#4

R/rawR.R

@@ -1,17 +1,23 @@
-#' readSpectrum of a raw file
+#' Read a Set of Spectra
 #'
-#' @param rawfile the name of the Thermo Fisher Scietific raw file which
-#' the data are to be read from.  
+#' @param rawfile the name of the Thermo Fisher Scietific raw file.
 #' @param scans a vector of requested scan numbers.
 #' @param tmpdir a non-empty character vector giving the directory name; default
 #' uses \code{tempdir()}.
-#' @author Christian Panse <[email protected]> 2018, 2019, 2020
+#' @author Tobias Kockmann and Christian Panse <[email protected]> 2018, 2019, 2020
 #' 
-#' @description the function reads scan information of a given set of scan
-#' number using a dot net interface and the ThermoFisher NewRawFileReader 
-#' libraries. 
+#' @description the function reads scan information, e.g., charge, mZ,
+#' or intensity of a given set of scan numbers using a dot net interface and
+#' the ThermoFisher NewRawFileReader libraries.
 #'  
-#' @references \url{https://doi.org/10.5281/zenodo.2640013}
+#' @seealso Thermo Fisher NewRawfileReader C# code snippets
+#' \url{https://planetorbitrap.com/rawfilereader}.
+#' 
+#' @references \itemize{
+#' \item{\url{https://doi.org/10.5281/zenodo.2640013}}
+#' \item{the R function 1st appeared in
+#' \url{https://doi.org/10.1021/acs.jproteome.8b00173}}
+#' }
 #' 
 #' @aliases readSpectrum
 #' 
@@ -26,11 +32,25 @@
 #' S <- readSpectrum(rawfile, scans = 1:9)
 #' 
 #' S[[1]]
+#' 
+#' names(S[[1]])
+#' 
+#' .plot.peaklist <- function(x, ...){
+#'   plot(x$mZ, x$intensity, type='h')
+#'   labels <- na.omit(lapply(x, function(y){if (length(y)==1){y}else{NA}}))
+#'   legend("topright", paste(names(labels), labels, sep=": "), ...)
+#'  }
 #'  
 readSpectrum <- function(rawfile, scans, tmpdir=tempdir()){
     mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE
     exe <- file.path(path.package(package = "rawR"), "exec", "rawR.exe")
 
+
+    if (!file.exists(rawfile)){
+        warning('file not available. return.')
+        return
+    }
+
     tfi <- tempfile(tmpdir=tmpdir)
     tfo <- tempfile(tmpdir=tmpdir)
     tfstdout <- tempfile(tmpdir=tmpdir)
@@ -54,3 +74,74 @@ readSpectrum <- function(rawfile, scans, tmpdir=tempdir()){
     return(lapply(e$PeakList,
                   function(x){class(x) <- c(class(x), 'peaklist'); x}))
 }
+
+
+#' read file header Information
+#'
+#' @param rawfile the name of the Thermo Fisher Scietific raw file
+#' @param mono enviroment
+#' @param exe path of the executable.
+#' @param mono_path default.
+#' @param argv arguments, default.
+#' @param system2_call system2 call, default.
+#' @param method instrument vendor
+#' @description The function extracts some meta information from a given rawfile.
+#' The R code output is parsed by the function and a list object is returned.
+#' @author Tobias Kockmann and Christian Panse 2018, 2019, 2020
+#' @seealso Thermo Fisher NewRawfileReader C# code snippets
+#' \url{https://planetorbitrap.com/rawfilereader}.
+#' 
+#' @return a list object
+#' @export readFileHeader
+#'
+#' @examples
+#' (rawfile <- file.path(path.package(package = 'rawR'), 'extdata',
+#'   'sample.raw'))
+#' 
+#' M <- readFileHeader(rawfile)
+readFileHeader <- function(rawfile,
+    mono = if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE,
+    exe = file.path(path.package(package = "rawR"), "exec", "rawR.exe"),
+    mono_path = "",
+    argv = "infoR",
+    system2_call = TRUE,
+    method = "thermo"){
+
+    if (!file.exists(rawfile)){
+        warning('file not available. return.')
+        return
+    }
+    if(system2_call && method == 'thermo'){
+
+        tf <- tempfile(fileext = '.R')
+        tf.err <- tempfile(fileext = '.err')
+
+        # message(paste("system2 is writting to tempfile ", tf, "..."))
+
+        if (mono){
+            rvs <- system2("mono", args = c(exe, shQuote(rawfile
+            ), argv),
+            stdout = tf)
+        }else{
+            rvs <- system2(exe, args = c(shQuote(rawfile
+            ), argv),
+            stderr = tf.err,
+            stdout = tf)
+        }
+
+        if (rvs == 0){
+
+            try({
+                source(tf)
+
+                #message(paste("unlinking", tf, "..."))
+                #unlink(tf)
+                return(e$info)
+            }, NULL)
+
+            # unlink(tfstdout)
+            return(rv)
+        }
+    }
+    NULL
+}