R/AllGenerics.R

In mzR: parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

setGeneric("runInfo", function(object) standardGeneric("runInfo"))
setGeneric("mzidInfo", function(object) standardGeneric("mzidInfo"))
setGeneric("para", function(object) standardGeneric("para"))
setGeneric("specParams", function(object) standardGeneric("specParams"))
setGeneric("substitutions", function(object) standardGeneric("substitutions"))
setGeneric("enzymes", function(object) standardGeneric("enzymes"))
setGeneric("instrumentInfo", function(object) standardGeneric("instrumentInfo"))
setGeneric("softwareInfo", function(object) standardGeneric("softwareInfo"))
setGeneric("sampleInfo", function(object) standardGeneric("sampleInfo"))
setGeneric("sourceInfo", function(object) standardGeneric("sourceInfo"))
setGeneric("writeMSfile", function(object, filename, outformat) standardGeneric("writeMSfile"))
## setGeneric("writeSpectrumList",
##            function(object, filename, outformat, header, data)
##                standardGeneric("writeSpectrumList"))
setGeneric("chromatogramsInfo", function(object) standardGeneric("chromatogramsInfo"))
setGeneric("chromatogramHeader", function(object, chrom)
    standardGeneric("chromatogramHeader"))
setGeneric("creationDate", function(object) standardGeneric("creationDate"))
setGeneric("manufacturer", function(object) standardGeneric("manufacturer"))
setGeneric("model", function(object) standardGeneric("model"))
setGeneric("ionisation", function(object) standardGeneric("ionisation"))
setGeneric("detector", function(object) standardGeneric("detector"))
setGeneric("isInitialized", function(object) standardGeneric("isInitialized"))
setGeneric("initializeRamp",
           signature = c("object"),
           function(object) standardGeneric("initializeRamp"))
setGeneric("header", function(object, scans, ...) standardGeneric("header"))
setGeneric("peaksCount",
           function(object, scans, ...) standardGeneric("peaksCount"))
setGeneric("get3Dmap",
           signature = c("object"),
           function(object, scans, lowMz, highMz, resMz, ...)
               standardGeneric("get3Dmap"))
setGeneric("isolationWindow",
           function(object, ...) standardGeneric("isolationWindow"))

### BiocGenerics
## setGeneric("score", function(x, ...) standardGeneric("score"))
## setGeneric("fileName", function(object, ...) standardGeneric("fileName"))

### ProtGenerics
## setGeneric("psms", function(object, ...) standardGeneric("psms"))
## setGeneric("peaks", function(object, ...) standardGeneric("peaks"))
## setGeneric("database", function(object, ...) standardGeneric("database"))
## setGeneric("modifications", function(object, ...) standardGeneric("modifications"))
## setGeneric("analyzer", function(object) standardGeneric("analyzer"))