Package de.isas.lipidomics.domain

Class LipidStructuralSubspecies

java.lang.Object

de.isas.lipidomics.domain.LipidSpecies

de.isas.lipidomics.domain.LipidMolecularSubspecies

de.isas.lipidomics.domain.LipidStructuralSubspecies

Direct Known Subclasses:

LipidIsomericSubspecies

public class LipidStructuralSubspecies
extends LipidMolecularSubspecies

A structural subspecies. Child of LipidMolecularSubspecies. Individual FAs and their sn positions are known, but not the double bond positions. Example: Phosphatidylinositol (8:0/8:0) or PI(8:0/8:0)

Author:

nils.hoffmann

See Also:

LipidMolecularSubspecies

Field Summary

Fields inherited from class de.isas.lipidomics.domain.LipidMolecularSubspecies

fa

Fields inherited from class de.isas.lipidomics.domain.LipidSpecies

info, NONE

Constructor Summary

Constructors

Constructor	Description
LipidStructuralSubspecies(HeadGroup headGroup, FattyAcid... fa)

Method Summary

Modifier and Type	Method	Description
String	getLipidString(LipidLevel level)	Returns a lipid string representation for the given LipidLevel, e.g.
String	getLipidString(LipidLevel level, boolean normalizeHeadGroup)	Returns a lipid string representation for the given LipidLevel, e.g.
String	getNormalizedLipidString()	Returns a lipid string representation for the native LipidLevel, e.g.
String	toString()

Methods inherited from class de.isas.lipidomics.domain.LipidMolecularSubspecies

buildLipidSubspeciesName, buildSubspeciesHeadGroupString, getFa, getHeadGroupSuffix, validate

Methods inherited from class de.isas.lipidomics.domain.LipidSpecies

buildLipidString, buildSpeciesHeadGroupString, getElements, getInfo, getLipidCategory, getLipidClass, getLipidString, getNormalizedHeadGroup, isEtherLipid

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

LipidStructuralSubspecies

public LipidStructuralSubspecies(HeadGroup headGroup,
                                 FattyAcid... fa)

Method Detail

getLipidString

public String getLipidString(LipidLevel level)

Description copied from class: LipidSpecies

Returns a lipid string representation for the given LipidLevel, e.g. Category, Species, etc. Please note that this method is overridden by specific implementations for molecular, structural and isomeric subspecies levels. This method does not normalize the head group.

Overrides:

getLipidString in class LipidMolecularSubspecies

Parameters:

level - the lipid level to report the name of this lipid on.

Returns:

the lipid name.

getLipidString

public String getLipidString(LipidLevel level,
                             boolean normalizeHeadGroup)

Description copied from class: LipidSpecies

Returns a lipid string representation for the given LipidLevel, e.g. Category, Species, etc. Please note that this method is overridden by specific implementations for molecular, structural and isomeric subspecies levels. This method normalizes the head group to the primary class-specific synonym. E.g. TG would be normalized to TAG.

Overrides:

getLipidString in class LipidMolecularSubspecies

Parameters:

level - the lipid level to report the name of this lipid on.

normalizeHeadGroup - if true, use class specific synonym for headGroup, if false, use head group as parsed.

Returns:

the lipid name.

getNormalizedLipidString

public String getNormalizedLipidString()

Description copied from class: LipidSpecies

Returns a lipid string representation for the native LipidLevel, e.g. Category, Species, etc, as returned by LipidSpecies.getInfo() of this lipid. This method normalizes the head group to the primary class-specific synonym. E.g. TG would be normalized to TAG.

Overrides:

getNormalizedLipidString in class LipidMolecularSubspecies

Returns:

the normalized lipid name.

toString

public String toString()

Overrides:

toString in class LipidMolecularSubspecies