@@ -2,7 +2,7 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.13.0

+Version: 2.13.1

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,

 	    Steffen Neumann <sneumann@ipb-halle.de>,

@@ -1,8 +1,10 @@

-CHANGES IN VERSION 2.11.12

+CHANGES IN VERSION 2.13.1

 --------------------------

  o Read filter string from mzML files and add it to the data.frame returned by

    the header function (see MSnbase issue #278).

-

+ o openMsFile automatically determine the backend to use based on file extension

+   and content.

+ 

 CHANGES IN VERSION 2.11.11

 --------------------------

  o Fix problem in writeMSData: ensure precursor data is saved even if precursor

@@ -1,10 +1,12 @@

 openMSfile <- function(filename,

-                       backend=c("pwiz", "Ramp", "netCDF"),

+                       backend = NULL,

                        verbose = FALSE) {

     if (!file.exists(filename))

         stop("File ",filename," not found.\n")

     filename <- path.expand(filename)

-    backend <- match.arg(backend)

+    if (is.null(backend))

+        backend <- .mzRBackend(filename)

+    backend <- match.arg(backend, c("pwiz", "Ramp", "netCDF"))

     if (backend == "Ramp") {

         rampModule <- new( Ramp ) 

@@ -38,6 +40,56 @@ openMSfile <- function(filename,

     }  

 }

+#' @title Define the type of mzR backend to use based on the file name or

+#'     content

+#'

+#' @description Simple helper to define the mzR backend that should/can be used

+#'     to read the file.

+#'

+#' @param x \code{character(1)} representing the file name.

+#'

+#' @return A \code{character(1)} with the name of the backend (either

+#'     \code{"netCDF"}, \code{"Ramp"} or \code{"pwiz"}.

+#'

+#' @author Johannes Rainer, Sebastian Gibb

+#'

+#' @noRd

+.mzRBackend <- function(x = character()) {

+    if (length(x) != 1)

+        stop("parameter 'x' has to be of length 1")

+    ## Use if/else conditions based on a suggestion from sgibb to avoid loops.

+    if (grepl("\\.mzml($|\\.)|\\.mzxml($|\\.)", x, ignore.case = TRUE)) {

+        return("pwiz")

+    } else if (grepl("\\.mzdata($|\\.)", x, ignore.case = TRUE)) {

+        return("Ramp")

+    } else if (grepl("\\.cdf($|\\.)|\\.nc($|\\.)", x, ignore.case = TRUE)) {

+        return("netCDF")

+    } else {

+        return(.mzRBackendFromContent(x))

+    }

+}

+

+#' Determine the backend from the (first few lines of the) file content.

+#' 

+#' @author Johannes Rainer

+#'

+#' @noRd

+.mzRBackendFromContent <- function(x = character()) {

+    if (length(x) != 1)

+        stop("parameter 'x' has to be of length 1")

+    suppressWarnings(

+        first_lines <- readLines(x, n = 4)

+    )

+    if (any(grepl("<mz[X]?ML", first_lines))) {

+        return("pwiz")

+    } else if (any(grepl("<mzData", first_lines))) {

+        return("Ramp")

+    } else if (substr(readBin(x, character(), n = 1), 1, 3) == "CDF") {

+        return("netCDF")

+    } else

+        stop("Could not determine file type for ", x)        

+}

+

 openIDfile <- function(filename, verbose = FALSE) {

   if (!file.exists(filename))

     stop("File ",filename," not found.\n")

@@ -9,7 +9,7 @@

   Create and check mzR objects from netCDF, mzXML, mzData or mzML files.

 }

 \usage{

- openMSfile(filename, backend=c("pwiz", "Ramp", "netCDF"), verbose = FALSE)

+ openMSfile(filename, backend = NULL, verbose = FALSE)

  initializeRamp(object)

@@ -20,10 +20,17 @@

  openIDfile(filename, verbose = FALSE)

 }

 \arguments{

-  \item{filename}{ Path name of the netCDF, mzData, mzXML or mzML file to

-    read/write. }

-  \item{backend}{ A \code{character} specifiying with backend API to

-    use. Currently 'Ramp', 'netCDF'  and 'pwiz' (default) are available.}

+  \item{filename}{

+    Path name of the netCDF, mzData, mzXML or mzML file to

+    read/write.

+  }

+  \item{backend}{

+    A \code{character(1)} specifiying which backend API to

+    use. Currently 'Ramp', 'netCDF'  and 'pwiz' are supported. If

+    \code{backend = NULL} (the default), the function tries to determine

+    the backend to be used based on either the file extension of the

+    file content.

+  }

   \item{object}{ An instantiated mzR object. }

   \item{verbose}{ Enable verbose output. }

   \item{...}{ Additional arguments, currently ignored. }