.peaks <- function(object, scans) {

     if (missing(scans))
         scans <- 1:length(object)
     res <- object@backend$getPeakList(scans)
     if (length(res) == 1)
         res[[1]]
     else res
 }
 

 setMethod("isolationWindow", "character",
           function(object, ...) .isolationWindow(object, ...))
 
 .isolationWindow <- function(x, unique. = TRUE, simplify = TRUE) {
     stopifnot(all(file.exists(x)))
     if (!requireNamespace("XML"))
         stop("Please install the XML package to use this functionality.")
     res <- lapply(x, function(xx) {
         xml <- XML::xmlParse(xx)
         ns <- c(x = "http://psi.hupo.org/ms/mzml")
         path <- c(low = "//x:isolationWindow/x:cvParam[@accession='MS:1000828']/@value",
                   high = "//x:isolationWindow/x:cvParam[@accession='MS:1000829']/@value")
         low <- as.numeric(XML::xpathSApply(xml, path["low"], namespaces = ns))
         high <- as.numeric(XML::xpathSApply(xml, path["high"], namespaces = ns))
         cbind(low, high)
     })
     if (.multipleIsolationWindows(res))
         message("Found multiple isolation windows in an acquisition.")
     if (unique.)
         res <- lapply(res, base::unique)
     if (simplify & length(x) == 1) res <- res[[1]]
     return(res)
 }
 
 .multipleIsolationWindows <- function(x) {
     x <- lapply(x, base::unique)
     any(sapply(x, function(xx) nrow(xx) > 1))
 }

 
 
 .hasSpectra <- function(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"))

     hdr <- chromatogramHeader(x)
     if (close_after)
         close(x)
     as.logical(nrow(hdr))

 }