Add tolerance

caetera · caetera · commit deb50cf33b9b · 2020-01-15T17:28:34.000+01:00
diff --git a/ThermoRawFileParserTest/ThermoRawFileParserTest.csproj b/ThermoRawFileParserTest/ThermoRawFileParserTest.csproj
@@ -174,6 +174,7 @@
     <Content Include="log4net.config">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </Content>
+    <Content Include="small2.RAW" />
   </ItemGroup>
   <ItemGroup>
     <Analyzer Include="..\packages\AWSSDK.CloudWatchLogs.3.3.101.14\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
diff --git a/ThermoRawFileParserTest/small2.RAW b/ThermoRawFileParserTest/small2.RAW
diff --git a/XIC/JSONParser.cs b/XIC/JSONParser.cs
@@ -21,6 +21,23 @@ public static XicData ParseJSON(string jsonPath)
 
             foreach (JSONInputUnit xic in jsonIn)
             {
+                if (xic.RtStart == 0) xic.RtStart = -1;
+                if (xic.RtEnd == 0) xic.RtEnd = -1;
+                if (xic.Tolerance != 0 && xic.ToleranceUnit != null && xic.Mz != 0)
+                {
+                    double delta;
+                    switch (xic.ToleranceUnit.ToLower())
+                    {
+                        case "ppm": delta = xic.Mz * xic.Tolerance * 1e-6; break;
+                        case "amu": delta = xic.Tolerance; break;
+                        case "mmu": delta = xic.Tolerance * 1e-3; break;
+                        case "da": delta = xic.Tolerance; break;
+                        default:
+                            throw new Exception(String.Format("Cannot parse tolerance unit: {0}", xic.ToleranceUnit));
+                    }
+                    data.content.Add(new XicUnit(xic.Mz - delta, xic.Mz + delta, xic.RtStart, xic.RtEnd));
+                }
+
                 if (xic.MzStart != 0 && xic.MzEnd != 0) data.content.Add(new XicUnit(xic.MzStart, xic.MzEnd, xic.RtStart, xic.RtEnd));
             }
 
