R/methods-mzRnetCDF.R

In sneumann/mzR-playground: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

## setMethod("get3Dmap",
##           signature="mzRnetCDF",
##           function(object,scans,lowMz,highMz,resMz) 
##           return(object@backend$get3DMap(scans,lowMz,highMz,resMz)))

## setMethod("initializeRamp",
##           signature="mzRnetCDF",
##           function(object) {
##             if (!file.exists(fileName(object)))
##               stop("File ",fileName(object)," not found.\n")
##             object@backend$open(fileName(object), declaredOnly = TRUE)
##             if (isInitialized(object)) invisible(TRUE)
##             else stop("Could not initialize ramp slot.")
##           })

setMethod("length",
          signature=c("mzRnetCDF"),
          function(x) {
            scanindex <- netCDFVarInt(x@backend, "scan_index")
            if (!is.null(attr(scanindex, "errortext")))
              stop("Couldn't read scan indicies from ", x@backend)
            return(length(scanindex))
          })

setMethod("peaks",
          signature=c("mzRnetCDF","numeric"),
          function(object,scans) {

            rawdata <- netCDFRawData(object@backend)

            if (length(scans)==1) {
              idx <- seq(rawdata$scanindex[scans]+1,
                         min(rawdata$scanindex[scans+1],
                             length(rawdata$mz), na.rm=TRUE))              
              return(cbind(mz=rawdata$mz[idx],intensity=rawdata$intensity[idx]))
            } else {
              return(sapply(scans,function(x) {
                idx <- seq(rawdata$scanindex[x]+1,
                           min(rawdata$scanindex[x+1],
                               length(rawdata$mz), na.rm=TRUE))
                cbind(mz=rawdata$mz[idx],intensity=rawdata$intensity[idx])
              }, simplify = FALSE))
            }
          })

setMethod("peaks",
          signature=c("mzRnetCDF","missing"),
          function(object) {
            n <- length(object)
            if (n==1)
              return(list(peaks(object,1:n))) ## full experiments are always returned as lists
            return(peaks(object,1:n))
          })

## setMethod("peaksCount",
##           signature=c("mzRnetCDF","numeric"),
##           function(object,scans) {
##             if (length(scans)==1) {
##               return(object@backend$getPeakList(scans)$peaksCount)
##             } else {
##               return(sapply(scans,function(x) object@backend$getPeakList(x)$peaksCount))
##             }
##           })

## setMethod("peaksCount",
##           signature=c("mzRnetCDF","missing"),
##           function(object) {
##             n <- length(object)
##             return(peaksCount(object,1:n))
##           })

setMethod("header",
          signature=c("mzRnetCDF","missing"),
          function(object) return(header(object, 1:length(object))))

setMethod("header",
          signature=c("mzRnetCDF","numeric"),
          function(object, scans) {
            
            result <- data.frame(seqNum=scans,
                            acquisitionNum=scans,
                            msLevel=rep(1, length(scans)),
                            peaksCount=rep(1, length(scans)),
                            totIonCurrent=netCDFVarDouble(object@backend, "total_intensity")[scans],
                            retentionTime=netCDFVarDouble(object@backend, "scan_acquisition_time")[scans], 
                            basePeakMZ=rep(-1, length(scans)),
                            basePeakIntensity=rep(-1, length(scans)),
                            collisionEnergy=rep(-1, length(scans)),
                            ionisationEnergy=rep(-1, length(scans)),
                            highMZ=rep(-1, length(scans)),
                            precursorScanNum=rep(-1, length(scans)),
                            precursorMZ=rep(-1, length(scans)),
                            precursorCharge=rep(-1, length(scans)),
                            precursorIntensity=rep(-1, length(scans)),
                            mergedScan=rep(-1, length(scans)),
                            mergedResultScanNum=rep(-1, length(scans)),
                            mergedResultStartScanNum=rep(-1, length(scans)),
                            mergedResultEndScanNum=rep(-1, length(scans)))

            return(result)
          })

setMethod("close", 
          signature="mzRnetCDF",
          function(con,...) return( netCDFClose(con@backend) ))

setMethod("isInitialized", 
          signature="mzRnetCDF",
          function(object) return(object@backend > 0))

## setMethod("runInfo",
##           signature="mzRnetCDF",
##           function(object) {
##             ##return(object@backend$getRunInfo())
##             hd <- header(object)
##             ll <- list()
##             ll$'scanCount' <- length(object)
##             ll$'lowMz' <- min(hd$lowMZ)
##             ll$'highMz' <- max(hd$highMZ)
##             ll$'dStartTime' <- min(hd$retentionTime)
##             ll$'dEndTime' <- max(hd$retentionTime)
##             ll$'msLevels' <- unique(hd$msLevel)
##             return(ll)
##           })


## setMethod("instrumentInfo",
##           signature="mzRnetCDF",
##           function(object) 
##           return(object@backend$getInstrumentInfo()))


## setMethod("manufacturer",
##           signature="mzRnetCDF",
##           function(object) {
##             info <- instrumentInfo(object)           
##             return(info$manufacturer)
##           })

## setMethod("model",
##           signature="mzRnetCDF",
##           function(object) {
##             info <- instrumentInfo(object)           
##             return(info$model)
##           })

## setMethod("ionisation",
##           signature="mzRnetCDF",
##           function(object) {
##             info <- instrumentInfo(object)           
##             return(info$ionisation)
##           })

## setMethod("analyzer",
##           signature="mzRnetCDF",
##           function(object) {
##             info <- instrumentInfo(object)           
##             return(info$analyzer)
##           })

## setMethod("detector",
##           signature="mzRnetCDF",
##           function(object) {
##             info <- instrumentInfo(object)           
##             return(info$detector)
##           })


setMethod("show",
          signature="mzRnetCDF",
          function(object) {
            if (!isInitialized(object)) {
              cat("Your object's netCDF slot is not initialized.\n")
            } else {
              filename <- fileName(object)
              cat("Mass Spectrometry file handle.\n")
              cat("Filename: ", filename, "\n")
              cat("Number of scans: ", length(object), "\n")
            }
            invisible(NULL)
          })