@@ -7,17 +7,6 @@

     else res

 }

-.peaks_ramp <- function(object, scans) {

-    if (missing(scans))

-        scans <- 1:length(object)

-    if (length(scans) == 1) {

-        object@backend$getPeakList(scans)$peaks

-    } else {

-        sapply(scans, function(x) object@backend$getPeakList(x)$peaks,

-               simplify = FALSE)

-    }

-}

-

 setMethod("isolationWindow", "character",

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

@@ -1,20 +1,26 @@

 .peaks <- function(object, scans) {

+    if (missing(scans))

+        scans <- 1:length(object)

+    res <- object@backend$getPeakList(scans)

+    if (length(res) == 1)

+        res[[1]]

+    else res

+}

+

+.peaks_ramp <- function(object, scans) {

     if (missing(scans))

         scans <- 1:length(object)

     if (length(scans) == 1) {

-        return(object@backend$getPeakList(scans)$peaks)

+        object@backend$getPeakList(scans)$peaks

     } else {

-        return(sapply(scans,

-                      function(x) object@backend$getPeakList(x)$peaks,

-                      simplify = FALSE))

+        sapply(scans, function(x) object@backend$getPeakList(x)$peaks,

+               simplify = FALSE)

     }

 }

-

 setMethod("isolationWindow", "character",

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

-

 .isolationWindow <- function(x, unique. = TRUE, simplify = TRUE) {

     stopifnot(all(file.exists(x)))

     if (!requireNamespace("XML"))

@@ -77,7 +77,8 @@ setMethod("isolationWindow", "character",

             "precursorIsolationWindowTargetMZ",

             "precursorIsolationWindowLowerOffset",

             "precursorIsolationWindowUpperOffset",

-            "precursorCollisionEnergy", "productIsolationWindowTargetMZ",

+            "precursorCollisionEnergy",

+            "productIsolationWindowTargetMZ",

             "productIsolationWindowLowerOffset",

             "productIsolationWindowUpperOffset")

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

@@ -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))

 }

@@ -40,3 +40,11 @@ setMethod("isolationWindow", "character",

     x <- lapply(x, base::unique)

     any(sapply(x, function(xx) nrow(xx) > 1))

 }

+

+

+.hasSpectra <- function(x) {

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

+        x <- mzR::openMSfile(x)

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

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

+}

@@ -1,3 +1,16 @@

+.peaks <- function(object, scans) {

+    if (missing(scans))

+        scans <- 1:length(object)

+    if (length(scans) == 1) {

+        return(object@backend$getPeakList(scans)$peaks)

+    } else {

+        return(sapply(scans,

+                      function(x) object@backend$getPeakList(x)$peaks,

+                      simplify = FALSE))

+    }

+}

+

+

 setMethod("isolationWindow", "character",

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

new file mode 100644

@@ -0,0 +1,29 @@

+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))

+}