All Classes and Interfaces
Class
Description
An acyl alkyl group as a functional group.
An adduct, generally, consists of a sum formula part, an adduct string, the
charge and the charge sign.
Abstract base class for parser event handling.
A linear hydrocarbon chain as a functional group.
Create a new command line parser for parsing of lipid names.
An exception that is thrown to indicate that preconditions have been
violated.
A cyclic hydrocarbon chain as a functional group.
A dictionary typing for
HashMap to align this
implementation with the other language implementations.An abstraction for double bond counts and positions.
Enumeration for typical chemical elements in lipids.
Utility class to look up element names, masses, shortcut names, and ordering.
Accounting table for chemical element frequency.
A fatty acid with a specific type.
Parser implementation for IUPAC Fatty acids nomenclature.
Event handler implementation for the
FattyAcidParser.A functional group of a fatty acid, it can contain nested functional groups.
A typing for
ArrayList of objects to align this
implementation with the other language implementations.Parser implementation for the Goslin lipid shorthand nomenclature.
Event handler implementation for the
GoslinParser.This class represents functional head groups of lipids.
Parser implementation for the HMDB lipid shorthand nomenclature.
Event handler implementation for the
HmdbParser.A lookup class that provides access to known functional groups defined in a
file following the format of functional-groups.csv.
Base class for lipid names parsed using the different grammars.
The lipid category nomenclature follows the shorthand notation of
Lookup class for lipid classes, consisting of
LipidClassMeta entries,
derived from lipid-list.csv.Metadata information about a lipid on class level.
Complete structure level according to the 2020 update of the Liebisch
shorthand nomenclature.
Base exception for exceptions that relate to lipid parsing or creation of
lipids.
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.
Full structure level according to the 2020 update of the Liebisch shorthand
nomenclature.
Defines the taxonomy of lipid levels, including UNDEFINED for lipids where
the level can not be inferred or does not apply.
Parser implementation for the LIPID MAPS lipid shorthand nomenclature.
Event handler implementation for the
LipidMapsParser.Molecular species level according to the 2020 update of the Liebisch shorthand
nomenclature.
Implementation that uses all available parsers to parse a given lipid name.
Specific exception that is thrown when errors are encountered in a lipid
name.
Sn position level according to the 2020 update of the Liebisch shorthand
nomenclature.
A lipid species is the factual root of the object hierarchy.
This class summarizes the FA parts of a lipid, independent of its head group.
Structure defined level according to the 2020 update of the Liebisch
shorthand nomenclature.
Abstract base class for parsers producing a parse result of type T.
Parser implementation for the updated 2020 Liebisch lipid shorthand
nomenclature.
Event handler implementation for the
ShorthandParser.Utility methods for strings and grammars.
Parser implementation for chemical sum formulas.
Event handler implementation for the
SumFormulaParser.Parser implementation for the updated 2020 Liebisch lipid shorthand
nomenclature.
Event handler implementation for the
SwissLipidsParser.A node representing an element in the parse tree.
This exception is thrown, if a certain type of lipid is not yet supported by
the grammar implementations.