Merge pull request #201 from lzivadinovic/master

BUGFIX MetadataWriter: Moving MSLevel counter out of the spectrum iteration loop

Author: caetera

Writer/MetadataWriter.cs

@@ -47,6 +47,9 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
         {
             if(rawFile.SelectMsData())
             {
+                // Get MS levels
+                msLevels = WriterUtil.CountScanOrder(rawFile);
+
                 for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
                 {
                     var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
@@ -57,9 +60,6 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
                     // Get the scan event for this scan number
                     var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
 
-                    // Get MS levels
-                    msLevels = WriterUtil.CountScanOrder(rawFile);
-                    
                     if (time > maxTime)
                         maxTime = time;
                     if (time < minTime)
@@ -174,10 +174,10 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
                     metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
                         msLevels[MSOrderType.Ms].ToString()));
                 if (msLevels[MSOrderType.Ms2] > 0)
-                    metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS1 spectra",
+                    metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
                         msLevels[MSOrderType.Ms2].ToString()));
                 if (msLevels[MSOrderType.Ms3] > 0)
-                    metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS1 spectra",
+                    metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
                         msLevels[MSOrderType.Ms3].ToString()));
 
                 metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",