DynamicXCMS: LC-MS and GC-MS Data Analysis

## # rampInit <- function() {
## #
## #     result <- .C("RampRInit",
## #                  PACKAGE = "xcms")
## # }
## #
## # rampPrintFiles <- function() {
## #
## #     result <- .C("RampRPrintFiles",
## #                  PACKAGE = "xcms")
## # }

## rampIsFile <- function(filename) {

##     ## The C version doesn't do anything extra
##     ##.C("RampRIsFile",
##     ##   as.character(filename),
##     ##   isfile = logical(1),
##     ##   PACKAGE = "xcms")$isfile

##     if (!file.exists(filename))
##         return(FALSE)
##     text <- readChar(filename, 1024)

##     length(text) > 0
## }

## # rampOpen <- function(filename) {
## #
## #     result <- .C("RampROpen",
## #                  as.character(filename),
## #                  rampid = integer(1),
## #                  status = integer(1),
## #                  PACKAGE = "xcms")
## #
## #     if (result$status)
## #         return(result$status)
## #
## #     return(result$rampid)
## # }

## # rampClose <- function(rampid) {
## #
## #     result <- .C("RampRClose",
## #                  as.integer(rampid),
## #                  PACKAGE = "xcms")
## # }

## # rampCloseAll <- function() {
## #
## #     result <- .C("RampRCloseAll",
## #                  PACKAGE = "xcms")
## # }

## # rampNumScans <- function(rampid) {
## #
## #     result <- .C("RampRNumScans",
## #                  as.integer(rampid),
## #                  numscans = integer(1),
## #                  status = integer(1),
## #                  PACKAGE = "xcms")
## #
## #     if (result$status)
## #         return(NA)
## #
## #     return(result$numscans)
## # }

## # rampScanHeaders <- function(rampid) {
## #
## #     .Call("RampRScanHeaders",
## #           as.integer(rampid),
## #           PACKAGE = "xcms")
## # }

## # rampSIPeaks <- function(rampid, seqNum, peaksCount) {
## #
## #     if (!is.integer(seqNum))
## #         seqNum <- as.integer(seqNum)
## #     if (!is.integer(peaksCount))
## #         peaksCount <- as.integer(peaksCount)
## #     .Call("RampRSIPeaks",
## #           as.integer(rampid),
## #           seqNum,
## #           peaksCount,
## #           PACKAGE = "xcms")
## # }

## rampRawData <- function(rampid) {

##     scanHeaders <- rampScanHeaders(rampid)

##     ## Some of these checks work around buggy RAMP indexing code
##     scans <- scanHeaders$msLevel == 1 & scanHeaders$seqNum > 0 &
##         !duplicated(scanHeaders$acquisitionNum) &
##             scanHeaders$peaksCount > 0
##     if ("Full" %in% levels(scanHeaders$scanType))
##         scans <- scans & scanHeaders$scanType == "Full"

##     scans <- which(scans)

##     sipeaks <- rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans])

##     return(list(rt = scanHeaders$retentionTime[scans],
##                 acquisitionNum = scanHeaders$acquisitionNum[scans],
##                 tic = scanHeaders$totIonCurrent[scans],
##                 scanindex = sipeaks$scanindex,
##                 mz = sipeaks$mz,
##                 intensity = sipeaks$intensity,
##                 polarity = scanHeaders$polarity[scans]))
## }

## mzRRawData <- function(mz, scanrange=NULL) {
##     ## TODO: missing in mzR are:
##     ## seqNum
##     ## scanType
##     ## polarity

##     scanHeaders <- header(mz)

##     if (!is.null(scanrange)) {
##         scanHeaders <- scanHeaders[seq(scanrange[1], scanrange[2]),]
##     }

##     scans <- scanHeaders$msLevel == 1 & scanHeaders$seqNum > 0 &
##         !duplicated(scanHeaders$acquisitionNum) &
##             scanHeaders$peaksCount > 0

##     scans <- which(scans)

##     scanlist <- mzR::peaks(mz, scans=scans)
##     if (class(scanlist) == "list")  {
##         ## concatenate multiple scans
##         sipeaks <- do.call(rbind, scanlist)
##         scanIndex <- as.integer(c(0, cumsum(sapply(scanlist[-length(scanlist)], nrow))))
##     } else {
##         ## no reshaping required
##         sipeaks <- scanlist
##         scanIndex <- as.integer(0) ##, nrow(sipeaks))
##     }

##     return(list(rt = scanHeaders$retentionTime[scans],
##                 acquisitionNum = scanHeaders$acquisitionNum[scans],
##                 tic = scanHeaders$totIonCurrent[scans],
##                 scanindex = scanIndex,
##                 mz = sipeaks[,1],
##                 intensity = sipeaks[,2],
##                 polarity = scanHeaders$polarity[scans]))
## }

## mzRRawDataMSn <- function(mz) {
##     ## TODO: missing in mzR are:
##     ## seqNum
##     ## scanType
##     ## polarity

##     scanHeaders <- header(mz)

##     ## Check if we have MSn at all
##     if (max(scanHeaders[,"msLevel"]) < 2) {
##         warning("MSn spectra requested but not found")
##         return (NULL);
##     }

##     ## Some of these checks work around buggy RAMP indexing code
##     scans <- scanHeaders$msLevel >= 2 & scanHeaders$seqNum > 0 &
##         !duplicated(scanHeaders$acquisitionNum) &
##             scanHeaders$peaksCount > 0

##     scans <- which(scans)

##     scanlist <- mzR::peaks(mz, scans=scans)
##     sipeaks <- do.call(rbind, scanlist)
##     scanIndex <- as.integer(c(0, cumsum(sapply(scanlist[-length(scanlist)], nrow))))

##     ##        sipeaks <- rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans])

##     retdata <- list(rt = scanHeaders$retentionTime[scans],
##                     acquisitionNum = scanHeaders$acquisitionNum[scans],
##                     tic = scanHeaders$totIonCurrent[scans],
##                     precursorNum=scanHeaders$precursorScanNum[scans],
##                     precursorMZ = scanHeaders$precursorMZ[scans],
##                     precursorIntensity = scanHeaders$precursorIntensity[scans],
##                     peaksCount=scanHeaders$peaksCount[scans],
##                     msLevel = scanHeaders$msLevel[scans],
##                     precursorCharge = scanHeaders$precursorCharge[scans],
##                     scanindex = scanIndex,
##                     polarity = scanHeaders$polarity[scans],
##                     collisionEnergy = scanHeaders$collisionEnergy[scans],
##                     mz = sipeaks[,1],
##                     intensity = sipeaks[,2]);

##     return(retdata)

## }

## rampRawDataMSn <- function(rampid) {

##     ## Check if we have MSn at all
##     scanHeaders <- rampScanHeaders(rampid)
##     if (max(scanHeaders[,"msLevel"]) < 2) {
##         warning("MSn spectra requested but not found")
##         return (NULL);
##     }

##     ## Some of these checks work around buggy RAMP indexing code
##     scans <- ( scanHeaders$msLevel >= 2 & scanHeaders$seqNum > 0
##               & !duplicated(scanHeaders$acquisitionNum)
##               & scanHeaders$peaksCount > 0)

##     scans <- which(scans)

##     sipeaks <- rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans])

##     retdata <- list(rt = scanHeaders$retentionTime[scans],
##                     acquisitionNum = scanHeaders$acquisitionNum[scans],
##                     precursorNum=scanHeaders$precursorScanNum[scans],
##                     precursorMZ = scanHeaders$precursorMZ[scans],
##                     precursorIntensity = scanHeaders$precursorIntensity[scans],
##                     peaksCount=scanHeaders$peaksCount[scans],
##                     msLevel = scanHeaders$msLevel[scans],
##                     precursorCharge = scanHeaders$precursorCharge[scans],
##                     scanindex = sipeaks$scanindex, collisionEnergy = scanHeaders$collisionEnergy[scans],
##                     mz = sipeaks$mz,
##                     intensity =sipeaks$intensity);

##     return(retdata)
## }