Package org.lifstools.jgoslin.parser

Class HmdbParser

java.lang.Object

org.lifstools.jgoslin.parser.Parser<LipidAdduct>

org.lifstools.jgoslin.parser.HmdbParser

public class HmdbParser
extends Parser<LipidAdduct>

Parser implementation for the HMDB lipid shorthand nomenclature.

Author:

Dominik Kopczynski, Nils Hoffmann

Nested Class Summary

Nested classes/interfaces inherited from class org.lifstools.jgoslin.parser.Parser

Parser.DPNode, Parser.ParsingErrors

Field Summary

Fields inherited from class org.lifstools.jgoslin.parser.Parser

avgPair, DEFAULT_QUOTE, EOF_RULE, EOF_RULE_NAME, EOF_SIGN, grammarName, MASK, nextFreeRuleIndex, NTtoNT, NTtoRule, originalTtoNT, quote, rightPair, RULE_ASSIGNMENT, RULE_SEPARATOR, RULE_TERMINAL, ruleToNT, SHIFT, START_RULE, substitution, TtoNT, usedEof

Constructor Summary

Constructors

Constructor	Description
HmdbParser()	Create a new instance of a HmdbParser with default grammar DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
HmdbParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a HmdbParser with default grammar DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
HmdbParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a HmdbParser.

Method Summary

Modifier and Type	Method	Description
HmdbParserEventHandler	newEventHandler()

Methods inherited from class org.lifstools.jgoslin.parser.Parser

add_terminal, collect_backwards, collect_backwards, collect_one_backwards, compute_rule_key, de_escape, extract_text_based_rules, fill_tree, get_next_free_rule_index, is_terminal, parse, parse, parse_regular, raise_events, readGrammar, top_nodes

Methods inherited from class java.lang.Object

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

Constructor Details

HmdbParser

public HmdbParser(KnownFunctionalGroups knownFunctionalGroups,
 String grammarContent,
 char quote)

Create a new instance of a HmdbParser.

Parameters:

knownFunctionalGroups - the known functional groups

grammarContent - the grammar text content

quote - the quotation character used in the grammar

HmdbParser

public HmdbParser(KnownFunctionalGroups knownFunctionalGroups)

Create a new instance of a HmdbParser with default grammar DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.

Parameters:

knownFunctionalGroups - the known functional groups

HmdbParser

public HmdbParser()

Create a new instance of a HmdbParser with default grammar DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.

Method Details

newEventHandler

public HmdbParserEventHandler newEventHandler()

Specified by:

newEventHandler in class Parser<LipidAdduct>