Package org.lifstools.jgoslin.domain

Class LipidSpecies

java.lang.Object

org.lifstools.jgoslin.domain.LipidSpecies

Direct Known Subclasses:

LipidMolecularSpecies

public class LipidSpecies
extends Object

A lipid species is the factual root of the object hierarchy. Lipid category and class are used as taxonomic roots of a lipid species. Partial structural knowledge, apart from the head group, is first encoded in the lipid species. A typical lipid species is PC 32:0 (SwissLipids SLM:000056493), where the head group is defined as PC (Glycerophosphocholines), with fatty acyl chains of unknown individual composition, but known total composition (32 carbon atoms, zero double bonds, no hydroxylations or other functions).

Author:

Dominik Kopczynski, Nils Hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
protected HashMap<String,FattyAcid>	fa
protected ArrayList<FattyAcid>	faList
protected Headgroup	headGroup
protected LipidSpeciesInfo	info

Constructor Summary

Constructors

Constructor	Description
LipidSpecies(Headgroup _headGroup, Collection<FattyAcid> _fa, KnownFunctionalGroups knownFunctionalGroups)
LipidSpecies(Headgroup _headgroup, KnownFunctionalGroups knownFunctionalGroups)

Method Summary

Modifier and Type	Method	Description
ElementTable	getElements()
String	getExtendedClass()
ArrayList<FattyAcid>	getFaList()
Headgroup	getHeadGroup()
LipidSpeciesInfo	getInfo()
LipidLevel	getLipidLevel()
String	getLipidString()	Returns the normalized lipid string on the native level.
String	getLipidString(LipidLevel level)	Returns the normalized lipid string on the provided level.

Methods inherited from class java.lang.Object

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

Field Details

headGroup

protected Headgroup headGroup

info

protected LipidSpeciesInfo info

fa

protected HashMap<String,FattyAcid> fa

faList

protected ArrayList<FattyAcid> faList

Constructor Details

LipidSpecies

public LipidSpecies(Headgroup _headgroup,
 KnownFunctionalGroups knownFunctionalGroups)

LipidSpecies

public LipidSpecies(Headgroup _headGroup,
 Collection<FattyAcid> _fa,
 KnownFunctionalGroups knownFunctionalGroups)

Method Details

getLipidLevel

public LipidLevel getLipidLevel()

getInfo

public LipidSpeciesInfo getInfo()

getHeadGroup

public Headgroup getHeadGroup()

getLipidString

public String getLipidString()

Returns the normalized lipid string on the native level.

Returns:

the normalized lipid string.

getLipidString

public String getLipidString(LipidLevel level)

Returns the normalized lipid string on the provided level.

Parameters:

level - the lipid level at which the lipid string should be generated.

Returns:

the normalized lipid string.

Throws:

IllegalArgumentException - when the provided level is not supported.

getExtendedClass

public String getExtendedClass()

getFaList

public ArrayList<FattyAcid> getFaList()

getElements

public ElementTable getElements()