Package org.lifstools.jgoslin.parser

Klasse LipidBaseParserEventHandler

java.lang.Object

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

org.lifstools.jgoslin.parser.LipidBaseParserEventHandler

Bekannte direkte Unterklassen:

GoslinParserEventHandler, HmdbParserEventHandler, LipidMapsParserEventHandler, ShorthandParserEventHandler, SwissLipidsParserEventHandler

public abstract class LipidBaseParserEventHandler
extends BaseParserEventHandler<LipidAdduct>

Autor:

Dominik Kopczynski, Nils Hoffmann

Feldübersicht

Felder

Modifizierer und Typ	Feld	Beschreibung
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

Von Klasse geerbte Felder org.lifstools.jgoslin.parser.BaseParserEventHandler

content, errorMessage, registeredEvents, ruleNames

Konstruktorübersicht

Konstruktoren

Konstruktor	Beschreibung
LipidBaseParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)

Methodenübersicht

Modifizierer und Typ	Methode	Beschreibung
protected LipidSpecies	assembleLipid(Headgroup headgroup)
protected boolean	check_full_structure(FunctionalGroup obj)
protected Headgroup	prepareHeadgroupAndChecks()
protected Headgroup	prepareHeadgroupAndChecks(boolean allowClassShift)
protected FattyAcid	resolveFaSynonym(String mediatorName)
protected void	setLipidLevel(LipidLevel _level)
protected boolean	spRegularLcb()

Von Klasse geerbte Methoden org.lifstools.jgoslin.parser.BaseParserEventHandler

getErrorMessage, handleEvent, resetParser, sanityCheck

Von Klasse geerbte Methoden java.lang.Object

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

Felddetails

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

Konstruktordetails

LipidBaseParserEventHandler

public LipidBaseParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)

Methodendetails

setLipidLevel

protected void setLipidLevel(LipidLevel _level)

spRegularLcb

protected boolean spRegularLcb()

check_full_structure

protected boolean check_full_structure(FunctionalGroup obj)

prepareHeadgroupAndChecks

protected Headgroup prepareHeadgroupAndChecks()

prepareHeadgroupAndChecks

protected Headgroup prepareHeadgroupAndChecks(boolean allowClassShift)

assembleLipid

protected LipidSpecies assembleLipid(Headgroup headgroup)

resolveFaSynonym

protected FattyAcid resolveFaSynonym(String mediatorName)