Merge pull request #169 from smith-chem-wisc/StefanBranch

alrighty

Author: stefanks

MetaMorpheusGUI/MainWindow.xaml.cs

@@ -62,9 +62,11 @@ public MainWindow()
             //xmlDBobservableCollection.Add(new XMLdb(@"C:\Users\stepa\Desktop\MM_error\cRAP_database.xml"));
             //xmlDBobservableCollection.Add(new XMLdb(@"C:\Users\stepa\Desktop\MM_error\MSQC4_heavy_light.xml"));
             //xmlDBobservableCollection.Add(new XMLdb(@"C:\Users\stepa\Desktop\MM_error\cRAP_database.xml"));
+            //xmlDBobservableCollection.Add(new XMLdb(@"C:\Users\stepa\Desktop\MM_error\sigma_rawFiles\2017-01-23-13-23-29\Task2Gptmd\cRAP_database-MSQC4_heavy_lightGPTMD.xml"));
 
             //rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Data\CalibrationPaperData\OrigData\Jurkat\120426_Jurkat_highLC_Frac17.raw"));
             //rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Data\CalibrationPaperData\Step2\Mouse\Calib-0.1.2\04-29-13_B6_Frac9_9p5uL-Calibrated.mzML"));
+            //rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Data\CalibrationPaperData\Step2\Mouse\Calib-0.1.2\04-29-13_B6_Frac9_9p5uL-Calibrated.mzML"));
 
             //rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Data\CalibrationPaperData\OrigData\Mouse\04-29-13_B6_Frac1_9uL.raw"));
             //rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Data\CalibrationPaperData\OrigData\Mouse\04-29-13_B6_Frac2_9p5uL.raw"));

OldInternalLogic/ProteomeDatabaseReader.cs

@@ -148,7 +148,7 @@ public static IEnumerable<MorpheusModification> ReadModFile(string v)
                                 break;
 
                             case "//":
-                                if (feature_type == "MOD_RES" && (!float.IsNaN(monoisotopic_mass_shift)))
+                                if (feature_type == "MOD_RES" && (!float.IsNaN(monoisotopic_mass_shift)) && ye != null)
                                 {
                                     if (labileOrSticky.Equals("Labile") || labileOrSticky.Equals("Both"))
                                         yield return new MorpheusModification(description, modification_type, amino_acid_residue, monoisotopic_mass_shift, Path.GetFileNameWithoutExtension(v), database_name, prevAA, alternative_mass, true, ye);