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

Packages that use FunctionalGroup

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

Uses of FunctionalGroup in org.lifstools.jgoslin.domain

Subclasses of FunctionalGroup in org.lifstools.jgoslin.domain

Modifier and Type	Class	Description
final class	AcylAlkylGroup	An acyl alkyl group as a functional group.
final class	CarbonChain	A linear hydrocarbon chain as a functional group.
final class	Cycle	A cyclic hydrocarbon chain as a functional group.
class	FattyAcid	A fatty acid with a specific type.
final class	HeadgroupDecorator
final class	LipidSpeciesInfo	This class summarizes the FA parts of a lipid, independent of its head group.

Fields in org.lifstools.jgoslin.domain with type parameters of type FunctionalGroup

Modifier and Type	Field	Description
protected Map<String,ArrayList<FunctionalGroup>>	FunctionalGroup.functionalGroups

Methods in org.lifstools.jgoslin.domain that return FunctionalGroup

Modifier and Type	Method	Description
FunctionalGroup	AcylAlkylGroup.copy()
FunctionalGroup	CarbonChain.copy()
FunctionalGroup	Cycle.copy()
FunctionalGroup	FattyAcid.copy()
FunctionalGroup	FunctionalGroup.copy()
FunctionalGroup	HeadgroupDecorator.copy()
FunctionalGroup	KnownFunctionalGroups.get(String s)

Methods in org.lifstools.jgoslin.domain that return types with arguments of type FunctionalGroup

Modifier and Type	Method	Description
Map<String,ArrayList<FunctionalGroup>>	FunctionalGroup.getFunctionalGroups()	Returns a copy of the internally used functional groups map, with the virtual [X] group for regular LCBs removed.
Map<String,ArrayList<FunctionalGroup>>	FunctionalGroup.getFunctionalGroupsInternal()	Returns the internal representation of the functional groups, including the virtual [X] group for regular LCBs.

Methods in org.lifstools.jgoslin.domain with parameters of type FunctionalGroup

Modifier and Type	Method	Description
void	Cycle.rearrangeFunctionalGroups(FunctionalGroup parent, int shift)

Method parameters in org.lifstools.jgoslin.domain with type arguments of type FunctionalGroup

Modifier and Type	Method	Description
void	FunctionalGroup.setFunctionalGroups(Map<String,ArrayList<FunctionalGroup>> functionalGroups)	Set the internal functional groups.

Constructor parameters in org.lifstools.jgoslin.domain with type arguments of type FunctionalGroup

Modifier	Constructor	Description
	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)
	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)
	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)