R/protgenerics.R

In lgatto/ProtGenerics: Generic infrastructure for Bioconductor mass spectrometry packages

## -------------------------------------------------------------
## Data slots
## -------------------------------------------------------------

setGeneric("processingData", function(object, ...) standardGeneric("processingData"))
setGeneric("processingData<-", function(object, ..., value) standardGeneric("processingData<-"))
setGeneric("spectraVariables", function(object, ...) standardGeneric("spectraVariables"))
setGeneric("spectraNames", function(object, ...) standardGeneric("spectraNames"))
setGeneric("spectraNames<-", function(object, ..., value) standardGeneric("spectraNames<-"))
setGeneric("spectraData", function(object, ...) standardGeneric("spectraData"))
setGeneric("spectraData<-", function(object, ..., value) standardGeneric("spectraData<-"))
setGeneric("dataOrigin", function(object, ...) standardGeneric("dataOrigin"))
setGeneric("dataOrigin<-", function(object, value) standardGeneric("dataOrigin<-"))
setGeneric("dataStorage", function(object, ...) standardGeneric("dataStorage"))
setGeneric("dataStorage<-", function(object, value) standardGeneric("dataStorage<-"))

## -------------------------------------------------------------
## Metadata
## -------------------------------------------------------------

setGeneric("ionCount", function(object, ...) standardGeneric("ionCount"))
setGeneric("scanIndex", function(object, ...) standardGeneric("scanIndex"))
setGeneric("precursorMz", function(object, ...) standardGeneric("precursorMz"))
setGeneric("precursorMz<-", function(object, ..., value) standardGeneric("precursorMz<-"))
setGeneric("precursorIntensity", function(object, ...) standardGeneric("precursorIntensity"))
setGeneric("precursorIntensity<-", function(object, ..., value) standardGeneric("precursorIntensity<-"))
setGeneric("precursorCharge", function(object, ...) standardGeneric("precursorCharge"))
setGeneric("precursorCharge<-", function(object, ..., value) standardGeneric("precursorCharge<-"))
setGeneric("acquisitionNum", function(object, ...) standardGeneric("acquisitionNum"))
setGeneric("precAcquisitionNum", function(object, ...) standardGeneric("precAcquisitionNum"))
setGeneric("precScanNum", function(object, ...) standardGeneric("precScanNum"))
setGeneric("msLevel", function(object, ...) standardGeneric("msLevel"))
setGeneric("msLevel<-", function(object, ..., value) standardGeneric("msLevel<-"))
setGeneric("uniqueMsLevels", function(object, ...) standardGeneric("uniqueMsLevels"))

setGeneric("collisionEnergy", function(object, ...) standardGeneric("collisionEnergy"))
setGeneric("collisionEnergy<-", function(object, ..., value) standardGeneric("collisionEnergy<-"))
setGeneric("polarity", function(object, ...) standardGeneric("polarity"))
setGeneric("polarity<-", function(object, ..., value) standardGeneric("polarity<-"))
setGeneric("tic", function(object, ...) standardGeneric("tic"))
setGeneric("rtime", function(object, ...) standardGeneric("rtime"))
setGeneric("rtime<-", function(object, ..., value) standardGeneric("rtime<-"))
setGeneric("centroided", function(object, ...) standardGeneric("centroided"))
setGeneric("centroided<-", function(object, ..., value) standardGeneric("centroided<-"))
setGeneric("smoothed", function(object) standardGeneric("smoothed"))
setGeneric("smoothed<-", function(object, ..., value) standardGeneric("smoothed<-"))
setGeneric("isCentroided", function(object, ...) standardGeneric("isCentroided"))

setGeneric("isolationWindowTargetMz", function(object, ...) standardGeneric("isolationWindowTargetMz"))
setGeneric("isolationWindowTargetMz<-", function(object, ..., value) standardGeneric("isolationWindowTargetMz<-"))
setGeneric("isolationWindowLowerMz", function(object, ...) standardGeneric("isolationWindowLowerMz"))
setGeneric("isolationWindowLowerMz<-", function(object, ..., value) standardGeneric("isolationWindowLowerMz<-"))
setGeneric("isolationWindowUpperMz", function(object, ...) standardGeneric("isolationWindowUpperMz"))
setGeneric("isolationWindowUpperMz<-", function(object, ..., value) standardGeneric("isolationWindowUpperMz<-"))

setGeneric("productMz", function(object, ...) standardGeneric("productMz"))
setGeneric("productMz<-", function(object, ..., value) standardGeneric("productMz<-"))

setGeneric("compounds", function(object, ...) standardGeneric("compounds"))

## -------------------------------------------------------------
## Raw data
## -------------------------------------------------------------

setGeneric("peaks", function(object, ...) standardGeneric("peaks"))
setGeneric("peaks<-", function(object, ..., value) standardGeneric("peaks<-"))
setGeneric("intensity", function(object, ...) standardGeneric("intensity"))
setGeneric("intensity<-", function(object, ..., value) standardGeneric("intensity<-"))
setGeneric("mz", function(object, ...) standardGeneric("mz"))
setGeneric("mz<-", function(object, ..., value) standardGeneric("mz<-"))
setGeneric("spectra", function(object, ...) standardGeneric("spectra"))
setGeneric("spectra<-", function(object, ..., value) standardGeneric("spectra<-"))
setGeneric("scans", function(object, ...) standardGeneric("scans"))
setGeneric("chromatograms", function(object, ...) standardGeneric("chromatograms"))
setGeneric("chromatogram", function(object, ...) standardGeneric("chromatogram"))
setGeneric("mass", function(object, ...) standardGeneric("mass"))
setGeneric("ions", function(object, ...) standardGeneric("ions"))

## -------------------------------------------------------------
## Identification
## -------------------------------------------------------------

setGeneric("modifications", function(object, ...) standardGeneric("modifications"))
setGeneric("database", function(object, ...) standardGeneric("database"))
setGeneric("psms", function(object, ...) standardGeneric("psms"))
setGeneric("peptides", function(object, ...) standardGeneric("peptides"))
setGeneric("proteins", function(object, ...) standardGeneric("proteins"))
setGeneric("accessions", function(object, ...) standardGeneric("accessions"))
setGeneric("tolerance", function(object, ...) standardGeneric("tolerance"))
setGeneric("calculateFragments", function(sequence, object, ...) standardGeneric("calculateFragments"))
setGeneric("adjacencyMatrix", function(object, ...) standardGeneric("adjacencyMatrix"))

## -------------------------------------------------------------
## Instrument
## -------------------------------------------------------------

setGeneric("msInfo", function(object) standardGeneric("msInfo"))
setGeneric("expemail", function(object) standardGeneric("expemail"))
setGeneric("exptitle", function(object) standardGeneric("exptitle"))
setGeneric("ionSource", function(object) standardGeneric("ionSource"))
setGeneric("ionSourceDetails", function(object) standardGeneric("ionSourceDetails"))
setGeneric("analyser", function(object) standardGeneric("analyser"))
setGeneric("analyzer", function(object) standardGeneric("analyzer"))
setGeneric("analyzerDetails", function(object) standardGeneric("analyzerDetails"))
setGeneric("analyserDetails", function(object) standardGeneric("analyserDetails"))
setGeneric("detectorType", function(object) standardGeneric("detectorType"))
setGeneric("instrumentManufacturer", function(object) standardGeneric("instrumentManufacturer"))
setGeneric("instrumentCustomisations", function(object) standardGeneric("instrumentCustomisations"))
setGeneric("instrumentModel", function(object) standardGeneric("instrumentModel"))

## -------------------------------------------------------------
## Data-processing
## -------------------------------------------------------------

setGeneric("smooth", function(x, ...) standardGeneric("smooth")) ## stats::smooth already exists
setGeneric("combineFeatures", function(object, ...) standardGeneric("combineFeatures"))
setGeneric("aggregateFeatures", function(object, ...) standardGeneric("aggregateFeatures"))
setGeneric("impute", function(object, ...) standardGeneric("impute"))
setGeneric("alignRt", function(x, y, ...) standardGeneric("alignRt"))
setGeneric("quantify", function(object, ...) standardGeneric("quantify"))
setGeneric("bin", function(x, ...) standardGeneric("bin"))
setGeneric("compareSpectra", function(x, y, ...)
    standardGeneric("compareSpectra"))
setGeneric("compareChromatograms", function(x, y, ...)
    standardGeneric("compareChromatograms"))
setGeneric("addProcessing", function(object, ...)
    standardGeneric("addProcessing"))
setGeneric("spectrapply", function(object, ...) standardGeneric("spectrapply"))

## -------------------------------------------------------------
## IO
## -------------------------------------------------------------

setGeneric("writeMSData", function(object, file, ...) standardGeneric("writeMSData"))

## -------------------------------------------------------------
## Filtering
## -------------------------------------------------------------

setGeneric("filterAcquisitionNum", function(object, ...) standardGeneric("filterAcquisitionNum"))
setGeneric("filterDataOrigin", function(object, ...) standardGeneric("filterDataOrigin"))
setGeneric("filterDataStorage", function(object, ...) standardGeneric("filterDataStorage"))
setGeneric("filterEmptySpectra", function(object, ...) standardGeneric("filterEmptySpectra"))
setGeneric("filterIsolationWindow", function(object, ...) standardGeneric("filterIsolationWindow"))
setGeneric("filterMsLevel", function(object, ...) standardGeneric("filterMsLevel"))
setGeneric("filterPolarity", function(object, ...) standardGeneric("filterPolarity"))
setGeneric("filterPrecursorMz", function(object, ...) standardGeneric("filterPrecursorMz"))
setGeneric("filterPrecursorMzRange", function(object, ...) standardGeneric("filterPrecursorMzRange"))
setGeneric("filterPrecursorMzValues", function(object, ...) standardGeneric("filterPrecursorMzValues"))
setGeneric("filterPrecursorCharge", function(object, ...) standardGeneric("filterPrecursorCharge"))
setGeneric("filterProductMz", function(object, ...) standardGeneric("filterProductMz"))
setGeneric("filterProductMzRange", function(object, ...) standardGeneric("filterProductMzRange"))
setGeneric("filterProductMzValues", function(object, ...) standardGeneric("filterProductMzValues"))
setGeneric("filterPrecursorScan", function(object, ...) standardGeneric("filterPrecursorScan"))
setGeneric("filterRt", function(object, ...) standardGeneric("filterRt"))
setGeneric("filterMz", function(object, ...) standardGeneric("filterMz"))
setGeneric("filterMzRange", function(object, ...) standardGeneric("filterMzRange"))
setGeneric("filterMzValues", function(object, ...) standardGeneric("filterMzValues"))
setGeneric("filterNA", function(object, ...) standardGeneric("filterNA"))
setGeneric("filterIntensity", function(object, ...) standardGeneric("filterIntensity"))
setGeneric("filterRanges", function(object, ...) standardGeneric("filterRanges"))
setGeneric("filterValues", function(object, ...) standardGeneric("filterValues"))

#' @title Filter features
#'
#' @description
#'
#' Implementations of this generic filter function are supposed to filter
#' *features* in `object` based on a filter criteria defined by
#' parameter `filter`.
#'
#' @param object The object to filter.
#'
#' @param filter The filtering criteria on which `object` should be filtered.
#'
#' @param ... Optional parameters.
#' 
#' @md
setGeneric("filterFeatures",
           function(object, filter, ...) standardGeneric("filterFeatures"))

#' @title Filter Spectra
#'
#' @description
#'
#' Implementations of this generic filter function are supposed to filter
#' *spectra* (e.g. within a `Spectra` object) based on filter criteria
#' defined with parameter `filter`.
#'
#' @param object The object to filter.
#'
#' @param filter The filtering criteria based on which `object` should be
#'     filtered.
#'
#' @param ... Optional parameters.
#' 
#' @md
setGeneric("filterSpectra", def = function(object, filter, ...)
    standardGeneric("filterSpectra"))

#' @title General backend methods
#'
#' @description
#'
#' These methods are used for implementations of *backends* e.g. for `Spectra`
#' or `Chromatograms` object to initialize the backend, merge backends or
#' extract specific information from them.
#' See the respective help pages (e.g. in the `Spectra` or `Chromatograms`
#' packages) for information on the actual implementations of these methods.
#'
#' @param backend A *backend* object.
#' 
#' @param object The *backend* object.
#'
#' @param ... Optional parameters.
#'
#' @md
#'
#' @name backendInitialize
setGeneric("backendInitialize", function(object, ...)
    standardGeneric("backendInitialize"))

#' @rdname backendInitialize
setGeneric("isReadOnly", function(object) standardGeneric("isReadOnly"))

#' @rdname backendInitialize
setGeneric("setBackend", function(object, backend, ...)
    standardGeneric("setBackend"))

#' @rdname backendInitialize
setGeneric("backendMerge", function(object, ...)
           standardGeneric("backendMerge"))

#' @rdname backendInitialize
setGeneric("backendBpparam", def = function(object, ...)
    standardGeneric("backendBpparam"))

#' @rdname backendInitialize
setGeneric("backendParallelFactor", def = function(object, ...)
    standardGeneric("backendParallelFactor"))

#' @rdname backendInitialize
setGeneric("supportsSetBackend", function(object, ...)
    standardGeneric("supportsSetBackend"))

#' @title Get or set MS peak data
#'
#' @description
#' 
#' These methods get or set mass spectrometry (MS) peaks data, which can be
#' m/z, intensity or retention time values.
#' See the respective help pages (e.g. in the `Spectra` or `Chromatograms`
#' packages) for information on the actual implementations of these methods.
#'
#' @param object A data object.
#'
#' @param value Replacement for peaks data.
#'
#' @param ... Optional parameters.
#' 
#' @md
#'
#' @name peaksData
setGeneric("peaksData", function(object, ...) standardGeneric("peaksData"))

#' @rdname peaksData
setGeneric("peaksData<-", function(object, value)
    standardGeneric("peaksData<-"))

#' @rdname peaksData
setGeneric("peaksVariables", function(object, ...)
    standardGeneric("peaksVariables"))