Parser
Class Newick

java.lang.Object
  |
  +--Parser.Newick

All Implemented Interfaces:

NewickConstants

public class Newick

extends java.lang.Object

implements NewickConstants

A static class used for parsing a Newick format file containing just one tree

Author:

Yunhong Zhou, Tamara Munzner

Field Summary

static Token	jj_nt
static boolean	lookingAhead
static Token	token
static NewickTokenManager	token_source

Fields inherited from interface Parser.NewickConstants

alpha, both_char, comment, DEFAULT, digit, double_number, EOF, exponent, number, only_quote_char, quoted_char, quoted_string, single_quote, tokenImage, unquoted_char, unquoted_string, whitespace

Constructor Summary

Newick(java.io.InputStream stream)

Newick(NewickTokenManager tm)

Newick(java.io.Reader stream)

Method Summary

static double	branch_length()
void	close()
static void	descendant_list()
static void	disable_tracing()
static void	enable_tracing()
static ParseException	generateParseException()
static Token	getNextToken()
static Token	getToken(int index)
static void	Input()
static java.lang.String	label()
void	parseTree(Tree t) function parseTree initiates field tree, call function Input to parse the input.
static java.lang.String	quoted_label() for each quoted label, we remove double quotes from the string
static void	ReInit(java.io.InputStream stream)
void	ReInit(NewickTokenManager tm)
static void	ReInit(java.io.Reader stream)
static void	subtree() function subtree will set name, length and weight for each tree node
static java.lang.String	unquoted_label() for each unquoted label, we need to replace '_' by ' '

Methods inherited from class java.lang.Object

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

Field Detail

token_source

public static NewickTokenManager token_source

token

public static Token token

jj_nt

public static Token jj_nt

lookingAhead

public static boolean lookingAhead

Constructor Detail

Newick

public Newick(java.io.InputStream stream)

Newick

public Newick(java.io.Reader stream)

Newick

public Newick(NewickTokenManager tm)

Method Detail

parseTree

public void parseTree(Tree t)

function parseTree initiates field tree, call function Input to parse the input.

Parameters:

t - Tree t will be initiated throught the parsing process

close

public void close()

Input

public static final void Input()
                        throws ParseException

ParseException

descendant_list

public static final void descendant_list()
                                  throws ParseException

ParseException

subtree

public static final void subtree()
                          throws ParseException

function subtree will set name, length and weight for each tree node

ParseException

label

public static final java.lang.String label()
                                    throws ParseException

ParseException

unquoted_label

public static final java.lang.String unquoted_label()
                                             throws ParseException

for each unquoted label, we need to replace '_' by ' '

ParseException

quoted_label

public static final java.lang.String quoted_label()
                                           throws ParseException

for each quoted label, we remove double quotes from the string

ParseException

branch_length

public static final double branch_length()
                                  throws ParseException

ParseException

ReInit

public static void ReInit(java.io.InputStream stream)

ReInit

public static void ReInit(java.io.Reader stream)

ReInit

public void ReInit(NewickTokenManager tm)

getNextToken

public static final Token getNextToken()

getToken

public static final Token getToken(int index)

generateParseException

public static ParseException generateParseException()

enable_tracing

public static final void enable_tracing()

disable_tracing

public static final void disable_tracing()