de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser

Class NewickParser

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser.NewickParser

public class NewickParser
extends Object

This class implements a simple newick parser and allows the construction of a PhyloTree

Author:

Michael Scharfe

Constructor Summary

Constructors

Constructor and Description
NewickParser(BufferedReader b) This constructor initialize the newick parser

Method Summary

Methods

Modifier and Type	Method and Description
PhyloTree	tokenize() This method construct a PhyloTree from the given input stream

Methods inherited from class java.lang.Object

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

Constructor Detail

NewickParser

public NewickParser(BufferedReader b)

This constructor initialize the newick parser

Parameters:

b - the BufferedReader which reads the newick file

Method Detail

tokenize

public PhyloTree tokenize()
                   throws NonParsableException

This method construct a PhyloTree from the given input stream

Returns:

the PhyloTree

Throws:

NonParsableException - if the stream is not parsable