/// <summary>
/// Create a new node from the initial node, recursively changing things.
/// </summary>
/// <param name="initialNode">The node found from the newick parser</param>
public SelectomeTreeNode(Node initialNode)
{
if (initialNode == null)
{
throw new NullReferenceException("initialNode");
}
this.MetaData = initialNode.MetaData;
this.children = new Dictionary<SelectomeTreeNode, Edge>();
this.Name = initialNode.Name;
//recursively update child nodes
foreach (var child in initialNode.Children)
{
this.children.Add(new SelectomeTreeNode(child.Key), child.Value);
}
}
/// <summary>
/// Gets the Branch node
/// </summary>
/// <param name="reader">TextReader we are working with</param>
/// <param name="isRoot"></param>
/// <returns>Branch object</returns>
private Node GetBranch(TextReader reader, bool isRoot)
{
Node branch = new Node { IsRoot = isRoot };
bool firstBranch = true;
while (true)
{
char peek = Peek(reader);
if (!firstBranch && peek == ')')
{
break;
}
char c = ReadChar(reader);
if (firstBranch)
{
if (c != '(')
{
throw new FormatException(string.Format
(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name,
"Missing [(] as a first branch"));
}
firstBranch = false;
}
else
{
if (c != ',')
{
throw new FormatException(string.Format
(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name,
"Missing [,] in between branches"));
}
}
var tmp = GetNode(reader, false);
branch.Children.Add(tmp.Key, tmp.Value);
}
//move to next char of ")"
char nextCloseChar = ReadChar(reader);
if (nextCloseChar != ')')
{
throw new FormatException(string.Format
(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name,
"Missing [)] branch is not closed"));
}
return branch;
}
/// <summary>
/// Gets the formatted object which is used for formatting
/// </summary>
/// <returns>Formatter tree.</returns>
private static Tree GetFormattedObject()
{
// Tree with three nodes are created
Node nd1 = new Node();
nd1.Name = "a";
Edge ed1 = new Edge();
ed1.Distance = 0.1;
Node nd2 = new Node();
nd2.Name = "b";
Edge ed2 = new Edge();
ed2.Distance = 0.2;
Node nd3 = new Node();
nd3.Name = "c";
Edge ed3 = new Edge();
ed3.Distance = 0.3;
Node nd4 = new Node();
nd4.Children.Add(nd1, ed1);
Edge ed4 = new Edge();
ed4.Distance = 0.4;
Node nd5 = new Node();
nd5.Children.Add(nd2, ed2);
nd5.Children.Add(nd3, ed3);
Edge ed5 = new Edge();
ed5.Distance = 0.5;
Node ndRoot = new Node();
ndRoot.Children.Add(nd4, ed4);
ndRoot.Children.Add(nd5, ed5);
// All the Node and Edges are combined to form a tree
Tree baseTree = new Tree();
baseTree.Root = ndRoot;
return baseTree;
}
/// <summary>
/// Recursive method to get each node into string
/// </summary>
/// <param name="node">tree node</param>
/// <param name="edge">edge</param>
/// <param name="stringBuilder">output newick string</param>
void Write(Node node, Edge edge, ref StringBuilder stringBuilder)
{
if (node.IsLeaf)
{
stringBuilder.Append(string.Format("{0}:{1}", node.Name, edge.Distance));
}
else
{
stringBuilder.Append("(");
bool firstNode = true;
foreach (KeyValuePair<Node, Edge> child in node.Children)
{
Edge localEdge = child.Value;
Node localNode = child.Key;
if (localNode == node)
{
throw new ArgumentException(string.Format
(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name,
"Tree object has more than one root"));
}
if (!firstNode)
{
stringBuilder.Append(",");
}
this.Write(localNode, localEdge, ref stringBuilder);
firstNode = false;
}
//last node
stringBuilder.Append(null == edge ? ")" : string.Format("):{0}", edge.Distance));
}
}
/// <summary>
/// Gets the leaves for the entire phylogenetic tree.
/// </summary>
/// <param name="nodeList">Phylogenetic tree node list.</param>
/// <param name="nodeName">Node names</param>
/// <param name="distance">edge distances</param>
void GetAllNodesAndEdges(Node rootNode,
ref List<string> nodeName, ref List<double> distance)
{
IList<Edge> edges = rootNode.Edges;
if (null != edges)
{
// Get all the edges distances
foreach (Edge ed in edges)
{
distance.Add(ed.Distance);
}
}
// Gets all the nodes
IList<Node> nodes = rootNode.Nodes;
if (null != nodes)
{
foreach (Node nd in nodes)
{
if (nd.IsLeaf)
{
nodeName.Add(nd.Name);
}
else
{
// Get the nodes and edges recursively until
// all the nodes and edges are retrieved.
GetAllNodesAndEdges(nd, ref nodeName, ref distance);
}
}
}
}