Merge pull request #2 from marinakiweler/master

Resolution for LTQ_orbitrap_MS added
loosolab · Jan 8, 2020 · 5f15a33 · 5f15a33
2 parents b05afef + e55f0e7
commit 5f15a33
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Showing 20 changed files with 58 additions and 14 deletions.
diff --git a/MARMoSET_C/MARMoSET/InstrumentMethod.cs b/MARMoSET_C/MARMoSET/InstrumentMethod.cs
@@ -59,12 +59,30 @@ public InstrumentMethod(IRawDataPlus rawFile, int index, bool toLower = false, o
             }
             else if (name[index].Equals("LTQ"))
             {
-                /*if (friendName[index].Equals("LTQ_Orbitrap_MS"))
+                Dictionary<string,object> methodWithResolution = ltqDictListCreate(methode);
+                // obtaining the resolution from all scans ('trailer data'), compare and add to method if all the same
+                if (friendName[index].Equals("LTQ Orbitrap MS"))
                 {
-                   this.Method = ltq2DictListCreate(methode);
-                    this.SharedTuneData = tuneData;
-                }*/
-                this.Method = ltqDictListCreate(methode);
+                    int sNumber = rawFile.RunHeaderEx.TrailerExtraCount;
+                    var seqSNumber = Enumerable.Range(1, sNumber);
+                    List<int> trailerD22List = new List<int>();
+
+                    foreach (int scan in seqSNumber)
+                    {
+                        Object aValue = rawFile.GetTrailerExtraValue(scan, 22);
+                        int intValue = Convert.ToInt32(aValue); 
+                        trailerD22List.Add(intValue);
+                    }
+                    // 1077 -> 0 ??? 
+
+
+                    var resolutionValues = new HashSet<int>(trailerD22List);
+                    resolutionValues.Remove(0);
+                    object resolution = resolutionValues;
+                    methodWithResolution.Add("Resolution", resolution);
+                }
+
+                this.Method = methodWithResolution;
                 this.SharedTuneData = tuneData;
             }   
             // if instrument is none of the above -> Method is List<string>
@@ -553,6 +571,7 @@ public List<string> MethodAsList(IRawDataPlus rawFile, int index, bool toLower =
                     }
                 }
             }
+
             // catch last entries
             if (dic.Count != 0)
             {

diff --git a/MARMoSET_C/MARMoSET/MARMoSET.csproj.user b/MARMoSET_C/MARMoSET/MARMoSET.csproj.user
@@ -7,7 +7,7 @@
     <StartArguments>E:\bspdaten</StartArguments>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|x64'">
-    <StartArguments>C:\Users\mkiwele\Desktop\RAW_07\20070326_JG_neuronalSC_01.RAW</StartArguments>
+    <StartArguments>C:\Users\mkiwele\Desktop\RAW_07\ afile.json</StartArguments>
     <StartWorkingDirectory>
     </StartWorkingDirectory>
   </PropertyGroup>

diff --git a/MARMoSET_C/MARMoSET/Program.cs b/MARMoSET_C/MARMoSET/Program.cs
@@ -56,14 +56,15 @@ public static void Main(string[] args)
                     "       For saving with full path set -r in front. If empty the output will be send to the standard output."
                     );
             }
+
             else
             {
                 // Output path
                 string outName = string.Empty;
                 if (args.Length > 1)
                 {   // 2nd argument is path + name
                     outName = args[1];
-                    if (outName.Equals("-r") || outName.Equals("-R"))
+                    if (outName.Equals("-r") || outName.Equals("-R")) // Mode for R Package
                     {
                         pathShort = true;
                         outName = args[2];
@@ -74,9 +75,11 @@ public static void Main(string[] args)
                 {   // no 2nd arg -> file on console
                     consoleOut = true;
                 }
-
-                // read all rawFiles, convert to JSON
+
+            //___________________________________________________
+            // main file handling:
                 var rawFiles = new FileSet(path, consoleOut);
+                // convert structure to JSON
                 string json = JsonConvert.SerializeObject(rawFiles, Formatting.Indented) + "\n";
                 // deleting ":" at the end of keys (tune data and instrument method)
                 json = json.Replace(":\":", "\":");
@@ -97,15 +100,16 @@ public static void Main(string[] args)
                     else
                     {
                         // is path to dir or file?
-                        if (path.EndsWith(".raw"))
+                        string lowPath = path.ToLower();
+                        if (lowPath.EndsWith(".raw"))
                         {
                             outPath = (System.IO.Path.GetDirectoryName(path));
                         }
                         else
                         {
                             outPath = path;
                         }
-                        fullOutPath = outPath + "\\" + outName;
+                        fullOutPath = System.IO.Path.Combine(outPath, outName);
                     }
                     System.IO.File.WriteAllText(fullOutPath, json);
                 }

diff --git a/MARMoSET_C/MARMoSET/bin/x64/Debug/MARMoSET.exe b/MARMoSET_C/MARMoSET/bin/x64/Debug/MARMoSET.exe
diff --git a/MARMoSET_C/MARMoSET/bin/x64/Debug/MARMoSET.pdb b/MARMoSET_C/MARMoSET/bin/x64/Debug/MARMoSET.pdb
diff --git a/MARMoSET_C/MARMoSET/bin/x64/Release/MARMoSET.exe b/MARMoSET_C/MARMoSET/bin/x64/Release/MARMoSET.exe
diff --git a/MARMoSET_C/MARMoSET/bin/x64/Release/MARMoSET.pdb b/MARMoSET_C/MARMoSET/bin/x64/Release/MARMoSET.pdb
diff --git a/MARMoSET_C/MARMoSET/obj/Debug/DesignTimeResolveAssemblyReferencesInput.cache b/MARMoSET_C/MARMoSET/obj/Debug/DesignTimeResolveAssemblyReferencesInput.cache
diff --git a/MARMoSET_C/MARMoSET/obj/Debug/MARMoSET.csproj.CoreCompileInputs.cache b/MARMoSET_C/MARMoSET/obj/Debug/MARMoSET.csproj.CoreCompileInputs.cache
@@ -1 +1 @@
-1005f4ce76369c18d99608c19a1b3ef7d845a78a
+accfaa5dd80ee39f64af26fa6b8ebcce153e648a
diff --git a/MARMoSET_C/MARMoSET/obj/Debug/MARMoSET.csprojAssemblyReference.cache b/MARMoSET_C/MARMoSET/obj/Debug/MARMoSET.csprojAssemblyReference.cache
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Debug/DesignTimeResolveAssemblyReferencesInput.cache b/MARMoSET_C/MARMoSET/obj/x64/Debug/DesignTimeResolveAssemblyReferencesInput.cache
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.csproj.CoreCompileInputs.cache b/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.csproj.CoreCompileInputs.cache
@@ -1 +1 @@
-6c7aab82043387192984052d277efc2be4a2c022
+0e07f3fdd32529e8f0140e5a46a6be6b427de4a6
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.csproj.FileListAbsolute.txt b/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.csproj.FileListAbsolute.txt
@@ -61,3 +61,14 @@ P:\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.pdb
 \\KI-S0138\Abt-A$\mkiwele\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.csproj.CopyComplete
 \\KI-S0138\Abt-A$\mkiwele\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.exe
 \\KI-S0138\Abt-A$\mkiwele\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Debug\MARMoSET.exe.config
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Debug\MARMoSET.exe
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Debug\MARMoSET.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Debug\Newtonsoft.Json.dll
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Debug\Newtonsoft.Json.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Debug\Newtonsoft.Json.xml
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.csproj.CoreCompileInputs.cache
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.csproj.CopyComplete
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.exe
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Debug\MARMoSET.csprojAssemblyReference.cache
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.csprojAssemblyReference.cache b/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.csprojAssemblyReference.cache
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.exe b/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.exe
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.pdb b/MARMoSET_C/MARMoSET/obj/x64/Debug/MARMoSET.pdb
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.csproj.CoreCompileInputs.cache b/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.csproj.CoreCompileInputs.cache
@@ -1 +1 @@
-36b4f4454047f5ca5b82504e0b30315c189cb3c3
+f2e199b9aef3cbda48b099284c4164caf57d681e
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.csproj.FileListAbsolute.txt b/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.csproj.FileListAbsolute.txt
@@ -61,3 +61,13 @@ P:\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.pdb
 \\KI-S0138\Abt-A$\mkiwele\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.csproj.CopyComplete
 \\KI-S0138\Abt-A$\mkiwele\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.exe
 \\KI-S0138\Abt-A$\mkiwele\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Release\MARMoSET.exe.config
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Release\MARMoSET.exe
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Release\MARMoSET.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Release\Newtonsoft.Json.dll
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Release\Newtonsoft.Json.pdb
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\bin\x64\Release\Newtonsoft.Json.xml
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.csproj.CoreCompileInputs.cache
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.csproj.CopyComplete
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.exe
+\\mpg-nki-winfs.kerckhoff.mpg.de\mkiwele$\allMARMoSET\MARMoSET_C\MARMoSET\obj\x64\Release\MARMoSET.pdb
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.exe b/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.exe
diff --git a/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.pdb b/MARMoSET_C/MARMoSET/obj/x64/Release/MARMoSET.pdb