public void AddBranch(TreeBranch branch)
{
// A node can only support three connections
if (branches.Count == 3)
{
throw new OverflowException("This node already has 3 connections.");
}
else
{
// If the branch being added connects this node to a leaf, and one of the other branches also
// connects to a leaf, this is a terminal node. Add this node to the list of terminal nodes.
if (branch.Follow(this).GetType() == typeof(TreeLeaf))
{
foreach (TreeBranch otherBranch in branches)
{
if (otherBranch.Follow(this).GetType() == typeof(TreeLeaf))
{
tree.terminalNodesList.Add(this);
}
}
}
branches.Add(branch);
}
}
public void RemoveBranch(TreeBranch branch)
{
// List's Remove method handles low-count and not-in-list conditions,
// so I won't handle them here.
// bool removeFlag = branches.Remove(branch); Not sure why I need the return code.
branches.Remove(branch);
if (childBranch1 == branch)
{
childBranch1 = null;
}
else if (childBranch2 == branch)
{
childBranch2 = null;
}
//if (!removeFlag)
//{
// return false;
//}
if (parentBranch == branch)
{
RemoveParent();
}
// If the branch removal results in no connections, the node can be removed from the tree.
if (branches.Count == 0)
{
tree.nodesList.Remove(this);
}
else if (true)
{
// If the branch was a terminal node and the branch being removed was connected to a leaf,
// if only one other branch is connected to a leaf, this is no longer a terminal node.
// Remove this node from the list of terminal nodes.
if (branch.Follow(this).GetType() == typeof(TreeLeaf))
{
int leafCount = 0;
foreach (TreeBranch otherBranch in branches)
{
if (otherBranch.Follow(this).GetType() == typeof(TreeLeaf))
{
leafCount += 1;
}
}
if (leafCount <= 1)
{
tree.terminalNodesList.Remove(this);
}
}
}
//return true;
}
void AssertPaternity()
// For each branch out from the given root which is not a parent branch, assign that branch
// as the child's parent branch.
// As this could be deeply recursive and could result in a stack overflow, this must be coded as a loop.
{
Stack <Tuple <TreeMember, TreeBranch> > arguments = new Stack <Tuple <TreeMember, TreeBranch> >();
TreeBranch prevBranch = new TreeBranch();
bool stepBack = false;
foreach (TreeBranch rootBranch in root.Branches)
{
arguments.Push(Tuple.Create(rootBranch.Follow(root), rootBranch));
while (arguments.Count > 0)
{
Tuple <TreeMember, TreeBranch> nextArgument = arguments.Peek();
TreeMember member = nextArgument.Item1;
TreeBranch parentBranch = nextArgument.Item2;
stepBack = false;
member.parentBranch = parentBranch;
((TreeNode)parentBranch.Follow(member)).SetChild(parentBranch);
if (member.GetType() == typeof(TreeNode))
{
TreeNode node = (TreeNode)member;
if (node.Branches.Contains(prevBranch))
// If the previously-used branch is a member of this node's branches, that means we've already used the
// branches of this node, and can discard it.
{
stepBack = true;
}
else
{
foreach (TreeBranch branch in node.Branches)
{
if (branch != parentBranch)
{
arguments.Push(Tuple.Create(branch.Follow(node), branch));
}
}
}
}
else
{
stepBack = true;
}
if (stepBack)
{
prevBranch = parentBranch;
arguments.Pop();
}
}
}
}
public TreeNode GetParent()
{
if (parentBranch != null)
{
return((TreeNode)parentBranch.Follow(this));
}
else
{
return(null);
}
}
void CountNodeChildren()
// Walk the tree up from the terminal nodes and count the children of each node.
{
if (!isRooted)
{
throw new InvalidOperationException("The tree must be rooted to count children.");
}
foreach (TreeNode terminalNode in terminalNodesList)
{
terminalNode.childCount = 2;
TreeNode currentNode = terminalNode;
while (currentNode != root)
{
TreeBranch parentBranch = currentNode.parentBranch;
TreeNode parentNode = (TreeNode)parentBranch.Follow(currentNode);
TreeBranch otherChildBranch;
if (parentNode.childBranch1 == parentBranch)
{
otherChildBranch = parentNode.childBranch2;
}
else // should be childBranch2
{
otherChildBranch = parentNode.childBranch1;
}
if (otherChildBranch.Follow(parentNode).GetType() == typeof(TreeLeaf))
{
parentNode.childCount = currentNode.childCount + 1;
}
else if (parentNode.childCount > 0)
{
parentNode.childCount += currentNode.childCount;
}
else
{
// Need to wait for another terminal node to propogate up.
parentNode.childCount += currentNode.childCount;
break;
}
currentNode = parentNode;
}
}
}
static double GetSumBranchLength(TreeMember member, TreeBranch baseBranch, bool includeBranch, out int numLeaves)
// This is a recursive function
//
{
// Algorithm:
// 1. Store the branch length to the current member in "distance" (except the first if includeBranch is true).
// 2. If the current member is a node, add the other branches to the stack and continue the loop.
// If the current member is a leaf, add 1 to the number of leaves, add the stemLength to the sumBranchLength, and subtract the length to this branch from the distance.
// 3.
double sumBranchLength = 0;
numLeaves = 0;
Stack <Tuple <TreeMember, TreeBranch> > arguments = new Stack <Tuple <TreeMember, TreeBranch> >();
double distance = 0;
arguments.Push(Tuple.Create(baseBranch.Follow(member), baseBranch));
TreeBranch prevBranch = new TreeBranch();
bool stepBack = false;
while (arguments.Count > 0)
{
Tuple <TreeMember, TreeBranch> nextArgument = arguments.Peek();
TreeMember nextMember = nextArgument.Item1;
TreeBranch nextBaseBranch = nextArgument.Item2;
if (nextMember.GetType() == typeof(TreeNode))
{
TreeNode node = (TreeNode)nextMember;
if (node.Branches.Contains(prevBranch))
// If the previously-used branch is a member of this node's branches, that means we've already used the
// branches of this node, and can discard it.
{
stepBack = true;
}
else
{
distance += nextBaseBranch.BranchLength;
foreach (TreeBranch branch in node.Branches)
{
if (branch != nextBaseBranch)
{
arguments.Push(Tuple.Create(branch.Follow(node), branch));
}
}
}
}
else
// This is a leaf, so add the distance to the sum, increment the leaf count, and step backward
{
distance += nextBaseBranch.BranchLength;
sumBranchLength += distance;
numLeaves++;
stepBack = true;
}
if (stepBack)
{
prevBranch = nextBaseBranch;
distance -= nextBaseBranch.BranchLength;
arguments.Pop();
stepBack = false;
}
}
if (!includeBranch)
{ // If we didn't want to include the base branch length, correct for that here.
sumBranchLength -= numLeaves * baseBranch.BranchLength;
}
return(sumBranchLength);
}
void DetermineSteps()
// Determine the groups to be used in each step of the alignment.
// Step through the tree to find the terminal leaf-only nodes and step back to join them together,
// with each step stored in a tuple, and the leaf groups 1 and 2 stored in lists in members 1 and 2 of the
// tuple, respectively.
// Possible to parallelize, but it looks like the overhead is generally too much for the work being done.
// may want to test that on larger sets, however.
{
if (!isRooted)
{
throw new InvalidOperationException("The tree must be rooted to determine alignment steps.");
}
Dictionary <TreeNode, List <TreeLeaf> > waitingList = new Dictionary <TreeNode, List <TreeLeaf> >(); // Store the members of one child of the node until the other child has been evaluated.
steps = new List <Tuple <ReadOnlyCollection <T>, ReadOnlyCollection <T>, double> >();
foreach (TreeNode terminalNode in terminalNodesList)
{
List <TreeLeaf> group1 = new List <TreeLeaf>();
TreeLeaf leaf1 = (TreeLeaf)terminalNode.childBranch1.Follow(terminalNode);
group1.Add(leaf1);
List <TreeLeaf> group2 = new List <TreeLeaf>();
TreeLeaf leaf2 = (TreeLeaf)terminalNode.childBranch2.Follow(terminalNode);
group2.Add(leaf2);
steps.Add(CreateStep(group1, group2));
TreeNode currentNode = terminalNode;
List <TreeLeaf> childLeaves = new List <TreeLeaf>();
childLeaves.Add(leaf1);
childLeaves.Add(leaf2);
while (currentNode != root)
{
TreeBranch parentBranch = currentNode.parentBranch;
TreeNode parentNode = (TreeNode)parentBranch.Follow(currentNode);
TreeBranch otherChildBranch;
group1 = new List <TreeLeaf>();
group2 = new List <TreeLeaf>();
if (parentNode.childBranch1 == parentBranch)
{
otherChildBranch = parentNode.childBranch2;
}
else // should be childBranch2
{
otherChildBranch = parentNode.childBranch1;
}
if (otherChildBranch.Follow(parentNode).GetType() == typeof(TreeLeaf))
// The other child is a leaf, so we're okay.
{
group1 = childLeaves;
TreeLeaf otherChildLeaf = (TreeLeaf)otherChildBranch.Follow(parentNode);
group2.Add(otherChildLeaf);
}
else if (waitingList.ContainsKey(parentNode))
// The other child is a node which was waiting for the other children to be evaluated.
{
group1 = childLeaves.ToList <TreeLeaf>();
group2 = waitingList[parentNode];
}
else
// The other child is a node. We'll need to save the current child and store the values
// for later. This also means we need to start over with another terminal node.
{
waitingList.Add(parentNode, childLeaves);
break;
}
steps.Add(CreateStep(group1, group2));
foreach (TreeLeaf leaf in group2)
{
childLeaves.Add(leaf);
}
currentNode = parentNode;
}
}
}
public void CalculateSimilarities()
// Construct a similarities matrix
// Clustal does this by storing the path to root for each leaf (storing the distance), then finds the common ancestor
// for each pair, storing the distance from the other sequence to it.
//
// I think a better implementation would be to loop over the leaves to get their paths to root, then for each pair,
// walk their paths until they diverge
{
similarityMatrix = new double[leavesCount, leavesCount];
Dictionary <TreeLeaf, List <Tuple <TreeNode, double> > > pathsToRoot = new Dictionary <TreeLeaf, List <Tuple <TreeNode, double> > >();
foreach (TreeLeaf leaf in leavesList)
{
List <Tuple <TreeNode, double> > pathToRoot = new List <Tuple <TreeNode, double> >();
double distance = 0;
TreeBranch parentBranch = leaf.parentBranch;
TreeNode parentNode = (TreeNode)parentBranch.Follow(leaf);
while (true)
{
distance += parentBranch.BranchLength;
pathToRoot.Add(Tuple.Create(parentNode, distance));
parentBranch = parentNode.parentBranch;
if (parentBranch != null)
{
parentNode = (TreeNode)parentBranch.Follow(parentNode);
}
else
{
break;
}
}
pathsToRoot.Add(leaf, pathToRoot);
}
for (int i = 0; i < leavesCount - 1; i++)
{
TreeLeaf leafI = leavesList[i];
List <Tuple <TreeNode, double> > pathToRootI = pathsToRoot[leafI];
for (int j = i + 1; j < leavesCount; j++)
{
TreeLeaf leafJ = leavesList[j];
List <Tuple <TreeNode, double> > pathToRootJ = pathsToRoot[leafJ];
bool found = false;
foreach (Tuple <TreeNode, double> pathMemberI in pathToRootI)
{
foreach (Tuple <TreeNode, double> pathmemberJ in pathToRootJ)
{
if (pathMemberI.Item1 == pathmemberJ.Item1)
{
found = true;
similarityMatrix[i, j] = 1 - (pathMemberI.Item2 + pathmemberJ.Item2);
break;
}
}
if (found)
{
break;
}
}
}
}
// Then Clustal forces any values less than 0.01 to be 0.01 (within the sequence ranges)
// and sets small values above 1 to 1, but values above 1.1 go into an error handling method.
// I won't implement this yet. Note that this is done while they are still in distances, not
// similarities.
}
