Index (jgoslin 2.1.0 API)

A B C D E F G H I K L M N O P Q R S T U V
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AcylAlkylGroup - Class in org.lifstools.jgoslin.domain: An acyl alkyl group as a functional group.
AcylAlkylGroup(FattyAcid, int, int, boolean, boolean, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.AcylAlkylGroup
AcylAlkylGroup(FattyAcid, int, int, boolean, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.AcylAlkylGroup
AcylAlkylGroup(FattyAcid, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.AcylAlkylGroup
add(ElementTable) - Method in class org.lifstools.jgoslin.domain.ElementTable: Add all elements and counts to those in this element table.
add(ElementTable, int) - Method in class org.lifstools.jgoslin.domain.ElementTable: Add all alements and counts to those in this element table, but use the count argument to multiply count values in the provided table.
add(FattyAcid) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
add_terminal(String) - Method in class org.lifstools.jgoslin.parser.Parser
addGrammarOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
addHelpOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
addLipidFileInputOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
addLipidNameInputOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
addOutputToFileOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
addPosition(int) - Method in class org.lifstools.jgoslin.domain.Cycle
addPosition(int) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
addStripWhitespaceOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
adduct - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
Adduct - Class in org.lifstools.jgoslin.domain: An adduct, generally, consists of a sum formula part, an adduct string, the charge and the charge sign.
Adduct(String, String) - Constructor for class org.lifstools.jgoslin.domain.Adduct
Adduct(String, String, int, int) - Constructor for class org.lifstools.jgoslin.domain.Adduct
ADDUCT_CHARGES - Static variable in class org.lifstools.jgoslin.domain.Adduct
ADDUCTS - Static variable in class org.lifstools.jgoslin.domain.Adduct
addVersionOption(Options) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser
AMIDE - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
As - Enum constant in enum class org.lifstools.jgoslin.domain.Element
assembleLipid(Headgroup) - Method in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
atomic - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
avgPair - Variable in class org.lifstools.jgoslin.parser.Parser

B

BaseParserEventHandler<T> - Class in org.lifstools.jgoslin.parser: Abstract base class for parser event handling.
BaseParserEventHandler() - Constructor for class org.lifstools.jgoslin.parser.BaseParserEventHandler
Br - Enum constant in enum class org.lifstools.jgoslin.domain.Element
buildLipidSubspeciesName() - Method in class org.lifstools.jgoslin.domain.LipidMolecularSpecies
buildLipidSubspeciesName(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidMolecularSpecies

C

C - Enum constant in enum class org.lifstools.jgoslin.domain.Element
C13 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
CarbonChain - Class in org.lifstools.jgoslin.domain: A linear hydrocarbon chain as a functional group.
CarbonChain(FattyAcid, int, int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.CarbonChain
CarbonChain(FattyAcid, int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.CarbonChain
CarbonChain(FattyAcid, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.CarbonChain
CATEGORY - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
CategoryString - Static variable in class org.lifstools.jgoslin.domain.Headgroup
Cl - Enum constant in enum class org.lifstools.jgoslin.domain.Element
CLASS - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
ClassString - Static variable in class org.lifstools.jgoslin.domain.Headgroup
CmdLineParser - Class in org.lifstools.jgoslin.cli: Create a new command line parser for parsing of lipid names.
CmdLineParser() - Constructor for class org.lifstools.jgoslin.cli.CmdLineParser
collect_backwards(long, long, HashSet<Long>, ArrayList<Long>, ArrayList<ArrayList<Long>>) - Method in class org.lifstools.jgoslin.parser.Parser
collect_backwards(Long, Long) - Method in class org.lifstools.jgoslin.parser.Parser
collect_one_backwards(Long) - Method in class org.lifstools.jgoslin.parser.Parser
compareTo(HeadgroupDecorator) - Method in class org.lifstools.jgoslin.domain.HeadgroupDecorator
COMPLETE_STRUCTURE - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
compute_rule_key(long, long) - Method in class org.lifstools.jgoslin.parser.Parser
computeAndCopyElements() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
computeElements() - Method in class org.lifstools.jgoslin.domain.Cycle
computeElements() - Method in class org.lifstools.jgoslin.domain.FattyAcid
computeElements() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
ConstraintViolationException - Exception in org.lifstools.jgoslin.domain: An exception that is thrown to indicate that preconditions have been violated.
ConstraintViolationException() - Constructor for exception org.lifstools.jgoslin.domain.ConstraintViolationException
ConstraintViolationException(String) - Constructor for exception org.lifstools.jgoslin.domain.ConstraintViolationException
ConstraintViolationException(String, Throwable) - Constructor for exception org.lifstools.jgoslin.domain.ConstraintViolationException
ConstraintViolationException(Throwable) - Constructor for exception org.lifstools.jgoslin.domain.ConstraintViolationException
content - Variable in class org.lifstools.jgoslin.parser.BaseParserEventHandler
copy() - Method in class org.lifstools.jgoslin.domain.AcylAlkylGroup
copy() - Method in class org.lifstools.jgoslin.domain.CarbonChain
copy() - Method in class org.lifstools.jgoslin.domain.Cycle
copy() - Method in class org.lifstools.jgoslin.domain.DoubleBonds
copy() - Method in class org.lifstools.jgoslin.domain.ElementTable: Copy all entries in this element table.
copy() - Method in class org.lifstools.jgoslin.domain.FattyAcid
copy() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
copy() - Method in class org.lifstools.jgoslin.domain.HeadgroupDecorator
copy() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
count - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
currentFa - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
Cycle - Class in org.lifstools.jgoslin.domain: A cyclic hydrocarbon chain as a functional group.
Cycle(int, int, int, HashMap<String, ArrayList<FunctionalGroup>>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.Cycle
Cycle(int, int, int, DoubleBonds, HashMap<String, ArrayList<FunctionalGroup>>, ArrayList<Element>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.Cycle
Cycle(int, int, int, DoubleBonds, HashMap<String, ArrayList<FunctionalGroup>>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.Cycle
Cycle(int, int, int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.Cycle
Cycle(int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.Cycle

D

D - Enum constant in enum class org.lifstools.jgoslin.domain.Element
de_escape(String, char) - Method in class org.lifstools.jgoslin.parser.Parser
DEFAULT_QUOTE - Static variable in class org.lifstools.jgoslin.domain.StringFunctions
DEFAULT_QUOTE - Static variable in class org.lifstools.jgoslin.parser.Parser
DEFAULT_SPLIT - Static variable in class org.lifstools.jgoslin.domain.StringFunctions
description - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
Dictionary - Class in org.lifstools.jgoslin.domain: A dictionary typing for HashMap to align this implementation with the other language implementations.
Dictionary() - Constructor for class org.lifstools.jgoslin.domain.Dictionary
doubleBondPositions - Variable in class org.lifstools.jgoslin.domain.DoubleBonds
doubleBonds - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
DoubleBonds - Class in org.lifstools.jgoslin.domain: An abstraction for double bond counts and positions.
DoubleBonds() - Constructor for class org.lifstools.jgoslin.domain.DoubleBonds
DoubleBonds(int) - Constructor for class org.lifstools.jgoslin.domain.DoubleBonds
DoubleBonds(TreeMap<Integer, String>) - Constructor for class org.lifstools.jgoslin.domain.DoubleBonds
DPNode(long, long, Parser.DPNode, Parser.DPNode) - Constructor for class org.lifstools.jgoslin.parser.Parser.DPNode

E

ELECTRON_REST_MASS - Static variable in class org.lifstools.jgoslin.domain.Elements
Element - Enum Class in org.lifstools.jgoslin.domain: Enumeration for typical chemical elements in lipids.
ELEMENT_MASSES - Static variable in class org.lifstools.jgoslin.domain.Elements
ELEMENT_ORDER - Static variable in class org.lifstools.jgoslin.domain.Elements
ELEMENT_POSITIONS - Static variable in class org.lifstools.jgoslin.domain.Elements
ELEMENT_SHORTCUT - Static variable in class org.lifstools.jgoslin.domain.Elements
elements - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
elements - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
Elements - Class in org.lifstools.jgoslin.domain: Utility class to look up element names, masses, shortcut names, and ordering.
Elements() - Constructor for class org.lifstools.jgoslin.domain.Elements
ElementTable - Class in org.lifstools.jgoslin.domain: Accounting table for chemical element frequency.
ElementTable() - Constructor for class org.lifstools.jgoslin.domain.ElementTable: Create a new element table.
EOF_RULE - Static variable in class org.lifstools.jgoslin.parser.Parser
EOF_RULE_NAME - Static variable in class org.lifstools.jgoslin.parser.Parser
EOF_SIGN - Static variable in class org.lifstools.jgoslin.parser.Parser
EOF_SIGN - Static variable in class org.lifstools.jgoslin.parser.TreeNode
errorMessage - Variable in class org.lifstools.jgoslin.parser.BaseParserEventHandler
ESTER - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
ETHER - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
ETHER_PLASMANYL - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
ETHER_PLASMENYL - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
ETHER_PREFIX - Static variable in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
ETHER_UNSPECIFIED - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
exceptionHeadgroups - Static variable in class org.lifstools.jgoslin.domain.Headgroup
extendedClass - Variable in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
extract_text_based_rules(String, char) - Method in class org.lifstools.jgoslin.parser.Parser

F

F - Enum constant in enum class org.lifstools.jgoslin.domain.Element
fa - Variable in class org.lifstools.jgoslin.domain.LipidSpecies
FA - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
faList - Variable in class org.lifstools.jgoslin.domain.LipidSpecies
faList - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
FattyAcid - Class in org.lifstools.jgoslin.domain: A fatty acid with a specific type.
FattyAcid(String, int, DoubleBonds) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcid(String, int, DoubleBonds, HashMap<String, ArrayList<FunctionalGroup>>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcid(String, int, DoubleBonds, HashMap<String, ArrayList<FunctionalGroup>>, LipidFaBondType, int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcid(String, int, DoubleBonds, HashMap<String, ArrayList<FunctionalGroup>>, LipidFaBondType, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcid(String, int, DoubleBonds, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcid(String, int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcid(String, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FattyAcid
FattyAcidParser - Class in org.lifstools.jgoslin.parser: Parser implementation for IUPAC Fatty acids nomenclature.
FattyAcidParser() - Constructor for class org.lifstools.jgoslin.parser.FattyAcidParser: Create a new instance of a FattyAcidParser with default grammar FattyAcidParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
FattyAcidParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.FattyAcidParser: Create a new instance of a FattyAcidParser with default grammar FattyAcidParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
FattyAcidParser(KnownFunctionalGroups, String, char) - Constructor for class org.lifstools.jgoslin.parser.FattyAcidParser: Create a new instance of a FattyAcidParser.
FattyAcidParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the FattyAcidParser.
FattyAcidParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.FattyAcidParserEventHandler: Create a new FattyAcidParserEventHandler.
fgExceptions - Static variable in class org.lifstools.jgoslin.domain.FattyAcid
fill_tree(TreeNode, Parser.DPNode) - Method in class org.lifstools.jgoslin.parser.Parser
forFullName(String) - Static method in enum class org.lifstools.jgoslin.domain.LipidCategory
FULL_STRUCTURE - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
FunctionalGroup - Class in org.lifstools.jgoslin.domain: A functional group of a fatty acid, it can contain nested functional groups.
FunctionalGroup(String, int, int, DoubleBonds, boolean, String, boolean, ElementTable, HashMap<String, ArrayList<FunctionalGroup>>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FunctionalGroup
FunctionalGroup(String, int, int, DoubleBonds, boolean, String, boolean, ElementTable, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FunctionalGroup
FunctionalGroup(String, int, int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FunctionalGroup
FunctionalGroup(String, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.FunctionalGroup
functionalGroups - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup

G

GenericList - Class in org.lifstools.jgoslin.domain: A typing for ArrayList of objects to align this implementation with the other language implementations.
GenericList() - Constructor for class org.lifstools.jgoslin.domain.GenericList
get(String) - Method in class org.lifstools.jgoslin.domain.KnownFunctionalGroups
get_next_free_rule_index() - Method in class org.lifstools.jgoslin.parser.Parser
getAdduct() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getAdductString() - Method in class org.lifstools.jgoslin.domain.Adduct
getBridgeChain() - Method in class org.lifstools.jgoslin.domain.Cycle
getCategory(String) - Static method in class org.lifstools.jgoslin.domain.Headgroup
getCategoryString(LipidCategory) - Static method in class org.lifstools.jgoslin.domain.Headgroup
getCharge() - Method in class org.lifstools.jgoslin.domain.Adduct: Returns the positive elementary charge times the charge sign.
getChargedMass(int) - Method in class org.lifstools.jgoslin.domain.ElementTable: Returns the total summed mass per number of elements, corrected for charge counts * electron rest mass.
getChargeSign() - Method in class org.lifstools.jgoslin.domain.Adduct
getClass(String) - Static method in class org.lifstools.jgoslin.domain.Headgroup
getClassName() - Method in class org.lifstools.jgoslin.domain.Headgroup
getClassName() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getClassName() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getClassString(int) - Static method in class org.lifstools.jgoslin.domain.Headgroup
getCount() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getCycle() - Method in class org.lifstools.jgoslin.domain.Cycle
getDecorators() - Method in class org.lifstools.jgoslin.domain.Headgroup
getDescription() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getDoubleBondPositions() - Method in class org.lifstools.jgoslin.domain.DoubleBonds
getDoubleBonds() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getElements() - Method in class org.lifstools.jgoslin.domain.Adduct
getElements() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getElements() - Method in class org.lifstools.jgoslin.domain.Headgroup
getElements() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getElements() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getElements() - Method in class org.lifstools.jgoslin.domain.LipidMolecularSpecies
getElements() - Method in class org.lifstools.jgoslin.domain.LipidSpecies
getElements() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getEnd() - Method in class org.lifstools.jgoslin.domain.Cycle
getErrorMessage() - Method in class org.lifstools.jgoslin.parser.BaseParserEventHandler
getExtendedClass() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getExtendedClass() - Method in class org.lifstools.jgoslin.domain.LipidSpecies
getExtendedClass() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getFaList() - Method in class org.lifstools.jgoslin.domain.LipidSpecies
getFullName() - Method in enum class org.lifstools.jgoslin.domain.LipidCategory
getFunctionalGroupElements() - Method in class org.lifstools.jgoslin.domain.FattyAcid
getFunctionalGroupElements() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getFunctionalGroups() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup: Returns a copy of the internally used functional groups map, with the virtual [X] group for regular LCBs removed.
getFunctionalGroupsInternal() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup: Returns the internal representation of the functional groups, including the virtual [X] group for regular LCBs.
getHeadgroup() - Method in class org.lifstools.jgoslin.domain.Headgroup
getHeadGroup() - Method in class org.lifstools.jgoslin.domain.LipidSpecies
getHeavyElements() - Method in class org.lifstools.jgoslin.domain.Adduct
getHeavyIsotopeString() - Method in class org.lifstools.jgoslin.domain.Adduct
getInfo() - Method in class org.lifstools.jgoslin.domain.LipidSpecies
getInstance() - Static method in class org.lifstools.jgoslin.domain.LipidClasses
getInt() - Method in class org.lifstools.jgoslin.parser.TreeNode
getLastSuccessfulGrammar() - Method in class org.lifstools.jgoslin.parser.LipidParser: Returns the grammar name of the last successful parser.
getLastSuccessfulParser() - Method in class org.lifstools.jgoslin.parser.LipidParser: Returns the last successful parser instance.
getLevel() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getLipid() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getLipidCategory() - Method in class org.lifstools.jgoslin.domain.Headgroup
getLipidCategory() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getLipidClass() - Method in class org.lifstools.jgoslin.domain.Headgroup
getLipidClass() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getLipidFaBondType() - Method in class org.lifstools.jgoslin.domain.FattyAcid
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidCompleteStructure
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidFullStructure
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidMolecularSpecies
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidSnPosition
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidSpecies
getLipidLevel() - Method in class org.lifstools.jgoslin.domain.LipidStructureDefined
getLipidString() - Method in class org.lifstools.jgoslin.domain.Adduct
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidCompleteStructure
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidFullStructure
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidMolecularSpecies
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidSnPosition
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidSpecies: Returns the normalized lipid string on the native level.
getLipidString() - Method in class org.lifstools.jgoslin.domain.LipidStructureDefined
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.Headgroup
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidCompleteStructure
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidFullStructure
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidMolecularSpecies
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidSnPosition
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidSpecies: Returns the normalized lipid string on the provided level.
getLipidString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidStructureDefined
getLowestVisibleLevel() - Method in class org.lifstools.jgoslin.domain.HeadgroupDecorator
getMass() - Method in class org.lifstools.jgoslin.domain.ElementTable: Returns the total summed mass per number of elements.
getMass() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getMass(Element) - Method in class org.lifstools.jgoslin.domain.ElementTable: Returns the individual total mass for the provided element.
getMaxNumFa() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getName() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getNDoubleBonds() - Method in class org.lifstools.jgoslin.domain.Cycle
getNDoubleBonds() - Method in class org.lifstools.jgoslin.domain.FattyAcid
getNDoubleBonds() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getNumCarbon() - Method in class org.lifstools.jgoslin.domain.FattyAcid
getNumDoubleBonds() - Method in class org.lifstools.jgoslin.domain.DoubleBonds
getNumEthers() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getNumSpecifiedFa() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getPosition() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getPossibleNumFa() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getPrefix(LipidFaBondType) - Method in class org.lifstools.jgoslin.domain.FattyAcid
getResourceAsString(String) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Read the provided resource path and return it as a string.
getResourceAsString(Resource) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Read the provided resource and return it as a string.
getResourceAsStringList(String) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Read the provided resource path, which is converted to a ClassPathResource and split it at default new line characters into a list for each line.
getResourceAsStringList(Resource) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Read the provided resource and split it at default new line characters into a list for each line.
getRingStereo() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getSpecialCases() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getStart() - Method in class org.lifstools.jgoslin.domain.Cycle
getStereoBound() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getStereochemistry() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
getSumFormula() - Method in class org.lifstools.jgoslin.domain.Adduct
getSumFormula() - Method in class org.lifstools.jgoslin.domain.ElementTable: Returns the sum formula for all elements in this table.
getSumFormula() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
getSynonyms() - Method in class org.lifstools.jgoslin.domain.LipidClassMeta
getText() - Method in class org.lifstools.jgoslin.parser.TreeNode
getTotalFa() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
getTotalFunctionalGroupCount(String) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup: Return the total count for the given functional group name, or 0.
GL - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
GoslinParser - Class in org.lifstools.jgoslin.parser: Parser implementation for the Goslin lipid shorthand nomenclature.
GoslinParser() - Constructor for class org.lifstools.jgoslin.parser.GoslinParser: Create a new instance of a GoslinParser with default grammar GoslinParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
GoslinParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.GoslinParser: Create a new instance of a GoslinParser with default grammar GoslinParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
GoslinParser(KnownFunctionalGroups, String, char) - Constructor for class org.lifstools.jgoslin.parser.GoslinParser: Create a new instance of a GoslinParser.
GoslinParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the GoslinParser.
GoslinParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.GoslinParserEventHandler: Create a new GoslinParserEventHandler.
GP - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
grammarName - Variable in class org.lifstools.jgoslin.parser.Parser

H

H - Enum constant in enum class org.lifstools.jgoslin.domain.Element
H2 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
handleEvent(String, TreeNode) - Method in class org.lifstools.jgoslin.parser.BaseParserEventHandler
headGroup - Variable in class org.lifstools.jgoslin.domain.LipidSpecies
headGroup - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
Headgroup - Class in org.lifstools.jgoslin.domain: This class represents functional head groups of lipids.
Headgroup(String) - Constructor for class org.lifstools.jgoslin.domain.Headgroup
Headgroup(String, ArrayList<HeadgroupDecorator>, boolean) - Constructor for class org.lifstools.jgoslin.domain.Headgroup
HeadgroupDecorator - Class in org.lifstools.jgoslin.domain
HeadgroupDecorator(String, int, int, ElementTable, boolean, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.HeadgroupDecorator
HeadgroupDecorator(String, int, int, ElementTable, boolean, LipidLevel, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.HeadgroupDecorator
HeadgroupDecorator(String, int, int, ElementTable, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.HeadgroupDecorator
HeadgroupDecorator(String, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.HeadgroupDecorator
headgroupDecorators - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
HEAVY_ELEMENT_TABLE - Static variable in class org.lifstools.jgoslin.domain.Elements
HEAVY_SHORTCUT - Static variable in class org.lifstools.jgoslin.domain.Elements
HEAVY_TO_REGULAR - Static variable in class org.lifstools.jgoslin.domain.Elements
HmdbParser - Class in org.lifstools.jgoslin.parser: Parser implementation for the HMDB lipid shorthand nomenclature.
HmdbParser() - Constructor for class org.lifstools.jgoslin.parser.HmdbParser: Create a new instance of a HmdbParser with default grammar HmdbParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
HmdbParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.HmdbParser: Create a new instance of a HmdbParser with default grammar HmdbParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
HmdbParser(KnownFunctionalGroups, String, char) - Constructor for class org.lifstools.jgoslin.parser.HmdbParser: Create a new instance of a HmdbParser.
HmdbParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the HmdbParser.
HmdbParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.HmdbParserEventHandler: Create a new HmdbParserEventHandler.

I

I - Enum constant in enum class org.lifstools.jgoslin.domain.Element
info - Variable in class org.lifstools.jgoslin.domain.LipidSpecies
is_terminal(String, char) - Method in class org.lifstools.jgoslin.parser.Parser
isAlkyl() - Method in class org.lifstools.jgoslin.domain.AcylAlkylGroup
isAtomic() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
isCardioLipin() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
isContainsEster() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
isContainsSugar() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
isLevel(LipidLevel, int) - Static method in enum class org.lifstools.jgoslin.domain.LipidLevel
isLyso() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
isNitrogenBond() - Method in class org.lifstools.jgoslin.domain.AcylAlkylGroup
isSpException() - Method in class org.lifstools.jgoslin.domain.Headgroup
isSpException() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
isSuffix() - Method in class org.lifstools.jgoslin.domain.HeadgroupDecorator
isUseHeadgroup() - Method in class org.lifstools.jgoslin.domain.Headgroup

K

knownFunctionalGroups - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
knownFunctionalGroups - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
KnownFunctionalGroups - Class in org.lifstools.jgoslin.domain: A lookup class that provides access to known functional groups defined in a file following the format of functional-groups.csv.
KnownFunctionalGroups() - Constructor for class org.lifstools.jgoslin.domain.KnownFunctionalGroups
KnownFunctionalGroups(List<String>, SumFormulaParser) - Constructor for class org.lifstools.jgoslin.domain.KnownFunctionalGroups

L

lcb - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
LCB_EXCEPTION - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
LCB_REGULAR - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
LCB_STATES - Static variable in class org.lifstools.jgoslin.domain.FattyAcid
left - Variable in class org.lifstools.jgoslin.parser.Parser.DPNode
level - Variable in enum class org.lifstools.jgoslin.domain.LipidLevel
level - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
LipidAdduct - Class in org.lifstools.jgoslin.domain: Base class for lipid names parsed using the different grammars.
LipidAdduct(LipidSpecies, Adduct) - Constructor for class org.lifstools.jgoslin.domain.LipidAdduct
LipidBaseParserEventHandler - Class in org.lifstools.jgoslin.parser
LipidBaseParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
lipidCategory - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
LipidCategory - Enum Class in org.lifstools.jgoslin.domain: The lipid category nomenclature follows the shorthand notation of
lipidClass - Variable in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
LipidClasses - Class in org.lifstools.jgoslin.domain: Lookup class for lipid classes, consisting of LipidClassMeta entries, derived from lipid-list.csv.
LipidClassMeta - Class in org.lifstools.jgoslin.domain: Metadata information about a lipid on class level.
LipidClassMeta(LipidCategory, String, String, int, int, Set<String>, ElementTable, List<String>) - Constructor for class org.lifstools.jgoslin.domain.LipidClassMeta: Create a new lipid class meta instance.
lipidClassName - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
LipidCompleteStructure - Class in org.lifstools.jgoslin.domain: Complete structure level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidCompleteStructure(Headgroup, Collection<FattyAcid>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidCompleteStructure
LipidCompleteStructure(Headgroup, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidCompleteStructure
LipidException - Exception in org.lifstools.jgoslin.domain: Base exception for exceptions that relate to lipid parsing or creation of lipids.
LipidException() - Constructor for exception org.lifstools.jgoslin.domain.LipidException
LipidException(String) - Constructor for exception org.lifstools.jgoslin.domain.LipidException
LipidException(String, Throwable) - Constructor for exception org.lifstools.jgoslin.domain.LipidException
LipidException(Throwable) - Constructor for exception org.lifstools.jgoslin.domain.LipidException
lipidFaBondType - Variable in class org.lifstools.jgoslin.domain.FattyAcid
LipidFaBondType - Enum Class in org.lifstools.jgoslin.domain: The lipid fatty acyl bond types define how the FA is connected to the head group or which variant of a particular bond type it is.
lipidFaBondTypePrefix(LipidFaBondType) - Method in class org.lifstools.jgoslin.domain.FattyAcid
LipidFullStructure - Class in org.lifstools.jgoslin.domain: Full structure level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidFullStructure(Headgroup, Collection<FattyAcid>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidFullStructure
LipidFullStructure(Headgroup, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidFullStructure
LipidLevel - Enum Class in org.lifstools.jgoslin.domain: Defines the taxonomy of lipid levels, including UNDEFINED for lipids where the level can not be inferred or does not apply.
LIPIDMAPS_CLASS_REGEXP - Static variable in class org.lifstools.jgoslin.cli.CmdLineParser
LipidMapsParser - Class in org.lifstools.jgoslin.parser: Parser implementation for the LIPID MAPS lipid shorthand nomenclature.
LipidMapsParser() - Constructor for class org.lifstools.jgoslin.parser.LipidMapsParser: Create a new instance of a LipidMapsParser with default grammar LipidMapsParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
LipidMapsParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.LipidMapsParser: Create a new instance of a LipidMapsParser with default grammar LipidMapsParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
LipidMapsParser(KnownFunctionalGroups, String, char) - Constructor for class org.lifstools.jgoslin.parser.LipidMapsParser: Create a new instance of a LipidMapsParser.
LipidMapsParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the LipidMapsParser.
LipidMapsParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.LipidMapsParserEventHandler: Create a new LipidMapsParserEventHandler.
LipidMolecularSpecies - Class in org.lifstools.jgoslin.domain: Molecular species level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidMolecularSpecies(Headgroup, Collection<FattyAcid>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidMolecularSpecies
LipidMolecularSpecies(Headgroup, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidMolecularSpecies
LipidParser - Class in org.lifstools.jgoslin.parser: Implementation that uses all available parsers to parse a given lipid name.
LipidParser() - Constructor for class org.lifstools.jgoslin.parser.LipidParser: Create a new lipid parser instance.
LipidParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.LipidParser: Create a new lipid parser instance.
LipidParsingException - Exception in org.lifstools.jgoslin.domain: Specific exception that is thrown when errors are encountered in a lipid name.
LipidParsingException() - Constructor for exception org.lifstools.jgoslin.domain.LipidParsingException
LipidParsingException(String) - Constructor for exception org.lifstools.jgoslin.domain.LipidParsingException
LipidParsingException(String, Throwable) - Constructor for exception org.lifstools.jgoslin.domain.LipidParsingException
LipidParsingException(Throwable) - Constructor for exception org.lifstools.jgoslin.domain.LipidParsingException
LipidSnPosition - Class in org.lifstools.jgoslin.domain: Sn position level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidSnPosition(Headgroup, Collection<FattyAcid>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidSnPosition
LipidSnPosition(Headgroup, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidSnPosition
LipidSpecies - Class in org.lifstools.jgoslin.domain: A lipid species is the factual root of the object hierarchy.
LipidSpecies(Headgroup, Collection<FattyAcid>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidSpecies
LipidSpecies(Headgroup, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidSpecies
LipidSpeciesInfo - Class in org.lifstools.jgoslin.domain: This class summarizes the FA parts of a lipid, independent of its head group.
LipidSpeciesInfo(int, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidSpeciesInfo
LipidStructureDefined - Class in org.lifstools.jgoslin.domain: Structure defined level according to the 2020 update of the Liebisch shorthand nomenclature.
LipidStructureDefined(Headgroup, Collection<FattyAcid>, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidStructureDefined
LipidStructureDefined(Headgroup, KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.domain.LipidStructureDefined

M

main(String[]) - Static method in class org.lifstools.jgoslin.cli.CmdLineParser: Runs the command line parser for jgoslin, including validation.
MASK - Static variable in class org.lifstools.jgoslin.parser.Parser
maxNumFa - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
MOLECULAR_SPECIES - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel

N

N - Enum constant in enum class org.lifstools.jgoslin.domain.Element
N15 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
name - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
newEventHandler() - Method in class org.lifstools.jgoslin.parser.FattyAcidParser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.GoslinParser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.HmdbParser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.LipidMapsParser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.Parser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.ShorthandParser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.SumFormulaParser
newEventHandler() - Method in class org.lifstools.jgoslin.parser.SwissLipidsParser
nextFreeRuleIndex - Variable in class org.lifstools.jgoslin.parser.Parser
NO_CATEGORY - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
NO_FA - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
NO_LEVEL - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
NTtoNT - Variable in class org.lifstools.jgoslin.parser.Parser
NTtoRule - Variable in class org.lifstools.jgoslin.parser.Parser
numCarbon - Variable in class org.lifstools.jgoslin.domain.FattyAcid
numEthers - Variable in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
numSpecifiedFa - Variable in class org.lifstools.jgoslin.domain.LipidSpeciesInfo

O

O - Enum constant in enum class org.lifstools.jgoslin.domain.Element
O17 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
O18 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
of(Map.Entry<Element, Integer>...) - Static method in class org.lifstools.jgoslin.domain.ElementTable: Create a new element table from the provided entries.
ONE_STR - Static variable in class org.lifstools.jgoslin.parser.TreeNode
org.lifstools.jgoslin.cli - package org.lifstools.jgoslin.cli: This package contains the command line interface for jgoslin.
org.lifstools.jgoslin.domain - package org.lifstools.jgoslin.domain: This package contains the main common domain models for lipids.
org.lifstools.jgoslin.parser - package org.lifstools.jgoslin.parser: This package contains the parser implementations for the lipid grammars.
originalTtoNT - Variable in class org.lifstools.jgoslin.parser.Parser

P

P - Enum constant in enum class org.lifstools.jgoslin.domain.Element
P32 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
parse(String) - Method in class org.lifstools.jgoslin.parser.LipidParser: This method tries multiple parsers in a defined order to parse the provided lipid name.If no parser is able to parse the name successfully, an exception is thrown.
parse(String, BaseParserEventHandler) - Method in class org.lifstools.jgoslin.parser.FattyAcidParser
parse(String, BaseParserEventHandler<T>) - Method in class org.lifstools.jgoslin.parser.Parser: Parse the given text, constructing the output object of type T using the provided parser event handler.
parse(String, BaseParserEventHandler<T>, boolean) - Method in class org.lifstools.jgoslin.parser.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.
parse(String, BaseParserEventHandler, boolean) - Method in class org.lifstools.jgoslin.parser.FattyAcidParser
parse_regular(String, BaseParserEventHandler<T>) - Method in class org.lifstools.jgoslin.parser.Parser
Parser<T> - Class in org.lifstools.jgoslin.parser: Abstract base class for parsers producing a parse result of type T.
Parser(String) - Constructor for class org.lifstools.jgoslin.parser.Parser
Parser(String, char) - Constructor for class org.lifstools.jgoslin.parser.Parser
Parser.DPNode - Class in org.lifstools.jgoslin.parser
Parser.ParsingErrors - Class in org.lifstools.jgoslin.parser
PK - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
position - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
possibleNumFa - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
prepareHeadgroupAndChecks() - Method in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler

Q

quote - Variable in class org.lifstools.jgoslin.parser.Parser

R

raise_events(TreeNode, BaseParserEventHandler) - Method in class org.lifstools.jgoslin.parser.Parser
readGrammar(String) - Method in class org.lifstools.jgoslin.parser.Parser
rearrangeFunctionalGroups(FunctionalGroup, int) - Method in class org.lifstools.jgoslin.domain.Cycle
registeredEvents - Variable in class org.lifstools.jgoslin.parser.BaseParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.BaseParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.FattyAcidParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.GoslinParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.HmdbParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.LipidMapsParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.ShorthandParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.SumFormulaParserEventHandler
resetParser(TreeNode) - Method in class org.lifstools.jgoslin.parser.SwissLipidsParserEventHandler
right - Variable in class org.lifstools.jgoslin.parser.Parser.DPNode
rightPair - Variable in class org.lifstools.jgoslin.parser.Parser
ringStereo - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
RULE_ASSIGNMENT - Static variable in class org.lifstools.jgoslin.parser.Parser
rule_index_1 - Variable in class org.lifstools.jgoslin.parser.Parser.DPNode
rule_index_2 - Variable in class org.lifstools.jgoslin.parser.Parser.DPNode
RULE_SEPARATOR - Static variable in class org.lifstools.jgoslin.parser.Parser
RULE_TERMINAL - Static variable in class org.lifstools.jgoslin.parser.Parser
ruleNames - Variable in class org.lifstools.jgoslin.parser.BaseParserEventHandler
ruleToNT - Variable in class org.lifstools.jgoslin.parser.Parser

S

S - Enum constant in enum class org.lifstools.jgoslin.domain.Element
S33 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
S34 - Enum constant in enum class org.lifstools.jgoslin.domain.Element
sanityCheck(Parser<T>) - Method in class org.lifstools.jgoslin.parser.BaseParserEventHandler
setAdductString(String) - Method in class org.lifstools.jgoslin.domain.Adduct
setAlkyl(boolean) - Method in class org.lifstools.jgoslin.domain.AcylAlkylGroup
setAtomic(boolean) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setCharge(int) - Method in class org.lifstools.jgoslin.domain.Adduct
setChargeSign(int) - Method in class org.lifstools.jgoslin.domain.Adduct
setCount(int) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setCycle(int) - Method in class org.lifstools.jgoslin.domain.Cycle
setDecorators(ArrayList<HeadgroupDecorator>) - Method in class org.lifstools.jgoslin.domain.Headgroup
setDoubleBonds(DoubleBonds) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setElements(ElementTable) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setEnd(int) - Method in class org.lifstools.jgoslin.domain.Cycle
setExtendedClass(LipidFaBondType) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
setFunctionalGroups(HashMap<String, ArrayList<FunctionalGroup>>) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup: Set the internal functional groups.
setHeadgroup(String) - Method in class org.lifstools.jgoslin.domain.Headgroup
setLevel(LipidLevel) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
setLipidCategory(LipidCategory) - Method in class org.lifstools.jgoslin.domain.Headgroup
setLipidClass(int) - Method in class org.lifstools.jgoslin.domain.Headgroup
setLipidClass(int) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
setLipidFaBondType(LipidFaBondType) - Method in class org.lifstools.jgoslin.domain.FattyAcid
setLipidLevel(LipidLevel) - Method in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
setName(String) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setNitrogenBond(boolean) - Method in class org.lifstools.jgoslin.domain.AcylAlkylGroup
setNumCarbon(int) - Method in class org.lifstools.jgoslin.domain.FattyAcid
setNumDoubleBonds(int) - Method in class org.lifstools.jgoslin.domain.DoubleBonds
setNumEthers(int) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
setNumSpecifiedFa(int) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
setPosition(int) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setRingStereo(String) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setSpException(boolean) - Method in class org.lifstools.jgoslin.domain.Headgroup
setStart(int) - Method in class org.lifstools.jgoslin.domain.Cycle
setStereoBound(boolean) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setStereochemistry(String) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
setSumFormula(String) - Method in class org.lifstools.jgoslin.domain.Adduct
setTotalFa(int) - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
setType(LipidFaBondType) - Method in class org.lifstools.jgoslin.domain.FattyAcid
setUseHeadgroup(boolean) - Method in class org.lifstools.jgoslin.domain.Headgroup
SHIFT - Static variable in class org.lifstools.jgoslin.parser.Parser
shiftPositions(int) - Method in class org.lifstools.jgoslin.domain.Cycle
shiftPositions(int) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
ShorthandParser - Class in org.lifstools.jgoslin.parser: Parser implementation for the updated 2020 Liebisch lipid shorthand nomenclature.
ShorthandParser() - Constructor for class org.lifstools.jgoslin.parser.ShorthandParser: Create a new instance of a ShorthandParser with default grammar ShorthandParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
ShorthandParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.ShorthandParser: Create a new instance of a ShorthandParser with default grammar ShorthandParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
ShorthandParser(KnownFunctionalGroups, String, char) - Constructor for class org.lifstools.jgoslin.parser.ShorthandParser: Create a new instance of a ShorthandParser.
ShorthandParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the ShorthandParser.
ShorthandParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.ShorthandParserEventHandler: Create a new ShorthandParserEventHandler.
SL - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
SN_POSITION - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
SP - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
SP_EXCEPTION_CLASSES - Static variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
specialCases - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta
SPECIES - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
splitString(String) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Split the provided text at StringFunctions.DEFAULT_SPLIT as separator, using StringFunctions.DEFAULT_QUOTE as the default quotation char.
splitString(String, char, char) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Split the provided text at separator, respecting the quote char to not split in between quoted parts.
splitString(String, char, char, boolean) - Static method in class org.lifstools.jgoslin.domain.StringFunctions: Split the provided text at separator, respecting the quote char to not split in between quoted parts.
spRegularLcb() - Method in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler
ST - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
START_RULE - Static variable in class org.lifstools.jgoslin.parser.Parser
stereoBound - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
stereochemistry - Variable in class org.lifstools.jgoslin.domain.FunctionalGroup
stereoInformationMissing() - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
StringCategory - Static variable in class org.lifstools.jgoslin.domain.Headgroup
StringClass - Static variable in class org.lifstools.jgoslin.domain.Headgroup
StringFunctions - Class in org.lifstools.jgoslin.domain: Utility methods for strings and grammars.
strip(String, char) - Static method in class org.lifstools.jgoslin.domain.StringFunctions
STRUCTURE_DEFINED - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
substitution - Variable in class org.lifstools.jgoslin.parser.Parser
SumFormulaParser - Class in org.lifstools.jgoslin.parser: Parser implementation for chemical sum formulas.
SumFormulaParser() - Constructor for class org.lifstools.jgoslin.parser.SumFormulaParser: Create a new instance of a SumFormulaParser with default grammar SumFormulaParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
SumFormulaParser(String, char) - Constructor for class org.lifstools.jgoslin.parser.SumFormulaParser: Create a new instance of a SumFormulaParser.
SumFormulaParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the SumFormulaParser.
SumFormulaParserEventHandler() - Constructor for class org.lifstools.jgoslin.parser.SumFormulaParserEventHandler: Create a new SumFormulaParserEventHandler instance.
SwissLipidsParser - Class in org.lifstools.jgoslin.parser: Parser implementation for the updated 2020 Liebisch lipid shorthand nomenclature.
SwissLipidsParser() - Constructor for class org.lifstools.jgoslin.parser.SwissLipidsParser: Create a new instance of a SwissLipidsParser with default grammar SwissLipidsParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE and default KnownFunctionalGroups.
SwissLipidsParser(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.SwissLipidsParser: Create a new instance of a SwissLipidsParser with default grammar SwissLipidsParser.DEFAULT_GRAMMAR and default quote StringFunctions.DEFAULT_QUOTE.
SwissLipidsParser(KnownFunctionalGroups, String, char) - Constructor for class org.lifstools.jgoslin.parser.SwissLipidsParser: Create a new instance of a SwissLipidsParser.
SwissLipidsParserEventHandler - Class in org.lifstools.jgoslin.parser: Event handler implementation for the SwissLipidsParser.
SwissLipidsParserEventHandler(KnownFunctionalGroups) - Constructor for class org.lifstools.jgoslin.parser.SwissLipidsParserEventHandler: Create a new SwissLipidsParserEventHandler.
synonyms - Variable in class org.lifstools.jgoslin.domain.LipidClassMeta

T

top_nodes(long) - Method in class org.lifstools.jgoslin.parser.Parser
toString() - Method in class org.lifstools.jgoslin.domain.LipidAdduct
toString() - Method in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
toString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.AcylAlkylGroup
toString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.CarbonChain
toString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.Cycle
toString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.FattyAcid
toString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.FunctionalGroup
toString(LipidLevel) - Method in class org.lifstools.jgoslin.domain.HeadgroupDecorator
totalFa - Variable in class org.lifstools.jgoslin.domain.LipidSpeciesInfo
TreeNode - Class in org.lifstools.jgoslin.parser: A node representing an element in the parse tree.
TreeNode(long, boolean) - Constructor for class org.lifstools.jgoslin.parser.TreeNode
TtoNT - Variable in class org.lifstools.jgoslin.parser.Parser

U

UNDEFINED - Enum constant in enum class org.lifstools.jgoslin.domain.LipidCategory
UNDEFINED_CLASS - Static variable in class org.lifstools.jgoslin.domain.KnownFunctionalGroups
UNDEFINED_CLASS - Static variable in class org.lifstools.jgoslin.domain.LipidClasses
UNDEFINED_FA - Enum constant in enum class org.lifstools.jgoslin.domain.LipidFaBondType
UNDEFINED_LEVEL - Enum constant in enum class org.lifstools.jgoslin.domain.LipidLevel
UnsupportedLipidException - Exception in org.lifstools.jgoslin.domain: This exception is thrown, if a certain type of lipid is not yet supported by the grammar implementations.
UnsupportedLipidException() - Constructor for exception org.lifstools.jgoslin.domain.UnsupportedLipidException
UnsupportedLipidException(String) - Constructor for exception org.lifstools.jgoslin.domain.UnsupportedLipidException
UnsupportedLipidException(String, Throwable) - Constructor for exception org.lifstools.jgoslin.domain.UnsupportedLipidException
UnsupportedLipidException(Throwable) - Constructor for exception org.lifstools.jgoslin.domain.UnsupportedLipidException
usedEof - Variable in class org.lifstools.jgoslin.parser.Parser
useHeadGroup - Variable in class org.lifstools.jgoslin.parser.LipidBaseParserEventHandler

V

valueOf(String) - Static method in enum class org.lifstools.jgoslin.domain.Element: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.lifstools.jgoslin.domain.LipidCategory: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.lifstools.jgoslin.domain.LipidFaBondType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.lifstools.jgoslin.domain.LipidLevel: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.lifstools.jgoslin.domain.Element: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.lifstools.jgoslin.domain.LipidCategory: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.lifstools.jgoslin.domain.LipidFaBondType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.lifstools.jgoslin.domain.LipidLevel: Returns an array containing the constants of this enum class, in the order they are declared.

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