Handling missing trailer

Author: caetera

Writer/MgfSpectrumWriter.cs

@@ -108,7 +108,18 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                             $"RTINSECONDS={(retentionTime * 60).ToString(CultureInfo.InvariantCulture)}");
 
                         // Trailer extra data list
-                        var trailerData = new ScanTrailer(rawFile.GetTrailerExtraInformation(scanNumber));
+                        ScanTrailer trailerData;
+
+                        try
+                        {
+                            trailerData = new ScanTrailer(rawFile.GetTrailerExtraInformation(scanNumber));
+                        }
+                        catch (Exception ex)
+                        {
+                            Log.WarnFormat("Cannot load trailer infromation for scan {0} due to following exception\n{1}", scanNumber, ex.Message);
+                            trailerData = new ScanTrailer();
+                        }
+
                         int? charge = trailerData.AsPositiveInt("Charge State:");
                         double? monoisotopicMz = trailerData.AsDouble("Monoisotopic M/Z:");
                         double? isolationWidth =

Writer/MzMlSpectrumWriter.cs

@@ -1199,7 +1199,17 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             };
 
             // Trailer extra data list
-            var trailerData = new ScanTrailer(_rawFile.GetTrailerExtraInformation(scanNumber));
+            ScanTrailer trailerData;
+
+            try
+            {
+                trailerData = new ScanTrailer(_rawFile.GetTrailerExtraInformation(scanNumber));
+            }
+            catch (Exception ex)
+            {
+                Log.WarnFormat("Cannot load trailer infromation for scan {0} due to following exception\n{1}", scanNumber, ex.Message);
+                trailerData = new ScanTrailer();
+            }
 
             int? charge = trailerData.AsPositiveInt("Charge State:");
             double? monoisotopicMz = trailerData.AsDouble("Monoisotopic M/Z:");

Writer/ScanTrailer.cs

@@ -35,6 +35,11 @@ public ScanTrailer(LogEntry trailerData)
             }
         }
 
+        public ScanTrailer()
+        {
+            data = new Dictionary<string, string>();
+        }
+
         /// <summary>
         /// Try returning selected trailer element as boolean value,
         /// if the element does not exist or cannot be converted to boolean return null