Package org.lifstools.jgoslin.parser

Class FattyAcidParser

java.lang.Object

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

org.lifstools.jgoslin.parser.FattyAcidParser

public final class FattyAcidParser
extends Parser<LipidAdduct>

Parser implementation for IUPAC Fatty acids 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
FattyAcidParser()	Create a new instance of a FattyAcidParser with default grammar DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
FattyAcidParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a FattyAcidParser with default grammar DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
FattyAcidParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a FattyAcidParser.

Method Summary

Modifier and Type	Method	Description
FattyAcidParserEventHandler	newEventHandler()
LipidAdduct	parse(String text, BaseParserEventHandler eventHandler)	Parse the given text, constructing the output object of type T using the provided parser event handler.
LipidAdduct	parse(String text, BaseParserEventHandler eventHandler, boolean with_exception)	Parse the given text, constructing the output object of type T using the provided parser event handler.Allows the user to specify, if exceptions should be thrown on errors.

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_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

FattyAcidParser

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

Create a new instance of a FattyAcidParser.

Parameters:

knownFunctionalGroups - the known functional groups

grammarContent - the grammar text content

quote - the quotation character used in the grammar

FattyAcidParser

public FattyAcidParser(KnownFunctionalGroups knownFunctionalGroups)

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

Parameters:

knownFunctionalGroups - the known functional groups

FattyAcidParser

public FattyAcidParser()

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

Method Details

parse

public LipidAdduct parse(String text,
 BaseParserEventHandler eventHandler)

Description copied from class: Parser

Parse the given text, constructing the output object of type T using the provided parser event handler.

Overrides:

parse in class Parser<LipidAdduct>

Parameters:

text - the text to parse.

eventHandler - the parser event handler to process events created by the parser.

Returns:

the parsed object of type T if successful, otherwise an exception will be thrown.

parse

public LipidAdduct parse(String text,
 BaseParserEventHandler eventHandler,
 boolean with_exception)

Description copied from class: Parser

Parse the given text, constructing the output object of type T using the provided parser event handler.Allows the user to specify, if exceptions should be thrown on errors.

Overrides:

parse in class Parser<LipidAdduct>

Parameters:

text - the text to parse.

eventHandler - the parser event handler to process events created by the parser.

with_exception - if true, throws exception if parsing was not successful.

Returns:

the parsed object of type T if successful, otherwise null, if throwError is false.

newEventHandler

public FattyAcidParserEventHandler newEventHandler()

Specified by:

newEventHandler in class Parser<LipidAdduct>