AffineAlignObj	AffineAlignObj-class
AffineAlignObj-class	AffineAlignObj-class
AffineAlignObjLight	AffineAlignObjLight-class
AffineAlignObjLight-class	AffineAlignObjLight-class
AffineAlignObjMedium	AffineAlignObjMedium-class
AffineAlignObjMedium-class	AffineAlignObjMedium-class
alignChromatogramsCpp	alignChromatogramsCpp
AlignObj	AlignObj-class
AlignObj-class	AlignObj-class
alignTargetedRuns	alignTargetedRuns
analytesFromFeatures	analytesFromFeatures
areaIntegrator	areaIntegrator
as.list,AffineAlignObj-method	as.list-AffineAlignObj-method
as.list,AffineAlignObjLight-method	as.list-AffineAlignObjLight-method
as.list,AffineAlignObjMedium-method	as.list-AffineAlignObjMedium-method
as.list,AlignObj-method	as.list-AlignObj-method
calculateIntensity	calculateIntensity
chromatogramIdAsInteger	chromatogramIdAsInteger
constrainSimCpp	constrainSimCpp
DIAlignR	DIAlignR
doAffineAlignmentCpp	doAffineAlignmentCpp
doAlignmentCpp	doAlignmentCpp
extractXIC_group	extractXIC_group
fetchAnalytesInfo	fetchAnalytesInfo
fetchFeaturesFromRun	fetchFeaturesFromRun
fetchPrecursorsInfo	fetchPrecursorsInfo
filenamesFromMZML	filenamesFromMZML
filenamesFromOSW	filenamesFromOSW
getAlignedFigs	getAlignedFigs
getAlignedIndices	getAlignedIndices
getAlignObj	getAlignObj
getAlignObjs	getAlignObjs
getAnalytesQuery	getAnalytesQuery
getBaseGapPenaltyCpp	getBaseGapPenaltyCpp
getChromatogramIndices	getChromatogramIndices
getChromSimMatCpp	getChromSimMatCpp
getFeatures	getFeatures
getFeaturesQuery	getFeaturesQuery
getGlobalAlignMaskCpp	getGlobalAlignMaskCpp
getGlobalAlignment	getGlobalAlignment
getGlobalFits	getGlobalFits
getLinearfit	getLinearfit
getLOESSfit	getLOESSfit
getMappedRT	getMappedRT
getMultipeptide	getMultipeptide
getMZMLpointers	getMZMLpointers
getOswAnalytes	getOswAnalytes
getOswFiles	getOswFiles
getPrecursorByID	getPrecursorByID
getPrecursors	getPrecursors
getPrecursorsQuery	getPrecursorsQuery
getPrecursorsQueryID	getPrecursorsQueryID
getQuery	getQuery
getRefRun	getRefRun
getRSE	getRSE
getRunNames	getRunNames
getSeqSimMatCpp	getSeqSimMatCpp
getXICs	getXICs
getXICs4AlignObj	getXICs4AlignObj
mapIdxToTime	mapIdxToTime
mappedRTfromAlignObj	mappedRTfromAlignObj
mapPrecursorToChromIndices	mapPrecursorToChromIndices
mergeOswAnalytes_ChromHeader	mergeOswAnalytes_ChromHeader
multipeptide_DIAlignR	multipeptide_DIAlignR
oswFiles_DIAlignR	oswFiles_DIAlignR
pickNearestFeature	pickNearestFeature
plotAlignedAnalytes	plotAlignedAnalytes
plotAlignmentPath	plotAlignmentPath
plotAnalyteXICs	plotAnalyteXICs
plotSingleAlignedChrom	plotSingleAlignedChrom
plotXICgroup	plotXICgroup
readChromatogramHeader	readChromatogramHeader
setAlignmentRank	setAlignmentRank
smoothSingleXIC	smoothSingleXIC
smoothXICs	smoothXICs
trimXICs	trimXICs
updateFileInfo	updateFileInfo
writeTables	writeTables
XIC_QFNNTDIVLLEDFQK_3_DIAlignR	XIC_QFNNTDIVLLEDFQK_3_DIAlignR
