Merge pull request #294 from smith-chem-wisc/StefanBranch

fix bug with precursorScanBestMass

Author: stefanks

EngineLayer/PsmParent.cs

@@ -36,6 +36,7 @@ public abstract class PsmParent
         #region Internal Fields
 
         internal readonly int notch;
+        internal double? precursorScanBestMass;
 
         #endregion Internal Fields
 

EngineLayer/PsmWithMultiplePossiblePeptides.cs

@@ -17,12 +17,6 @@ public class PsmWithMultiplePossiblePeptides
 
         #endregion Public Fields
 
-        #region Private Fields
-
-        private double? precursorScanBestMass;
-
-        #endregion Private Fields
-
         #region Public Constructors
 
         public PsmWithMultiplePossiblePeptides(PsmParent newPsm, HashSet<PeptideWithSetModifications> peptidesWithSetModifications, Tolerance fragmentTolerance, IMsDataFile<IMsDataScan<IMzSpectrum<IMzPeak>>> myMsDataFile, List<ProductType> lp)
@@ -70,10 +64,10 @@ public PsmWithMultiplePossiblePeptides(PsmParent newPsm, HashSet<PeptideWithSetM
             PeptideMonoisotopicMass = representative.MonoisotopicMass;
 
             // Look for better match in MS1 spectrum!!!
-            if (myMsDataFile != null && !precursorScanBestMass.HasValue)
+            if (myMsDataFile != null && !newPsm.precursorScanBestMass.HasValue)
             {
                 var precursorScan = myMsDataFile.GetOneBasedScan(newPsm.precursorScanNumber);
-                precursorScanBestMass = precursorScan.MassSpectrum.GetClosestPeakXvalue(this.PeptideMonoisotopicMass.ToMz(this.newPsm.scanPrecursorCharge)).ToMass(this.newPsm.scanPrecursorCharge);
+                newPsm.precursorScanBestMass = precursorScan.MassSpectrum.GetClosestPeakXvalue(this.PeptideMonoisotopicMass.ToMz(this.newPsm.scanPrecursorCharge)).ToMass(this.newPsm.scanPrecursorCharge);
             }
 
             FullSequence = representative.Sequence;
@@ -187,9 +181,9 @@ public override string ToString()
             sb.Append((ScanPrecursorMass - PeptideMonoisotopicMass).ToString("F5", CultureInfo.InvariantCulture) + '\t');
             sb.Append(((ScanPrecursorMass - PeptideMonoisotopicMass) / PeptideMonoisotopicMass * 1e6).ToString("F5", CultureInfo.InvariantCulture) + '\t');
 
-            sb.Append(precursorScanBestMass.Value.ToString("F5", CultureInfo.InvariantCulture) + '\t');
-            sb.Append((precursorScanBestMass - PeptideMonoisotopicMass).Value.ToString("F5", CultureInfo.InvariantCulture) + '\t');
-            sb.Append(((precursorScanBestMass - PeptideMonoisotopicMass) / PeptideMonoisotopicMass * 1e6).Value.ToString("F5", CultureInfo.InvariantCulture) + '\t');
+            sb.Append(newPsm.precursorScanBestMass.Value.ToString("F5", CultureInfo.InvariantCulture) + '\t');
+            sb.Append((newPsm.precursorScanBestMass - PeptideMonoisotopicMass).Value.ToString("F5", CultureInfo.InvariantCulture) + '\t');
+            sb.Append(((newPsm.precursorScanBestMass - PeptideMonoisotopicMass) / PeptideMonoisotopicMass * 1e6).Value.ToString("F5", CultureInfo.InvariantCulture) + '\t');
 
             if (IsDecoy)
                 sb.Append("D");