DeBruijnNode graphNode in linkStartNode.GetExtensionNodes())
{
// Condition to avoid updating other linkStartNode's dictionary. Reduces conflicts.
if (!lastNodes.Contains(graphNode))
{
graphNode.RemoveExtensionThreadSafe(linkStartNode);
}
}
}
/// <summary>
/// Visits all connected nodes, not caring about orientation here. Hope the graph
/// is not so big this leads to an OOM exception.
/// </summary>
/// <param name="startNode">Start node.</param>
private void visitAllConnectedNodes(DeBruijnNode startNode)
{
Stack <DeBruijnNode> toProcess = new Stack <DeBruijnNode> (16000);
toProcess.Push(startNode);
//Visit all nodes, avoid function all recursion with stack.
do
{
DeBruijnNode next = toProcess.Pop();
next.IsVisited = true;
foreach (DeBruijnNode neighbor in next.GetExtensionNodes())
{
if (neighbor.IsVisited)
{
continue;
}
else
{
toProcess.Push(neighbor);
}
}
}while(toProcess.Count > 0);
}