fix refinement bug, update version number

kevinkovalchik · Nov 9, 2018 · 69b754f · 69b754f
1 parent 74b5d82
commit 69b754f
Show file tree

Hide file tree

Showing 4 changed files with 38 additions and 5 deletions.
diff --git a/RawTools/Program.cs b/RawTools/Program.cs
@@ -384,7 +384,7 @@ static int DoStuff(ArgumentParser.ParseOptions opts)
                     if (opts.WriteMGF)
                     {
                         MGF.WriteMGF(rawData: rawData, rawFile: rawFile, outputDirectory: opts.OutputDirectory, cutoff: opts.MassCutOff,
-                            intensityCutoff: opts.IntensityCutoff);
+                            intensityCutoff: opts.IntensityCutoff, refineMassCharge: opts.RefineMassCharge);
                     }
 
                     if (opts.Metrics)

diff --git a/RawTools/Properties/AssemblyInfo.cs b/RawTools/Properties/AssemblyInfo.cs
@@ -34,6 +34,6 @@
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
 [assembly: AssemblyVersion("1.0.0.0")]
-[assembly: AssemblyFileVersion("7.11.2018.10")]
+[assembly: AssemblyFileVersion("9.11.2018.2")]
 
-[assembly: AssemblyInformationalVersion("1.3.1")]
+[assembly: AssemblyInformationalVersion("1.3.2")]
diff --git a/RawTools/Write/DataWrite.cs b/RawTools/Write/DataWrite.cs
@@ -27,6 +27,7 @@
 using RawTools.Data.Extraction;
 using RawTools.Utilities;
 using RawTools.QC;
+using RawTools.Algorithms;
 using ThermoFisher;
 using ThermoFisher.CommonCore.Data.Business;
 using ThermoFisher.CommonCore.Data.Interfaces;
@@ -209,7 +210,7 @@ public static void WriteMatrix(RawDataCollection rawData, ScanMetaDataCollection
 
     static class MGF
     {
-        public static void WriteMGF(RawDataCollection rawData, IRawDataPlus rawFile, string outputDirectory, double cutoff = 0, int[] scans = null, double intensityCutoff = 0.01)
+        public static void WriteMGF(RawDataCollection rawData, IRawDataPlus rawFile, string outputDirectory, double cutoff = 0, int[] scans = null, double intensityCutoff = 0.01, bool refineMassCharge = false)
         {
             double intCutoff = 0;
             string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, ".mgf");
@@ -227,8 +228,38 @@ public static void WriteMGF(RawDataCollection rawData, IRawDataPlus rawFile, str
                 operations.Add(Operations.Ms2SegmentedScans);
             }
 
+            if (refineMassCharge) operations.Add(Operations.Ms1CentroidStreams);
+
             CheckIfDone.Check(rawData, rawFile, operations);
 
+            if (refineMassCharge)
+            {
+                ProgressIndicator P = new ProgressIndicator(rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2].Length, "Refining precursor charge state and monoisotopic mass");
+                P.Start();
+                int refinedCharge;
+                double refinedMass;
+
+                //if (!rawData.Performed.Contains(Operations.PeakRetAndInt))
+                //{
+                //    rawData.CalcPeakRetTimesAndInts(rawFile);
+                //}
+
+                foreach (int scan in rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2])
+                {
+                    // refine precursor mass and charge
+                    // var centroid = rawData.GetAverageScan(rawFile, scan);
+                    //rawData.centroidStreams[rawData.precursorScans[scan].MasterScan]
+
+                    (refinedCharge, refinedMass) =
+                        MonoIsoPredictor.GetMonoIsotopicMassCharge(rawData.centroidStreams[rawData.precursorScans[scan].MasterScan],
+                        rawData.precursorMasses[scan].ParentMZ, rawData.trailerExtras[scan].ChargeState);
+                    rawData.trailerExtras[scan].ChargeState = refinedCharge;
+                    rawData.precursorMasses[scan].MonoisotopicMZ = refinedMass;
+                    P.Update();
+                }
+                P.Done();
+            }
+
             const int BufferSize = 65536;  // 64 Kilobytes
 
             using (StreamWriter f = new StreamWriter(fileName, false, Encoding.UTF8, BufferSize)) //Open a new file, the MGF file

diff --git a/changelog.md b/changelog.md
@@ -10,10 +10,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 but the meta data was incomplete. To address this, the scan lists RawTools uses to process are now built off of the scan dependents found in the
 raw file meta data. This means scans which are missing meta data will not appear in the output data table. Note that these occurances are rare, and
 we are planning to add a text output to alert the user when this happens.
+- The examples have been updated. There are now two sections to the examples function: --interface and --modifications.
 
 ### Fixed
-- MS3ScanRate was not referecing the correct data. Is fixed now.
+- MS3ScanRate was not referencing the correct data. Is fixed now.
 - Fixed a bug which caused a crash when MS scan data was absent or corrupted for a scan.
+- Fixed a bug where precursor charge state and monoisotopic m/z was not refined when the only output was an MGF file.
 
 ## [1.3.1] 2018-10-26
 ### Fixed