## AbstractMassObject
setGeneric("plotMsiSlice", function(x, ...) standardGeneric("plotMsiSlice"))
setGeneric(".prepareShow", function(object) standardGeneric(".prepareShow"))
setGeneric(
"transformIntensity",
function(object, ...) standardGeneric("transformIntensity")
)
setGeneric(
".transformIntensity",
function(object, ...) standardGeneric(".transformIntensity")
)
setGeneric("trim", function(object, range, ...) standardGeneric("trim"))
## get/set slots
setGeneric("mass", function(object, ...) standardGeneric("mass"))
setGeneric("mass<-", function(object, value) standardGeneric("mass<-"))
# from ProtGenerics (same as mass)
setGeneric("mz", function(object, ...) standardGeneric("mz"))
setGeneric("mz<-", function(object, value) standardGeneric("mz<-"))
setGeneric("intensity", function(object, ...) standardGeneric("intensity"))
setGeneric(
"intensity<-",
function(object, value) standardGeneric("intensity<-")
)
setGeneric("isEmpty", function(x) standardGeneric("isEmpty"))
setGeneric(".isEmptyWarning", function(x) standardGeneric(".isEmptyWarning"))
setGeneric("metaData", function(object) standardGeneric("metaData"))
setGeneric("metaData<-", function(object, value) standardGeneric("metaData<-"))
setGeneric("coordinates", function(object, ...) standardGeneric("coordinates"))
setGeneric(
"coordinates<-",
function(object, value) standardGeneric("coordinates<-")
)
## end of AbstractMassObject
## MassSpectrum
setGeneric(
"calibrateIntensity",
function(object, ...) standardGeneric("calibrateIntensity")
)
setGeneric("detectPeaks", function(object, ...) standardGeneric("detectPeaks"))
setGeneric(
"estimateBaseline",
function(object, method=c("SNIP", "ConvexHull", "Median"), ...)
standardGeneric("estimateBaseline"))
setGeneric(
"estimateNoise", function(object, ...) standardGeneric("estimateNoise")
)
setGeneric(
".findLocalMaxima",
function(object, halfWindowSize=20L) standardGeneric(".findLocalMaxima")
)
setGeneric(
".findLocalMaximaLogical",
function(object, halfWindowSize=20L)
standardGeneric(".findLocalMaximaLogical")
)
setGeneric("isRegular", function(object, ...) standardGeneric("isRegular"))
setGeneric(
"removeBaseline", function(object, ...) standardGeneric("removeBaseline")
)
setGeneric(
"smoothIntensity", function(object, ...) standardGeneric("smoothIntensity")
)
setGeneric(
"totalIonCurrent", function(object) standardGeneric("totalIonCurrent")
)
## end of MassSpectrum
## MassPeaks
setGeneric("labelPeaks", function(object, ...) standardGeneric("labelPeaks"))
setGeneric(
"monoisotopicPeaks",
function(object, ...) standardGeneric("monoisotopicPeaks")
)
setGeneric("snr", function(object) standardGeneric("snr"))
## end of MassPeaks
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