Package org.lifstools.jgoslin.parser

Class LipidBaseParserEventHandler

java.lang.Object

org.lifstools.jgoslin.parser.BaseParserEventHandler<LipidAdduct>

org.lifstools.jgoslin.parser.LipidBaseParserEventHandler

Direct Known Subclasses:

GoslinParserEventHandler, HmdbParserEventHandler, LipidMapsParserEventHandler, ShorthandParserEventHandler, SwissLipidsParserEventHandler

public abstract class LipidBaseParserEventHandler
extends BaseParserEventHandler<LipidAdduct>

Author:

Dominik Kopczynski, Nils Hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
protected Adduct	adduct
protected FattyAcid	currentFa
protected List<FattyAcid>	faList
protected String	headGroup
protected ArrayList<HeadgroupDecorator>	headgroupDecorators
protected KnownFunctionalGroups	knownFunctionalGroups
protected FattyAcid	lcb
protected LipidLevel	level
protected static HashSet<String>	SP_EXCEPTION_CLASSES
protected boolean	useHeadGroup

Fields inherited from class org.lifstools.jgoslin.parser.BaseParserEventHandler

content, errorMessage, registeredEvents, ruleNames

Constructor Summary

Constructors

Constructor	Description
LipidBaseParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)

Method Summary

Modifier and Type	Method	Description
protected LipidSpecies	assembleLipid(Headgroup headgroup)
protected Headgroup	prepareHeadgroupAndChecks()
protected void	setLipidLevel(LipidLevel _level)
protected boolean	spRegularLcb()

Methods inherited from class org.lifstools.jgoslin.parser.BaseParserEventHandler

getErrorMessage, handleEvent, resetParser, sanityCheck

Methods inherited from class java.lang.Object

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

Field Details

level

protected LipidLevel level

headGroup

protected String headGroup

lcb

protected FattyAcid lcb

faList

protected List<FattyAcid> faList

currentFa

protected FattyAcid currentFa

adduct

protected Adduct adduct

headgroupDecorators

protected ArrayList<HeadgroupDecorator> headgroupDecorators

useHeadGroup

protected boolean useHeadGroup

knownFunctionalGroups

protected KnownFunctionalGroups knownFunctionalGroups

SP_EXCEPTION_CLASSES

protected static HashSet<String> SP_EXCEPTION_CLASSES

Constructor Details

LipidBaseParserEventHandler

public LipidBaseParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)

Method Details

setLipidLevel

protected void setLipidLevel(LipidLevel _level)

spRegularLcb

protected boolean spRegularLcb()

prepareHeadgroupAndChecks

protected Headgroup prepareHeadgroupAndChecks()

assembleLipid

protected LipidSpecies assembleLipid(Headgroup headgroup)