Uses of Class
broadwick.phylo.PhyloNode

Packages that use PhyloNode

Package	Description
broadwick.phylo	This package contains parsers for phylogenetic trees.

Uses of PhyloNode in broadwick.phylo

Methods in broadwick.phylo that return PhyloNode

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.

Methods in broadwick.phylo that return types with arguments of type PhyloNode

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() 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.
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 PhyloNode

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.

Method parameters in broadwick.phylo with type arguments of type PhyloNode

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 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.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.
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.