Package de.isas.lipidomics.domain

Class LipidIsomericSubspecies

java.lang.Object

de.isas.lipidomics.domain.LipidSpecies

de.isas.lipidomics.domain.LipidMolecularSubspecies

de.isas.lipidomics.domain.LipidStructuralSubspecies

de.isas.lipidomics.domain.LipidIsomericSubspecies

public class LipidIsomericSubspecies
extends LipidStructuralSubspecies

An isomeric subspecies. Child of LipidStructuralSubspecies. Individual FAs, their sn positions, and the double bond positions are known. Example: PE(P-18:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z))

Author:

nils.hoffmann

See Also:

LipidStructuralSubspecies

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
LipidIsomericSubspecies(HeadGroup headGroup, FattyAcid... fa)	Creates a new LipidIsomericSubspecies.

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

LipidIsomericSubspecies

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

Creates a new LipidIsomericSubspecies.

Parameters:

headGroup - the head group for this lipid.

fa - the FattyAcids attached to this lipid.

Method Detail

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 LipidStructuralSubspecies

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.

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 LipidStructuralSubspecies

Parameters:

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

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 LipidStructuralSubspecies

Returns:

the normalized lipid name.

toString

public String toString()

Overrides:

toString in class LipidStructuralSubspecies