public IEnumerable <PossibleAssembly> ExtendFromStartNode(DeBruijnNode start)
{
//TODO: I believe this handles figure 8s and palindromes just fine, should verify though.
//First go Right
var rightNeighbors = start.GetRightExtensionNodesWithOrientationMarkingEdgeAsVisited(false);
List <PossibleAssembly> rights = new List <PossibleAssembly>();
foreach (var direction in rightNeighbors)
{
PossibleAssembly pa = new PossibleAssembly(start, true);
rights.AddRange(ExtendChain(pa, direction.Key, true, direction.Value));
}
List <PossibleAssembly> lefts = new List <PossibleAssembly>();
var leftNeighbors = start.GetLeftExtensionNodesWithOrientationMarkingEdgeAsVisited(false);
foreach (var direction in leftNeighbors)
{
PossibleAssembly pa = new PossibleAssembly(start, false);
lefts.AddRange(ExtendChain(pa, direction.Key, false, direction.Value));
}
//Now to combine a left and right chain
if (lefts.Count > 0 && rights.Count > 0)
{
foreach (var right in rights)
{
foreach (var left in lefts)
{
yield return(new PossibleAssembly(left, right));
}
}
}
else if (lefts.Count > 0)
{
foreach (var left in lefts)
{
yield return(left);
}
}
else if (rights.Count > 0)
{
foreach (var right in rights)
{
yield return(right);
}
}
}
private IEnumerable <PossibleAssembly> ExtendChain(PossibleAssembly currentPath, DeBruijnNode nextNeighbor, bool goingRight, bool sameOrientation)
{
byte nextSymbol = MetaNode.GetNextSymbol(nextNeighbor, KmerLength, !goingRight);
currentPath.Add(nextNeighbor, nextSymbol);
nextNeighbor.IsVisited = true;
bool nextRight = !goingRight ^ sameOrientation;
List <KeyValuePair <DeBruijnNode, bool> > nextNodes = nextRight ? nextNeighbor.GetRightExtensionNodesWithOrientationMarkingEdgeAsVisited() :
nextNeighbor.GetLeftExtensionNodesWithOrientationMarkingEdgeAsVisited();
DeBruijnNode next;
//DeBruijnNode last = currentPath.constituentNodes[currentPath.constituentNodes.Count-1];
//DeBruijnNode first=currentPath.constituentNodes[0];
while (nextNodes.Count == 1)
{
var nextSet = nextNodes.First();
next = nextSet.Key;
sameOrientation = nextSet.Value;
nextRight = (!nextRight) ^ sameOrientation;
nextSymbol = MetaNode.GetNextSymbol(next, KmerLength, !nextRight);
//now check if we are in a circle or a loop at the end, these are very annoying situtations, basic criteria, can't leave
//the same node the same way twice
if (next.IsVisited && currentPath.constituentNodes.Contains(next))
{
//okay, if we are equal to the first node or the last node, we can't leave or return the same way we came, otherwise we are done.
var excludedNextNodes = currentPath.GetPreviousWaysNodeWasLeft(next);
//how many neighbors dow we have in this group?
var temp = nextRight ? next.GetRightExtensionNodesWithOrientationMarkingEdgeAsVisited() : next.GetLeftExtensionNodesWithOrientationMarkingEdgeAsVisited();
temp = temp.Where(x => !excludedNextNodes.Contains(x.Key)).ToList();
//only one way to go
if (temp.Count == 1)
{
nextNodes = temp;
//currentPath.contigSequence.Add(nextSymbol);
currentPath.Add(next, nextSymbol);
next.IsVisited = true; //flag not actually used though
}
else if (temp.Count == 0) //done
{
if (currentPath.constituentNodes[0] == next)
{
currentPath.CircularLoop = true;
}
yield return(currentPath);
//nextNodes.Clear();//we are done
yield break;
}
else //Extend path using all feasible options, then continue.
{
foreach (var neighbor in temp)
{
foreach (var v in ExtendChain(currentPath.Clone(), neighbor.Key, nextRight, neighbor.Value))
{
yield return(v);
}
}
//nextNodes.Clear();//done
yield break;
}
}
else
{
//currentPath.contigSequence.Add(nextSymbol);
currentPath.Add(next, nextSymbol);
next.IsVisited = true;//flag not actually used though
nextNodes = nextRight ? next.GetRightExtensionNodesWithOrientationMarkingEdgeAsVisited() : next.GetLeftExtensionNodesWithOrientationMarkingEdgeAsVisited();
}
}
//If we have more than one node remaining, have to kick it off.
if (nextNodes.Count > 1)
{
foreach (var neighbor in nextNodes)
{
foreach (var v in ExtendChain(currentPath.Clone(), neighbor.Key, nextRight, neighbor.Value))
{
yield return(v);
}
}
}
if (nextNodes.Count == 0)
{
yield return(currentPath);
}
}