broadwick.phylo

Class NewickTreeParser

java.lang.Object

broadwick.phylo.NewickTreeParser

public class NewickTreeParser
extends Object

Parser for a Newick tree. This has limited functionality and only works for Newick trees

• with unique node names (e.g. one node can be unnamed but the rest must be uniquely named)
• with defined branch lengths (e.g. (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F:0.0;)

Field Summary

Fields

Modifier and Type	Field and Description
private int	branchLabel
private String	newickString

Constructor Summary

Constructors

Constructor and Description
NewickTreeParser() Create the parser.
NewickTreeParser(String newickFile) Create the parser.

Method Summary

Modifier and Type	Method and Description
private PhyloNode	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 Collection<String>	findNodes(String tree) Parse a tree splitting it into top level nodes and subtrees.
private int	getClosingParenthesis(String strng) Get the index of the closing parenthesis in a string that starts with an opening parenthesis.
Tree<PhyloNode,Edge<PhyloNode>>	parse() Parse a string from a Newick file.
Tree<PhyloNode,Edge<PhyloNode>>	parse(String newickStr) Parse a given string that MUST be a valid Newick format.
private void	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	parseString(String stringToParse, PhyloNode parent, Tree<PhyloNode,Edge<PhyloNode>> tree) Parse a string in Newick format (where the root node has been removed) recursively.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

newickString

private String newickString

branchLabel

private int branchLabel

Constructor Detail

NewickTreeParser

public NewickTreeParser(String newickFile)

Create the parser.

Parameters:

newickFile - the name of the file containing the tree.

NewickTreeParser

public NewickTreeParser()

Create the parser.

Method Detail

parse

public final Tree<PhyloNode,Edge<PhyloNode>> parse(String newickStr)

Parse a given string that MUST be a valid Newick format.

Parameters:

newickStr - the string to parse.

Returns:

a Tree created from the parsed string.

parse

public final Tree<PhyloNode,Edge<PhyloNode>> parse()

Parse a string from a Newick file.

Returns:

a generated Tree object.

parseString

private void parseString(String stringToParse,
                         PhyloNode parent,
                         Tree<PhyloNode,Edge<PhyloNode>> tree)

Parse a string in Newick format (where the root node has been removed) recursively.

Parameters:

stringToParse - the string to be parsed.

parent - the parent node for the string (initially this is the root node but will be a brach node if this method is called recursively).

tree - the tree to which the created nodes will be attached.

findNodes

private Collection<String> findNodes(String tree)

Parse a tree splitting it into top level nodes and subtrees.

Parameters:

tree - the tree tp be parsed.

Returns:

a collection of nodes and subtrees contained in the parsed string

getClosingParenthesis

private int getClosingParenthesis(String strng)

Get the index of the closing parenthesis in a string that starts with an opening parenthesis. If the string does not start with an opening parenthesis then an IllegalArgumentException is thrown. The algorithm for finding the closing parenthesis is simple - keep reading the string incrementing a count of the number of opening parentheses we find and decrementing the count if we encounter a closing parenthesis. When we read a closing parenthesis AND the count becomes zero we have our closing parenthesis.

Parameters:

strng - the string to examine.

Returns:

the index in the string of the closing parenthesis, -1 if none is found.

parseNode

private void 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.

Parameters:

node - the string containing the node information.

tree - the tree to which the created node will be attached.

parent - the node on the tree to which the new node will be created.

addNodeToTree

private PhyloNode 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. If the string is empty then a dummy node is added, this is useful fro creating (unnamed) branches.

Parameters:

node - the string representing the node.

tree - the tree object on which the node will be placed.

parent - the parent node to which this node is attached.

createUniqueName - if the name of the node is not unique then add create a unique one if this is true.

Returns:

the node added to the tree.