R/AllGenerics.R

In xcms: LC-MS and GC-MS Data Analysis

## On the long run it would be nice to have all generics in here.
## Alphabetically ordered.

## A
setGeneric("absent", function(object, class, minfrac) standardGeneric("absent"))
setGeneric("absMz", function(object, ...) standardGeneric("absMz"))
setGeneric("absMz<-", function(object, value) standardGeneric("absMz<-"))
setGeneric("absRt", function(object, ...) standardGeneric("absRt"))
setGeneric("absRt<-", function(object, value) standardGeneric("absRt<-"))
setGeneric("addParams", function(object, ...) standardGeneric("addParams"))
setGeneric("addParams<-", function(object, value) standardGeneric("addParams<-"))
setGeneric("addProcessHistory", function(object, ...)
    standardGeneric("addProcessHistory"))
setGeneric("adjustRtime", function(object, param, ...)
    standardGeneric("adjustRtime"))
setGeneric("adjustedRtime", function(object, ...) standardGeneric("adjustedRtime"))
setGeneric("adjustedRtime<-", function(object, value)
    standardGeneric("adjustedRtime<-"))
setGeneric("align", function(x, y, ...) standardGeneric("align"))
setGeneric("ampTh", function(object, ...) standardGeneric("ampTh"))
setGeneric("ampTh<-", function(object, value) standardGeneric("ampTh<-"))
setGeneric("AutoLockMass", function(object) standardGeneric("AutoLockMass"))

## B
setGeneric("baseValue", function(object, ...) standardGeneric("baseValue"))
setGeneric("baseValue<-", function(object, value) standardGeneric("baseValue<-"))
setGeneric("binSize", function(object, ...) standardGeneric("binSize"))
setGeneric("binSize<-", function(object, value) standardGeneric("binSize<-"))
setGeneric("bw", function(object) standardGeneric("bw"))
setGeneric("bw<-", function(object, value) standardGeneric("bw<-"))

## C
setGeneric("calibrate", function(object, ...) standardGeneric("calibrate"))
setGeneric("checkBack", function(object, ...) standardGeneric("checkBack"))
setGeneric("centerSample", function(object) standardGeneric("centerSample"))
setGeneric("centerSample<-", function(object, value)
    standardGeneric("centerSample<-"))
setGeneric("checkBack<-", function(object, value) standardGeneric("checkBack<-"))
setGeneric("chromPeaks", function(object, ...) standardGeneric("chromPeaks"))
setGeneric("chromPeaks<-", function(object, value)
    standardGeneric("chromPeaks<-"))
setGeneric("chromPeakData", function(object, ...) standardGeneric("chromPeakData"))
setGeneric("chromPeakData<-", function(object, value)
    standardGeneric("chromPeakData<-"))
setGeneric("collect", function(object, ...) standardGeneric("collect"))
setGeneric("consecMissedLimit", function(object, ...)
    standardGeneric("consecMissedLimit"))
setGeneric("consecMissedLimit<-", function(object, value)
    standardGeneric("consecMissedLimit<-"))
setGeneric("correlate", function(x, y, ...) standardGeneric("correlate"))
setGeneric("criticalValue", function(object, ...)
    standardGeneric("criticalValue"))
setGeneric("criticalValue<-", function(object, value)
    standardGeneric("criticalValue<-"))

## D
setGeneric("deepCopy", function(object) standardGeneric("deepCopy"))
setGeneric("diffreport", function(object, ...) standardGeneric("diffreport"))
setGeneric("distance", function(object, ...) standardGeneric("distance"))
setGeneric("distance<-", function(object, value) standardGeneric("distance<-"))
setGeneric("distFun", function(object) standardGeneric("distFun"))
setGeneric("distFun<-", function(object, value) standardGeneric("distFun<-"))
setGeneric("dropAdjustedRtime", function(object, ...)
    standardGeneric("dropAdjustedRtime"))
setGeneric("dropChromPeaks", function(object, ...)
    standardGeneric("dropChromPeaks"))
setGeneric("dropFeatureDefinitions", function(object, ...)
    standardGeneric("dropFeatureDefinitions"))
setGeneric("dropFilledChromPeaks", function(object, ...)
    standardGeneric("dropFilledChromPeaks"))

## E
setGeneric("expandMz", function(object, ...)
    standardGeneric("expandMz"))
setGeneric("expandMz<-", function(object, value)
    standardGeneric("expandMz<-"))
setGeneric("expandRt", function(object, ...)
    standardGeneric("expandRt"))
setGeneric("expandRt<-", function(object, value)
    standardGeneric("expandRt<-"))
setGeneric("extraPeaks", function(object, ...)
    standardGeneric("extraPeaks"))
setGeneric("extraPeaks<-", function(object, value)
    standardGeneric("extraPeaks<-"))
setGeneric("extractMsData", function(object, ...)
    standardGeneric("extractMsData"))

## F
setGeneric("factorDiag", function(object) standardGeneric("factorDiag"))
setGeneric("factorDiag<-", function(object, value) standardGeneric("factorDiag<-"))
setGeneric("factorGap", function(object) standardGeneric("factorGap"))
setGeneric("factorGap<-", function(object, value) standardGeneric("factorGap<-"))
setGeneric("family", function(object, ...) standardGeneric("family"))
setGeneric("family<-", function(object, value) standardGeneric("family<-"))
setGeneric("featureDefinitions", function(object, ...)
    standardGeneric("featureDefinitions"))
setGeneric("featureDefinitions<-", function(object, value)
    standardGeneric("featureDefinitions<-"))
setGeneric("featureValues", function(object, ...)
    standardGeneric("featureValues"))
setGeneric("fileIndex", function(object) standardGeneric("fileIndex"))
setGeneric("fileIndex<-", function(object, value) standardGeneric("fileIndex<-"))
setGeneric("filepaths", function(object) standardGeneric("filepaths"))
setGeneric("filepaths<-", function(object, value) standardGeneric("filepaths<-"))
setGeneric("fillChromPeaks", function(object, param, ...)
    standardGeneric("fillChromPeaks"))
setGeneric("fillPeaks.chrom", function(object, ...)
    standardGeneric("fillPeaks.chrom"))
setGeneric("fillPeaks.MSW", function(object, ...)
    standardGeneric("fillPeaks.MSW"))
setGeneric("fillPeaks", function(object, ...) standardGeneric("fillPeaks"))
setGeneric("filterColumnsIntensityAbove", function(object, ...)
    standardGeneric("filterColumnsIntensityAbove"))
setGeneric("filterColumnsKeepTop", function(object, ...)
    standardGeneric("filterColumnsKeepTop"))
setGeneric("findChromPeaks", function(object, param, ...)
           standardGeneric("findChromPeaks"))
setGeneric("findMZ", function(object, find, ppmE=25, print=TRUE)
    standardGeneric("findMZ"))
setGeneric("findmzROI", function(object, ...) standardGeneric("findmzROI"))
setGeneric("findneutral", function(object, find, ppmE=25, print=TRUE)
    standardGeneric("findneutral"))
setGeneric("findKalmanROI", function(object, ...)
    standardGeneric("findKalmanROI"))
setGeneric("findPeaks", function(object, ...) standardGeneric("findPeaks"))
setGeneric("findPeaks.centWave", function(object, ...)
    standardGeneric("findPeaks.centWave"))
setGeneric("findPeaks.addPredictedIsotopeFeatures", function(object, ...)
    standardGeneric("findPeaks.addPredictedIsotopeFeatures"))
setGeneric("findPeaks.centWaveWithPredictedIsotopeROIs", function(object, ...)
    standardGeneric("findPeaks.centWaveWithPredictedIsotopeROIs"))
setGeneric("findPeaks.massifquant", function(object, ...)
    standardGeneric("findPeaks.massifquant"))
setGeneric("findPeaks.matchedFilter", function(object, ...)
    standardGeneric("findPeaks.matchedFilter"))
setGeneric("findPeaks.MSW", function(object, ...)
    standardGeneric("findPeaks.MSW"))
setGeneric("findPeaks.MS1", function(object, ...)
    standardGeneric("findPeaks.MS1"))
setGeneric("firstBaselineCheck", function(object, ...)
    standardGeneric("firstBaselineCheck"))
setGeneric("firstBaselineCheck<-", function(object, value)
    standardGeneric("firstBaselineCheck<-"))
setGeneric("fitgauss", function(object, ...) standardGeneric("fitgauss"))
setGeneric("fitgauss<-", function(object, value) standardGeneric("fitgauss<-"))
setGeneric("fwhm", function(object, ...) standardGeneric("fwhm"))
setGeneric("fwhm<-", function(object, value) standardGeneric("fwhm<-"))

## G
setGeneric("gapExtend", function(object) standardGeneric("gapExtend"))
setGeneric("gapExtend<-", function(object, value) standardGeneric("gapExtend<-"))
setGeneric("gapInit", function(object) standardGeneric("gapInit"))
setGeneric("gapInit<-", function(object, value) standardGeneric("gapInit<-"))
setGeneric("getEIC", function(object, ...) standardGeneric("getEIC"))
setGeneric("getMsnScan", function(object, ...) standardGeneric("getMsnScan"))
setGeneric("getPeaks", function(object, ...) standardGeneric("getPeaks"))
setGeneric("getScan", function(object, ...) standardGeneric("getScan"))
setGeneric("getSpec", function(object, ...) standardGeneric("getSpec"))
setGeneric("getXcmsRaw", function(object, ...) standardGeneric("getXcmsRaw"))
## There's too many "group" methods here...
setGeneric("group.density", function(object, ...) standardGeneric("group.density"))
setGeneric("group.mzClust", function(object, ...) standardGeneric("group.mzClust"))
setGeneric("group.nearest", function(object, ...) standardGeneric("group.nearest"))
setGeneric("group", function(object, ...) standardGeneric("group"))
setGeneric("groupChromPeaks", function(object, param, ...)
           standardGeneric("groupChromPeaks"))
setGeneric("groupidx", function(object) standardGeneric("groupidx"))
setGeneric("groupidx<-", function(object, value) standardGeneric("groupidx<-"))
setGeneric("groupnames", function(object, ...) standardGeneric("groupnames"))
setGeneric("groups", function(object) standardGeneric("groups"))
setGeneric("groups<-", function(object, value) standardGeneric("groups<-"))
setGeneric("groupval", function(object, ...) standardGeneric("groupval"))

## H
setGeneric("hasMSn", function(object, ...) standardGeneric("hasMSn"))
setGeneric("hasAdjustedRtime", function(object, ...)
    standardGeneric("hasAdjustedRtime"))
setGeneric("hasFeatures", function(object, ...)
    standardGeneric("hasFeatures"))
setGeneric("hasChromPeaks", function(object, ...)
    standardGeneric("hasChromPeaks"))
setGeneric("hasFilledChromPeaks", function(object, ...)
    standardGeneric("hasFilledChromPeaks"))


## I
setGeneric("image", function(x, ...) standardGeneric("image"))
setGeneric("impute<-", function(object, value) standardGeneric("impute<-"))
setGeneric("index", function(object, ...) standardGeneric("index"))
setGeneric("index<-", function(object, value) standardGeneric("index<-"))
setGeneric("integrate")
##setGeneric("integrate", function(object, ...) standardGeneric("integrate"))
setGeneric("integrate<-", function(object, value) standardGeneric("integrate<-"))
setGeneric("initPenalty", function(object) standardGeneric("initPenalty"))
setGeneric("initPenalty<-", function(object, value) standardGeneric("initPenalty<-"))

## K
setGeneric("kNN", function(object, ...) standardGeneric("kNN"))
setGeneric("kNN<-", function(object, value) standardGeneric("kNN<-"))


## L
setGeneric("levelplot", function(x, data, ...) standardGeneric("levelplot"))
setGeneric("localAlignment", function(object) standardGeneric("localAlignment"))
setGeneric("localAlignment<-", function(object, value) standardGeneric("localAlignment<-"))
setGeneric("loadRaw", function(object, ...) standardGeneric("loadRaw"))

## M
##setGeneric("max", function(x, ...) standardGeneric("max"))
setGeneric("max")
setGeneric("max<-", function(object, value) standardGeneric("max<-"))
setGeneric("maxCharge", function(object) standardGeneric("maxCharge"))
setGeneric("maxCharge<-", function(object, value) standardGeneric("maxCharge<-"))
setGeneric("maxFeatures", function(object) standardGeneric("maxFeatures"))
setGeneric("maxFeatures<-", function(object, value) standardGeneric("maxFeatures<-"))
setGeneric("maxIso", function(object) standardGeneric("maxIso"))
setGeneric("maxIso<-", function(object, value) standardGeneric("maxIso<-"))
setGeneric("makeacqNum", function(object, freq, start=1) standardGeneric("makeacqNum"))
setGeneric("minFraction", function(object) standardGeneric("minFraction"))
setGeneric("minFraction<-", function(object, value) standardGeneric("minFraction<-"))
setGeneric("minNoiseLevel", function(object, ...) standardGeneric("minNoiseLevel"))
setGeneric("minNoiseLevel<-", function(object, value)
    standardGeneric("minNoiseLevel<-"))
setGeneric("minSamples", function(object) standardGeneric("minSamples"))
setGeneric("minSamples<-", function(object, value) standardGeneric("minSamples<-"))
setGeneric("mslevel", function(object, ...) standardGeneric("mslevel"))
setGeneric("mslevel<-", function(object, value) standardGeneric("mslevel<-"))
setGeneric("msnparent2ms", function(object, ...) standardGeneric("msnparent2ms"))
setGeneric("msn2ms", function(object, ...) standardGeneric("msn2ms"))
setGeneric("mzdiff", function(object, ...) standardGeneric("mzdiff"))
setGeneric("mzdiff<-", function(object, value) standardGeneric("mzdiff<-"))
setGeneric("mzrange", function(object, ...) standardGeneric("mzrange"))
setGeneric("mzCenterFun", function(object, ...) standardGeneric("mzCenterFun"))
setGeneric("mzCenterFun<-", function(object, value)
    standardGeneric("mzCenterFun<-"))
setGeneric("mzIntervalExtension", function(object, ...)
    standardGeneric("mzIntervalExtension"))
setGeneric("mzIntervalExtension<-", function(object, value)
    standardGeneric("mzIntervalExtension<-"))
setGeneric("mzVsRtBalance", function(object, ...)
    standardGeneric("mzVsRtBalance"))
setGeneric("mzVsRtBalance<-", function(object, value)
    standardGeneric("mzVsRtBalance<-"))

## N
setGeneric("nearbyPeak", function(object, ...) standardGeneric("nearbyPeak"))
setGeneric("nearbyPeak<-", function(object, value) standardGeneric("nearbyPeak<-"))
setGeneric("noise", function(object, ...) standardGeneric("noise"))
setGeneric("noise<-", function(object, value) standardGeneric("noise<-"))

## P
setGeneric("peakGroupsMatrix", function(object, ...)
    standardGeneric("peakGroupsMatrix"))
setGeneric("peakGroupsMatrix<-", function(object, value)
    standardGeneric("peakGroupsMatrix<-"))
setGeneric("peakScaleRange", function(object, ...)
    standardGeneric("peakScaleRange"))
setGeneric("peakScaleRange<-", function(object, value)
    standardGeneric("peakScaleRange<-"))
setGeneric("peakTable", function(object, ...) standardGeneric("peakTable"))
setGeneric("peakThr", function(object, ...) standardGeneric("peakThr"))
setGeneric("peakThr<-", function(object, value) standardGeneric("peakThr<-"))
setGeneric("peakwidth", function(object, ...) standardGeneric("peakwidth"))
setGeneric("peakwidth<-", function(object, value) standardGeneric("peakwidth<-"))
setGeneric("plotChrom", function(object, ...) standardGeneric("plotChrom"))
setGeneric("plotChromPeakDensity", function(object, ...)
    standardGeneric("plotChromPeakDensity"))
setGeneric("plotEIC", function(object, ...) standardGeneric("plotEIC"))
setGeneric("plotPeaks", function(object, ...) standardGeneric("plotPeaks"))
setGeneric("plotRaw", function(object, ...) standardGeneric("plotRaw"))
setGeneric("plotrt", function(object, ...) standardGeneric("plotrt"))
setGeneric("plotScan", function(object, ...) standardGeneric("plotScan"))
setGeneric("plotSpec", function(object, ...) standardGeneric("plotSpec"))
setGeneric("plotSurf", function(object, ...) standardGeneric("plotSurf"))
setGeneric("plotTIC", function(object, ...) standardGeneric("plotTIC"))
setGeneric("plotTree", function(object, ...) standardGeneric("plotTree"))
setGeneric("ppm", function(object, ...) standardGeneric("ppm"))
setGeneric("ppm<-", function(object, value) standardGeneric("ppm<-"))
setGeneric("prefilter", function(object, ...) standardGeneric("prefilter"))
setGeneric("prefilter<-", function(object, value) standardGeneric("prefilter<-"))
setGeneric("present", function(object, class, minfrac) standardGeneric("present"))
setGeneric("processDate", function(object, ...) standardGeneric("processDate"))
setGeneric("processDate<-", function(object, value) standardGeneric("processDate<-"))
setGeneric("processInfo", function(object, ...) standardGeneric("processInfo"))
setGeneric("processInfo<-", function(object, value) standardGeneric("processInfo<-"))
setGeneric("processParam", function(object, ...) standardGeneric("processParam"))
setGeneric("processParam<-", function(object, value)
    standardGeneric("processParam<-"))
setGeneric("processType", function(object, ...) standardGeneric("processType"))
setGeneric("processType<-", function(object, value) standardGeneric("processType<-"))
setGeneric("processHistory", function(object, ...) standardGeneric("processHistory"))
setGeneric("profinfo", function(object) standardGeneric("profinfo"))
setGeneric("profinfo<-", function(object, value) standardGeneric("profinfo<-"))
setGeneric("profMat", function(object, ...) standardGeneric("profMat"))
setGeneric("profMedFilt", function(object, ...) standardGeneric("profMedFilt"))
setGeneric("profMethod", function(object) standardGeneric("profMethod"))
setGeneric("profMethod<-", function(object, value) standardGeneric("profMethod<-"))
setGeneric("profRange", function(object, ...) standardGeneric("profRange"))
setGeneric("profStep", function(object) standardGeneric("profStep"))
setGeneric("profStep<-", function(object, value) standardGeneric("profStep<-"))
setGeneric("profStepPad<-", function(object, value) standardGeneric("profStepPad<-"))
setGeneric("profMz", function(object) standardGeneric("profMz"))
setGeneric("progressCallback", function(object) standardGeneric("progressCallback"))
setGeneric("progressCallback<-", function(object, value) standardGeneric("progressCallback<-"))
setGeneric("progressInfoUpdate", function(object) standardGeneric("progressInfoUpdate"))

## R
setGeneric("rawEIC", function(object, ...) standardGeneric("rawEIC"))
setGeneric("rawMat", function(object, ...) standardGeneric("rawMat"))
setGeneric("rawMZ", function(object, ...) standardGeneric("rawMZ"))
setGeneric("refineChromPeaks", function(object, param, ...)
    standardGeneric("refineChromPeaks"))
setGeneric("removeIntensity", function(object, ...) standardGeneric("removeIntensity"))
setGeneric("response", function(object) standardGeneric("response"))
setGeneric("response<-", function(object, value) standardGeneric("response<-"))
setGeneric("retcor", function(object, ...) standardGeneric("retcor"))
setGeneric("retcor.peakgroups", function(object, ...) standardGeneric("retcor.peakgroups"))
setGeneric("retcor.obiwarp", function(object, ...) standardGeneric("retcor.obiwarp"))
setGeneric("revMz", function(object, ...) standardGeneric("revMz"))
setGeneric("ridgeLength", function(object, ...) standardGeneric("ridgeLength"))
setGeneric("ridgeLength<-", function(object, value) standardGeneric("ridgeLength<-"))
setGeneric("roiList", function(object, ...) standardGeneric("roiList"))
setGeneric("roiList<-", function(object, value) standardGeneric("roiList<-"))
setGeneric("roiScales", function(object, ...) standardGeneric("roiScales"))
setGeneric("roiScales<-", function(object, value) standardGeneric("roiScales<-"))
setGeneric("rtrange", function(object) standardGeneric("rtrange"))

## S
setGeneric("sampclass", function(object) standardGeneric("sampclass"))
setGeneric("sampclass<-", function(object, value) standardGeneric("sampclass<-"))
setGeneric("sampleGroups", function(object) standardGeneric("sampleGroups"))
setGeneric("sampleGroups<-", function(object, value)
    standardGeneric("sampleGroups<-"))
setGeneric("sampnames", function(object) standardGeneric("sampnames"))
setGeneric("sampnames<-", function(object, value) standardGeneric("sampnames<-"))
setGeneric("scales", function(object, ...) standardGeneric("scales"))
setGeneric("scales<-", function(object, value) standardGeneric("scales<-"))
setGeneric("scanrange", function(object, ...) standardGeneric("scanrange"))
setGeneric("scanrange<-", function(object, value) standardGeneric("scanrange<-"))
setGeneric("sigma", function(object, value) standardGeneric("sigma"))
setGeneric("sigma<-", function(object, value) standardGeneric("sigma<-"))
setGeneric("showError", function(object, ...) standardGeneric("showError"))
setGeneric("smooth<-", function(object, value) standardGeneric("smooth<-"))
setGeneric("snthresh", function(object, ...) standardGeneric("snthresh"))
setGeneric("snthresh<-", function(object, value) standardGeneric("snthresh<-"))
setGeneric("snthreshIsoROIs", function(object, ...)
    standardGeneric("snthreshIsoROIs"))
setGeneric("snthreshIsoROIs<-", function(object, value)
    standardGeneric("snthreshIsoROIs<-"))
setGeneric("sortMz", function(object, ...) standardGeneric("sortMz"))
setGeneric("span", function(object, ...) standardGeneric("span"))
setGeneric("span<-", function(object, value) standardGeneric("span<-"))
setGeneric("specDist", function(object, ...) standardGeneric("specDist"))
setGeneric("specDist.meanMZmatch",
           function(peakTable1, peakTable2, matchdist=1, matchrate=1,
                    mzabs=0.001, mzppm=10, symmetric=TRUE)
               standardGeneric("specDist.meanMZmatch"))
setGeneric("specDist.cosine",
           function(peakTable1, peakTable2, mzabs = 0.001, mzppm = 10,
                    mzExp = 0.6, intExp = 3, nPdiff = 2, nPmin = 8,
                    symmetric = FALSE)
               standardGeneric("specDist.cosine"))
setGeneric("specDist.peakCount",
           function(peakTable1, peakTable2, mzabs=0.001, mzppm=10,symmetric=FALSE)
               standardGeneric("specDist.peakCount"))
setGeneric("steps", function(object, ...) standardGeneric("steps"))
setGeneric("steps<-", function(object, value) standardGeneric("steps<-"))
setGeneric("stitch", function(object, lockMass, ...) standardGeneric("stitch"))
setGeneric("stitch.xml", function(object, lockMass) standardGeneric("stitch.xml"))
setGeneric("stitch.netCDF", function(object, lockMass) standardGeneric("stitch.netCDF"))
setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stitch.netCDF.new"))
setGeneric("subset<-", function(object, value) standardGeneric("subset<-"))
setGeneric("subsetAdjust", function(object, ...) standardGeneric("subsetAdjust"))
setGeneric("subsetAdjust<-", function(object, value) standardGeneric("subsetAdjust<-"))


## T
setGeneric("tuneIn", function(object, ...) standardGeneric("tuneIn"))
setGeneric("tuneIn<-", function(object, value) standardGeneric("tuneIn<-"))

## U
setGeneric("unions", function(object, ...) standardGeneric("unions"))
setGeneric("unions<-", function(object, value) standardGeneric("unions<-"))

## V
setGeneric("verboseColumns", function(object, ...) standardGeneric("verboseColumns"))
setGeneric("verboseColumns<-", function(object, value)
    standardGeneric("verboseColumns<-"))

## W
setGeneric("withWave", function(object, ...) standardGeneric("withWave"))
setGeneric("withWave<-", function(object, value) standardGeneric("withWave<-"))
setGeneric("write.cdf", function(object, ...) standardGeneric("write.cdf"))
setGeneric("write.mzdata", function(object, ...) standardGeneric("write.mzdata"))
setGeneric("write.mzQuantML", function(object, ...) standardGeneric("write.mzQuantML"))

## X
setGeneric("xcmsSource", function(object, ...) standardGeneric("xcmsSource"))