added tmpdir in readscan

added centroidStream
fgcz · Aug 20, 2020 · 71ba35a · 71ba35a
1 parent 8098407
commit 71ba35a
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Showing 4 changed files with 23 additions and 6 deletions.
diff --git a/R/rawDiag.R b/R/rawDiag.R
@@ -487,16 +487,16 @@ plot.XICs <- function(x, y, method='ggplot', ...){
 #' op <- par(mfrow = c(3, 3))
 #' lapply(S, function(x){ plot.peaklist(x, sub=x$scanType) })
 #' 
-readScans <- function(rawfile, scans){
+readScans <- function(rawfile, scans, tmpdir=tempdir()){
   mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE
   exe <- file.path(path.package(package = "rawDiag"), "exec", "fgcz_raw.exe")
 
   # TODO(cp): replace asap we have an R .Net binding similar as Rcpp
   # the current solution writting and reading from a file is pain-of-the-art
   # https://github.com/fgcz/rawDiag/issues/46
-  tfi <- tempfile()
-  tfo <- tempfile()
-  tfstdout <- tempfile()
+  tfi <- tempfile(tmpdir=tmpdir)
+  tfo <- tempfile(tmpdir=tmpdir)
+  tfstdout <- tempfile(tmpdir=tmpdir)
 
   cat(scans, file = tfi, sep="\n")
 

diff --git a/exec/fgcz_raw.exe b/exec/fgcz_raw.exe
diff --git a/src/Makefile b/src/Makefile
@@ -1,5 +1,10 @@
 CSC=mcs
 CSCFLAGS=-lib:../exec /r:ThermoFisher.CommonCore.Data.dll /r:ThermoFisher.CommonCore.MassPrecisionEstimator.dll /r:ThermoFisher.CommonCore.RawFileReader.dll /optimize /platform:anycpu
 
+
+#	$(CSC) /target:library rawDiag.cs  /out:../exec/rawDiag.dll  $(CSCFLAGS)
+exe:
+	$(CSC) /out:../exec/fgcz_raw.exe fgcz_raw.cs $(CSCFLAGS)
+
 dll:
-	$(CSC) /target:library rawDiag.cs  /out:../exec/rawDiag.dll  $(CSCFLAGS)
+	$(CSC) /target:library ../src/fgcz_raw.cs  /out:../exec/fgcz_raw.dll  $(CSCFLAGS)
diff --git a/src/fgcz_raw.cs b/src/fgcz_raw.cs
@@ -362,6 +362,7 @@ public static void PrintScanAsRcode(this IRawDataPlus rawFile, string filename,
                         monoisotopicMz = "NA";
                     }
 
+                        var scan = Scan.FromFile(rawFile, scanNumber);
 
                         if (scanStatistics.IsCentroidScan && centroidStream.Length > 0)
                         {
@@ -375,6 +376,12 @@ public static void PrintScanAsRcode(this IRawDataPlus rawFile, string filename,
                             file.WriteLine("\tpepmass = c({0}, {1}),", pepmass, basepeakIntensity);
                             file.WriteLine("\tcentroidStream = TRUE,");
 
+                            file.WriteLine("\tHasCentroidStream = '{0}, Length={1}',", scan.HasCentroidStream, scan.CentroidScan.Length);
+			    if(scan.HasCentroidStream){
+                                file.WriteLine("\tcentroid.mZ = c(" + string.Join(",", scan.CentroidScan.Masses.ToArray()) + "),");
+                                file.WriteLine("\tcentroid.intensity = c(" + string.Join(",", scan.CentroidScan.Intensities.ToArray()) + "),");
+			    }
+
                             file.WriteLine("\ttitle = \"File: {0}; SpectrumID: {1}; scans: {2}\",",
                                 Path.GetFileName(rawFile.FileName),
                                 null,
@@ -389,7 +396,6 @@ public static void PrintScanAsRcode(this IRawDataPlus rawFile, string filename,
                         }
                         else
                         {
-                            var scan = Scan.FromFile(rawFile, scanNumber);
 
                             file.WriteLine("e$PeakList[[{0}]] <- list(", count++);
                             file.WriteLine("\tscan = {0},", scanNumber);
@@ -399,6 +405,12 @@ public static void PrintScanAsRcode(this IRawDataPlus rawFile, string filename,
                             file.WriteLine("\tpepmass = c({0}, {1}),", pepmass, basepeakIntensity);
                             file.WriteLine("\tcentroidStream = FALSE,");
 
+                            file.WriteLine("\tHasCentroidStream = '{0}, Length={1}',", scan.HasCentroidStream, scan.CentroidScan.Length);
+			    if(scan.HasCentroidStream){
+                                file.WriteLine("\tcentroid.mZ = c(" + string.Join(",", scan.CentroidScan.Masses.ToArray()) + "),");
+                                file.WriteLine("\tcentroid.intensity = c(" + string.Join(",", scan.CentroidScan.Intensities.ToArray()) + "),");
+			    }
+
                             file.WriteLine("\ttitle = \"File: {0}; SpectrumID: {1}; scans: {2}\",",
                                 Path.GetFileName(rawFile.FileName),
                                 null,