Merge branch 'eubic2020hackathon' of https://github.com/compomics/ThermoRawFileParser into eubic2020hackathon

Author: edeutsch

Query/ProxiSpectrumReader.cs

@@ -75,6 +75,8 @@ public List<PROXISpectrum> Retrieve()
                         // Get the scan event for this scan number
                         var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
 
+                        var isCentroid = true;
+
                         IReaction reaction = null;
                         switch (scanFilter.MSOrder)
                         {
@@ -87,7 +89,7 @@ public List<PROXISpectrum> Retrieve()
                                 {
                                     Log.Warn("No reaction found for scan " + scanNumber);
                                 }
-                                
+
                                 goto default;
                             case MSOrderType.Ms3:
                             {
@@ -195,6 +197,20 @@ public List<PROXISpectrum> Retrieve()
                                         rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
                                     proxiSpectrum.AddMz(segmentedScan.Positions);
                                     proxiSpectrum.AddIntensities(segmentedScan.Intensities);
+
+                                    if (scanEvent.ScanData.Equals(ScanDataType.Profile))
+                                    {
+                                        isCentroid = false;
+                                    }
+                                }
+
+                                if (isCentroid)
+                                {
+                                    proxiSpectrum.AddAttribute(accession: "MS:1000127", name: "centroid spectrum");
+                                }
+                                else
+                                {
+                                    proxiSpectrum.AddAttribute(accession: "MS:1000128", name: "profile spectrum");
                                 }
 
                                 resultList.Add(proxiSpectrum);

XIC/JSONParser.cs

@@ -53,7 +53,7 @@ public static XicData ParseJSON(string jsonPath)
                 }
                 else
                 {
-                    throw new Exception(String.Format("Unparsable JSON element:\n{0}", JsonConvert.SerializeObject(xic)));
+                    throw new Exception(String.Format("Unparsable JSON element:\n{0}", JsonConvert.SerializeObject(xic, Formatting.Indented)));
                 }
             }
 

XIC/XicExecutor.cs

@@ -51,16 +51,10 @@ public void StdOutputXicData(XicData outputData){
             Console.WriteLine(outputString);
         }
 
-        
-        
         public void OutputXicData(XicData outputData, string outputFileName){
             string outputString = JsonConvert.SerializeObject(outputData);
             File.WriteAllText(outputFileName, outputString);
         }
 
-        public double PepseqToMass(String pep_seq){
-
-            throw new NotImplementedException();
-        }
     }
 }

XIC/XicReader.cs

@@ -54,6 +54,10 @@ public static void ReadXic(string rawFilePath, bool base64, XicData xicData)
                 //var generator = new ChromatogramBatchGenerator();
                 //ParallelChromatogramFactory.FromRawData(generator, rawFile);
 
+                //update global metadata
+                xicData.outputmeta.base64 = base64;
+                xicData.outputmeta.timeunit = "minutes";
+
                 foreach (var xicUnit in xicData.content)
                 {
                     IChromatogramSettings settings;