1. mzR
  2. Commit 7886df399816c6fae569e58c4906f636e574fd55
Browse code

back-ported the old XCMS rampR interface, which is much faster than cramp

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@63802 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 13/03/2012 11:40:20
Showing 2 changed files
.gitignore
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+# editor backup files
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+*~
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+\#*\#
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+
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+# compiled code
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+*.o
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+*.so
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+*.dll
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+*.a
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+
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+# SVN stuff
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+.svn
R/ramp.R
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+rampInit <- function() {
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+
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+    result <- .C("RampRInit",
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+                 PACKAGE = "mzR")
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+}
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+
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+rampPrintFiles <- function() {
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+
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+    result <- .C("RampRPrintFiles",
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+                 PACKAGE = "mzR")
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+}
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+
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+rampIsFile <- function(filename) {
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+
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+    # The C version doesn't do anything extra
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+    #.C("RampRIsFile",
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+    #   as.character(filename),
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+    #   isfile = logical(1),
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+    #   PACKAGE = "mzR")$isfile
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+
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+    if (!file.exists(filename))
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+        return(FALSE)
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+    text <- readChar(filename, 1024)
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+
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+    length(text) > 0
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+}
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+
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+rampOpen <- function(filename) {
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+
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+    result <- .C("RampROpen",
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+                 as.character(filename),
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+                 rampid = integer(1),
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+                 status = integer(1),
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+                 PACKAGE = "mzR")
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+
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+    if (result$status)
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+        return(result$status)
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+
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+    return(result$rampid)
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+}
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+
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+rampClose <- function(rampid) {
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+
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+    result <- .C("RampRClose",
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+                 as.integer(rampid),
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+                 PACKAGE = "mzR")
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+}
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+
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+rampCloseAll <- function() {
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+
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+    result <- .C("RampRCloseAll",
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+                 PACKAGE = "mzR")
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+}
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+
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+rampNumScans <- function(rampid) {
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+
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+    result <- .C("RampRNumScans",
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+                 as.integer(rampid),
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+                 numscans = integer(1),
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+                 status = integer(1),
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+                 PACKAGE = "mzR")
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+
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+    if (result$status)
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+        return(NA)
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+
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+    return(result$numscans)
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+}
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+
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+rampScanHeaders <- function(rampid) {
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+
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+    .Call("RampRScanHeaders",
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+          as.integer(rampid),
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+          PACKAGE = "mzR")
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+}
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+
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+rampSIPeaks <- function(rampid, seqNum, peaksCount) {
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+
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+    if (!is.integer(seqNum))
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+        seqNum <- as.integer(seqNum)
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+    if (!is.integer(peaksCount))
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+        peaksCount <- as.integer(peaksCount)
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+    .Call("RampRSIPeaks",
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+          as.integer(rampid),
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+          seqNum,
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+          peaksCount,
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+          PACKAGE = "mzR")
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+}
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+
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+rampRawData <- function(rampid) {
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+
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+    scanHeaders <- rampScanHeaders(rampid)
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+
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+    # Some of these checks work around buggy RAMP indexing code
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+    scans <- scanHeaders$msLevel == 1 & scanHeaders$seqNum > 0 &
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+             !duplicated(scanHeaders$acquisitionNum) &
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+             scanHeaders$peaksCount > 0
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+    if ("Full" %in% levels(scanHeaders$scanType))
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+        scans <- scans & scanHeaders$scanType == "Full"
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+
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+    scans <- which(scans)
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+
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+    sipeaks <- rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans])
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+
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+    return(list(rt = scanHeaders$retentionTime[scans],
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+                acquisitionNum = scanHeaders$acquisitionNum[scans],
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+                tic = scanHeaders$totIonCurrent[scans],
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+                scanindex = sipeaks$scanindex,
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+                mz = sipeaks$mz,
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+                intensity = sipeaks$intensity,
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+                polarity = scanHeaders$polarity[scans]))
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+}
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+
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+rampRawDataMSn <- function(rampid) {
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+
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+    # Check if we have MSn at all
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+    scanHeaders <- rampScanHeaders(rampid)
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+    if (max(scanHeaders[,"msLevel"]) < 2) {
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+        warning("MSn spectra requested but not found")
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+        return (NULL);
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+    }
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+
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+    # Some of these checks work around buggy RAMP indexing code
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+    scans <- ( scanHeaders$msLevel >= 2 & scanHeaders$seqNum > 0
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+              & !duplicated(scanHeaders$acquisitionNum)
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+              & scanHeaders$peaksCount > 0)
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+
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+    scans <- which(scans)
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+
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+    sipeaks <- rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans])
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+
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+    retdata <- list(rt = scanHeaders$retentionTime[scans],
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+                    acquisitionNum = scanHeaders$acquisitionNum[scans],
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+                    precursorNum=scanHeaders$precursorScanNum[scans],
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+                    precursorMZ = scanHeaders$precursorMZ[scans],
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+                    precursorIntensity = scanHeaders$precursorIntensity[scans],
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+                    peaksCount=scanHeaders$peaksCount[scans],
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+                    msLevel = scanHeaders$msLevel[scans],
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+                    precursorCharge = scanHeaders$precursorCharge[scans],
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+                    scanindex = sipeaks$scanindex, collisionEnergy = scanHeaders$collisionEnergy[scans],
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+                    mz = sipeaks$mz,
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+                    intensity =sipeaks$intensity);
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+
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+    return(retdata)
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+}