Uses of Class
broadwick.graph.Tree

Packages that use Tree

Package	Description
broadwick.graph	This package contains classes for reading and manipulating graphs.
broadwick.phylo	This package contains parsers for phylogenetic trees.

Uses of Tree in broadwick.graph

Methods in broadwick.graph that return Tree

Modifier and Type	Method and Description
Tree<V,E>	Tree.getSubTree(V vertex) Obtain the sub-tree with vertex as it's root.

Methods in broadwick.graph with parameters of type Tree

Modifier and Type	Method and Description
void	Tree.addSubtree(Tree<V,E> subtree, V node, E connectingEdge) Add a [sub]tree to the current tree.
private void	DepthFirstIterator.traverseTree(Tree<V,E> tree) Perform a depth first traversal through the tree recording, in a linked list, the vertices visited in order.

Constructors in broadwick.graph with parameters of type Tree

Constructor and Description
DepthFirstIterator(Tree<V,E> tree) Create the iterator over a tree.

Uses of Tree in broadwick.phylo

Methods in broadwick.phylo that return Tree

Modifier and Type	Method and Description
Tree<PhyloNode,Edge<PhyloNode>>	NewickTreeParser.parse() Parse a string from a Newick file.
Tree<PhyloNode,Edge<PhyloNode>>	NewickTreeParser.parse(String newickStr) Parse a given string that MUST be a valid Newick format.

Methods in broadwick.phylo with parameters of type Tree

Modifier and Type	Method and Description
private PhyloNode	NewickTreeParser.addNodeToTree(String node, Tree<PhyloNode,Edge<PhyloNode>> tree, PhyloNode parent, boolean createUniqueName) Given a string that represents a node in the tree, split in into its constituent name and distance components and add it to the tree.
private void	NewickTreeParser.parseNode(String node, Tree<PhyloNode,Edge<PhyloNode>> tree, PhyloNode parent) Parse a string containing information on a node in Newick format and attach it to a given tree.
private void	NewickTreeParser.parseString(String stringToParse, PhyloNode parent, Tree<PhyloNode,Edge<PhyloNode>> tree) Parse a string in Newick format (where the root node has been removed) recursively.