@@ -169,3 +169,13 @@ setMethod("show",

             invisible(NULL)

           })

+setMethod("chromatograms", "mzRnetCDF", function(object, chrom)

+    chromatogram(object, chrom))

+setMethod("chromatogram", "mzRnetCDF", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram()

+})

+setMethod("chromatogramHeader", "mzRnetCDF", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram_header()

+})

@@ -163,3 +163,14 @@ setMethod("show",

 setMethod("isolationWindow", "mzRramp",

           function(object, ...) .isolationWindow(fileName(object), ...))

+

+setMethod("chromatograms", "mzRramp", function(object, chrom)

+    chromatogram(object, chrom))

+setMethod("chromatogram", "mzRramp", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram()

+})

+setMethod("chromatogramHeader", "mzRramp", function(object, chrom) {

+    warning("The mzRnetCdf backend does not support chromatographic data")

+    .empty_chromatogram_header()

+})

@@ -43,8 +43,56 @@ setMethod("isolationWindow", "character",

 .hasSpectra <- function(x) {

-    if (is.character(x) & file.exists(x))

+    close_after <- FALSE

+    if (is.character(x) && file.exists(x)) {

         x <- mzR::openMSfile(x)

+        ## Ensure we are closing the file later

+        close_after <- TRUE

+    }

+    stopifnot(inherits(x, "mzR"))

+    len <- length(x)

+    if (close_after)

+        close(x)

+    return(as.logical(len))

+}

+

+#' Create return data for MS backends not supporting chromatographic data. This

+#' function is supposed to be called by the chromatogram(s) methods for these

+#' backends

+#'

+#' @author Johannes Rainer

+#'

+#' @noRd

+.empty_chromatogram <- function() {

+    list()

+}

+

+#' Create return data for MS backends not supporting chromatographic data.

+#'

+#' @author Johannes Rainer

+#'

+#' @noRd

+.empty_chromatogram_header <- function() {

+    cn <- c("chromatogramId", "chromatogramIndex", "polarity",

+            "precursorIsolationWindowTargetMZ",

+            "precursorIsolationWindowLowerOffset",

+            "precursorIsolationWindowUpperOffset",

+            "precursorCollisionEnergy", "productIsolationWindowTargetMZ",

+            "productIsolationWindowLowerOffset",

+            "productIsolationWindowUpperOffset")

+    data.frame(matrix(nrow = 0, ncol = length(cn),

+                      dimnames = list(character(), cn)))

+}

+

+.hasChromatograms <- function(x) {

+    close_after <- FALSE

+    if (is.character(x) && file.exists(x)) {

+        x <- mzR::openMSfile(x)

+        close_after <- TRUE

+    }

     stopifnot(inherits(x, "mzR"))

-    return(as.logical(length(x)))

+    hdr <- chromatogramHeader(x)

+    if (close_after)

+        close(x)

+    as.logical(nrow(hdr))

 }

@@ -58,3 +58,27 @@ test_header <- function() {

   close(cdf)

 }

+

+test_chromatogram <- function() {

+    file <- system.file('cdf/ko15.CDF', package = "msdata")

+    x <- openMSfile(file, backend="netCDF")        

+    suppressWarnings(

+        chr <- chromatogram(x)

+    )

+    checkTrue(length(chr) == 0)

+    suppressWarnings(

+        chr <- chromatograms(x)

+    )

+    checkTrue(length(chr) == 0)

+    close(x)

+}

+

+test_chromatogramHeader <- function() {

+    file <- system.file('cdf/ko15.CDF', package = "msdata")

+    x <- openMSfile(file, backend="netCDF")        

+    suppressWarnings(

+        ch <- chromatogramHeader(x)

+    )

+    checkTrue(nrow(ch) == 0)

+    close(x)

+}

@@ -102,4 +102,32 @@ test_peaks_spectra <- function() {

     p <- peaks(x, 1:10)

     s <- spectra(x, 1:10)

     checkIdentical(p, s)

+    close(x)

 }

+

+test_chromatogram <- function() {

+    library("msdata")

+    f <- proteomics(full.names = TRUE)

+    x <- openMSfile(f[1], backend = "Ramp")

+    suppressWarnings(

+        chr <- chromatogram(x)

+    )

+    checkTrue(length(chr) == 0)

+    suppressWarnings(

+        chr <- chromatograms(x)

+    )

+    checkTrue(length(chr) == 0)

+    close(x)

+}

+

+test_chromatogramHeader <- function() {

+    library("msdata")

+    f <- proteomics(full.names = TRUE)

+    x <- openMSfile(f[1], backend = "Ramp")

+    suppressWarnings(

+        ch <- chromatogramHeader(x)

+    )

+    checkTrue(nrow(ch) == 0)

+    close(x)

+}

+

new file mode 100644

@@ -0,0 +1,20 @@

+test_hasChromatograms <- function() {

+    fl <- system.file("proteomics/MRM-standmix-5.mzML.gz", package = "msdata")

+    x <- mzR::openMSfile(fl, backend = "pwiz")

+    checkTrue(mzR:::.hasChromatograms(x))

+    checkTrue(mzR:::.hasChromatograms(fl))

+    close(x)

+    

+    fl <- system.file("cdf/ko15.CDF", package = "msdata")

+    x <- openMSfile(fl, backend = "netCDF")        

+    suppressWarnings(checkTrue(!mzR:::.hasChromatograms(x)))

+    suppressWarnings(checkTrue(!mzR:::.hasChromatograms(fl)))

+    close(x)

+

+    fl <- system.file("sciex/20171016_POOL_POS_1_105-134.mzML",

+                      package = "msdata")

+    x <- mzR::openMSfile(fl, backend = "pwiz")

+    checkTrue(!mzR:::.hasChromatograms(x))

+    checkTrue(!mzR:::.hasChromatograms(fl))

+    close(x)

+}

@@ -29,6 +29,12 @@

 \alias{chromatogram,mzRpwiz-method}

 \alias{chromatogramHeader,mzRpwiz-method}

 \alias{chromatograms,mzRpwiz-method}

+\alias{chromatogram,mzRramp-method}

+\alias{chromatogramHeader,mzRramp-method}

+\alias{chromatograms,mzRramp-method}

+\alias{chromatogram,mzRnetCDF-method}

+\alias{chromatogramHeader,mzRnetCDF-method}

+\alias{chromatograms,mzRnetCDF-method}

 \alias{tic,mzRpwiz-method}

 \alias{nChrom}

 \alias{chromatogram}

@@ -885,10 +885,11 @@ Rcpp::DataFrame RcppPwiz::getAllChromatogramHeaderInfo ( ) {

   if (msd != NULL) {

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

     int N = clp->size();

-    

-    return getChromatogramHeaderInfo(Rcpp::seq(1, N));

+    if (N > 0)

+      return getChromatogramHeaderInfo(Rcpp::seq(1, N));

+  } else {

+    Rprintf("Warning: pwiz not yet initialized.\n ");

   }

-  Rprintf("Warning: pwiz not yet initialized.\n ");

   return Rcpp::DataFrame::create( );

 }