Package de.isas.lipidomics.domain

Class LipidMolecularSubspecies

java.lang.Object

de.isas.lipidomics.domain.LipidSpecies

de.isas.lipidomics.domain.LipidMolecularSubspecies

Direct Known Subclasses:

LipidStructuralSubspecies

public class LipidMolecularSubspecies
extends LipidSpecies

A molecular subspecies. Child of LipidSpecies. Individual FAs are known, but neither their sn positions nor double bond positions. Example: Phosphatidylinositol (8:0-8:0) or PI(8:0-8:0)

Author:

nils.hoffmann

See Also:

LipidSpecies

Field Summary

Fields

Modifier and Type	Field	Description
protected Map<String,FattyAcid>	fa

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

info, NONE

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected String	buildLipidSubspeciesName(LipidLevel level, String faSeparator, String headGroup, boolean isNormalized)
protected StringBuilder	buildSubspeciesHeadGroupString(String headGroup, boolean normalizeHeadGroup)
Map<String,FattyAcid>	getFa()	Returns the fatty acyls registered for this lipid.
protected String	getHeadGroupSuffix()
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()
boolean	validate()	Validate this lipid against the class-specific available FA types and slots.

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

Field Detail

fa

protected final Map<String,FattyAcid> fa

Constructor Detail

LipidMolecularSubspecies

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

Method Detail

getFa

public Map<String,FattyAcid> getFa()

Description copied from class: LipidSpecies

Returns the fatty acyls registered for this lipid.

Overrides:

getFa in class LipidSpecies

Returns:

the fatty acyls.

getHeadGroupSuffix

protected String getHeadGroupSuffix()

buildSubspeciesHeadGroupString

protected StringBuilder buildSubspeciesHeadGroupString(String headGroup,
                                                       boolean normalizeHeadGroup)

buildLipidSubspeciesName

protected String buildLipidSubspeciesName(LipidLevel level,
                                          String faSeparator,
                                          String headGroup,
                                          boolean isNormalized)

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 LipidSpecies

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 LipidSpecies

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 LipidSpecies

Returns:

the normalized lipid name.

validate

public boolean validate()

Description copied from class: LipidSpecies

Validate this lipid against the class-specific available FA types and slots.

Overrides:

validate in class LipidSpecies

Returns:

true if this lipid's FA types and their number match the class definition, false otherwise.

toString

public String toString()

Overrides:

toString in class LipidSpecies