Uses of Class
org.lifstools.jgoslin.domain.KnownFunctionalGroups

Packages that use KnownFunctionalGroups

Package	Description
org.lifstools.jgoslin.domain	This package contains the main common domain models for lipids.
org.lifstools.jgoslin.parser	This package contains the parser implementations for the lipid grammars.

Uses of KnownFunctionalGroups in org.lifstools.jgoslin.domain

Fields in org.lifstools.jgoslin.domain declared as KnownFunctionalGroups

Modifier and Type	Field	Description
protected KnownFunctionalGroups	FunctionalGroup.knownFunctionalGroups

Constructors in org.lifstools.jgoslin.domain with parameters of type KnownFunctionalGroups

Modifier	Constructor	Description
	AcylAlkylGroup(FattyAcid _fa, int _position, int _count, boolean _alkyl, boolean _N_bond, KnownFunctionalGroups knownFunctionalGroups)
	AcylAlkylGroup(FattyAcid _fa, int _position, int _count, boolean _alkyl, KnownFunctionalGroups knownFunctionalGroups)
	AcylAlkylGroup(FattyAcid _fa, KnownFunctionalGroups knownFunctionalGroups)
	CarbonChain(FattyAcid _fa, int _position, int _count, KnownFunctionalGroups knownFunctionalGroups)
	CarbonChain(FattyAcid _fa, int _position, KnownFunctionalGroups knownFunctionalGroups)
	CarbonChain(FattyAcid _fa, KnownFunctionalGroups knownFunctionalGroups)
	Cycle(int _cycle, int _start, int _end, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
	Cycle(int _cycle, int _start, int _end, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, ArrayList<Element> _bridge_chain, KnownFunctionalGroups knownFunctionalGroups)
	Cycle(int _cycle, int _start, int _end, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
	Cycle(int _cycle, int _start, int _end, KnownFunctionalGroups knownFunctionalGroups)
	Cycle(int _cycle, KnownFunctionalGroups knownFunctionalGroups)
	FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
	FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, LipidFaBondType _lipid_FA_bond_type, int _position, KnownFunctionalGroups knownFunctionalGroups)
	FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, LipidFaBondType _lipid_FA_bond_type, KnownFunctionalGroups knownFunctionalGroups)
	FattyAcid(String _name, int _num_carbon, DoubleBonds _double_bonds, KnownFunctionalGroups knownFunctionalGroups)
	FattyAcid(String _name, int _num_carbon, KnownFunctionalGroups knownFunctionalGroups)
	FattyAcid(String _name, KnownFunctionalGroups knownFunctionalGroups)
	FunctionalGroup(String _name, int _position, int _count, DoubleBonds _double_bonds, boolean _is_atomic, String _stereochemistry, ElementTable _elements, HashMap<String,ArrayList<FunctionalGroup>> _functional_groups, KnownFunctionalGroups knownFunctionalGroups)
	FunctionalGroup(String _name, int _position, int _count, DoubleBonds _double_bonds, boolean _is_atomic, String _stereochemistry, ElementTable _elements, KnownFunctionalGroups knownFunctionalGroups)
	FunctionalGroup(String _name, int _position, int _count, KnownFunctionalGroups knownFunctionalGroups)
	FunctionalGroup(String _name, KnownFunctionalGroups knownFunctionalGroups)
	HeadgroupDecorator(String _name, int _position, int _count, ElementTable _elements, boolean _suffix, KnownFunctionalGroups knownFunctionalGroups)
	HeadgroupDecorator(String _name, int _position, int _count, ElementTable _elements, boolean _suffix, LipidLevel _level, KnownFunctionalGroups knownFunctionalGroups)
	HeadgroupDecorator(String _name, int _position, int _count, ElementTable _elements, KnownFunctionalGroups knownFunctionalGroups)
	HeadgroupDecorator(String _name, KnownFunctionalGroups knownFunctionalGroups)
	LipidCompleteStructure(Headgroup _headgroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
	LipidCompleteStructure(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)
	LipidFullStructure(Headgroup _headgroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
	LipidFullStructure(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)
	LipidMolecularSpecies(Headgroup _headgroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
	LipidMolecularSpecies(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)
	LipidSnPosition(Headgroup _headgroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
	LipidSnPosition(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)
	LipidSpecies(Headgroup _headGroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
	LipidSpecies(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)
	LipidSpeciesInfo(int _lipid_class, KnownFunctionalGroups knownFunctionalGroups)
	LipidStructureDefined(Headgroup _headgroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
	LipidStructureDefined(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)

Uses of KnownFunctionalGroups in org.lifstools.jgoslin.parser

Fields in org.lifstools.jgoslin.parser declared as KnownFunctionalGroups

Modifier and Type	Field	Description
protected KnownFunctionalGroups	LipidBaseParserEventHandler.knownFunctionalGroups

Constructors in org.lifstools.jgoslin.parser with parameters of type KnownFunctionalGroups

Modifier	Constructor	Description
	FattyAcidParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a FattyAcidParser with default grammar FattyAcidParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
	FattyAcidParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a FattyAcidParser.
	FattyAcidParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)	Create a new FattyAcidParserEventHandler.
	GoslinParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a GoslinParser with default grammar GoslinParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
	GoslinParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a GoslinParser.
	GoslinParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)	Create a new GoslinParserEventHandler.
	HmdbParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a HmdbParser with default grammar HmdbParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
	HmdbParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a HmdbParser.
	HmdbParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)	Create a new HmdbParserEventHandler.
	LipidBaseParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)
	LipidMapsParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a LipidMapsParser with default grammar LipidMapsParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
	LipidMapsParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a LipidMapsParser.
	LipidMapsParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)	Create a new LipidMapsParserEventHandler.
	LipidParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new lipid parser instance.
	ShorthandParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a ShorthandParser with default grammar ShorthandParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
	ShorthandParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a ShorthandParser.
	ShorthandParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)	Create a new ShorthandParserEventHandler.
	SwissLipidsParser(KnownFunctionalGroups knownFunctionalGroups)	Create a new instance of a SwissLipidsParser with default grammar SwissLipidsParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
	SwissLipidsParser(KnownFunctionalGroups knownFunctionalGroups, String grammarContent, char quote)	Create a new instance of a SwissLipidsParser.
	SwissLipidsParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)	Create a new SwissLipidsParserEventHandler.