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Fix logging and mzML
* Log4net configuration moved to App.config * Fixed unhandled exception during mzML precursor creation * Explicit usings * Properties (some build/debug information from VS) ignored TODO Check all "possibly null reference" warnings
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+55
-82
lines changed

10 files changed

+55
-82
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‎.gitignore‎

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@@ -6,3 +6,4 @@ obj/
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.vs/
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*.csproj.user
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.vscode/
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Properties/

‎App.config‎

Lines changed: 29 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -1,44 +1,35 @@
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<?xml version="1.0" encoding="utf-8"?>
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<configuration>
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<configSections>
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<section name="log4net" type="System.Configuration.IgnoreSectionHandler" />
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</configSections>
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<log4net>
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<root>
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<level value="INFO" />
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<appender-ref ref="console" />
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<!-- <appender-ref ref="file" /> -->
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</root>
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<appender name="console" type="log4net.Appender.ConsoleAppender">
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<layout type="log4net.Layout.PatternLayout">
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<conversionPattern value="%date{yyyy-MM-dd HH:mm:ss} %level %message%newline" />
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</layout>
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</appender>
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<!--<appender name="file" type="log4net.Appender.RollingFileAppender">
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<file value="ThermoRawFileParser.log" />
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<appendToFile value="true" />
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<rollingStyle value="Size" />
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<maxSizeRollBackups value="5" />
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<maximumFileSize value="10MB" />
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<staticLogFileName value="true" />
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<layout type="log4net.Layout.PatternLayout">
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<conversionPattern value="%date{yyyy-MM-dd HH:mm:ss} [%thread] %message%newline" />
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</layout>
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</appender>-->
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</log4net>
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<runtime>
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<loadFromRemoteSources enabled="true" />
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<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
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<dependentAssembly>
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<assemblyIdentity name="System.Buffers" publicKeyToken="cc7b13ffcd2ddd51" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-4.0.3.0" newVersion="4.0.3.0" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="Newtonsoft.Json" publicKeyToken="30ad4fe6b2a6aeed" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-13.0.0.0" newVersion="13.0.0.0" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="OpenMcdf" publicKeyToken="fdbb1629d7c00800" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-2.2.1.9" newVersion="2.2.1.9" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="System.Runtime.CompilerServices.Unsafe" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="ThermoFisher.CommonCore.Data" publicKeyToken="1aef06afb5abd953" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-5.0.0.88" newVersion="5.0.0.88" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="System.IO.FileSystem.AccessControl" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="OpenMcdf.Extensions" publicKeyToken="fdbb1629d7c00800" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-2.3.0.0" newVersion="2.3.0.0" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="System.Security.Principal.Windows" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="System.Security.AccessControl" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
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<bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
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</dependentAssembly>
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</assemblyBinding>
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</runtime>
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</configuration>

‎MainClass.cs‎

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@@ -13,12 +13,14 @@
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using System.Text.RegularExpressions;
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using System.Data;
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[assembly: log4net.Config.XmlConfigurator()]
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namespace ThermoRawFileParser
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{
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public static class MainClass
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{
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private static readonly ILog Log =
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LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
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LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
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public const string Version = "1.4.5";
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public static void Main(string[] args)
@@ -125,7 +127,7 @@ private static void XicParametersParsing(string[] args)
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126128
if (parameters.help)
127129
{
128-
ShowHelp("usage is:", null,
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ShowHelp("usage is:", new OptionException(),
129131
optionSet);
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return;
131133
}
@@ -253,12 +255,12 @@ private static void XicParametersParsing(string[] args)
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{
254256
if (parameters.help)
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{
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ShowHelp("usage is:", null,
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ShowHelp("usage is:", new OptionException(),
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optionSet);
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}
259261
else
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{
261-
ShowHelp("Error - usage is:", null,
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ShowHelp("Error - usage is:", new OptionException(),
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optionSet);
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}
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}
@@ -374,7 +376,7 @@ private static void SpectrumQueryParametersParsing(string[] args)
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375377
if (parameters.help)
376378
{
377-
ShowHelp("usage is:", null,
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ShowHelp("usage is:", new OptionException(),
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optionSet);
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return;
380382
}
@@ -416,12 +418,12 @@ private static void SpectrumQueryParametersParsing(string[] args)
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{
417419
if (parameters.help)
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{
419-
ShowHelp("usage is:", null,
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ShowHelp("usage is:", new OptionException(),
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optionSet);
421423
}
422424
else
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{
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ShowHelp("Error - usage is:", null,
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ShowHelp("Error - usage is:", new OptionException(),
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optionSet);
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}
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}
@@ -623,7 +625,7 @@ private static void RegularParametersParsing(string[] args)
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{
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var helpMessage =
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$"Usage is {Assembly.GetExecutingAssembly().GetName().Name}.exe [subcommand] [options]\noptional subcommands are xic|query (use [subcommand] -h for more info]):";
626-
ShowHelp(helpMessage, null, optionSet);
628+
ShowHelp(helpMessage, new OptionException(), optionSet);
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return;
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}
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@@ -788,12 +790,12 @@ private static void RegularParametersParsing(string[] args)
788790
{
789791
if (help)
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{
791-
ShowHelp("usage is:", null,
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ShowHelp("usage is:", new OptionException(),
792794
optionSet);
793795
}
794796
else
795797
{
796-
ShowHelp("Error - usage is:", null,
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ShowHelp("Error - usage is:", new OptionException(),
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optionSet);
798800
}
799801
}

‎Query/ProxiSpectrum.cs‎

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@@ -1,8 +1,5 @@
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using System;
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using System.Collections.Generic;
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using System.Collections.Generic;
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using System.Linq;
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using System.Text;
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using System.Threading.Tasks;
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using ThermoRawFileParser.Writer;
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namespace ThermoRawFileParser.Query

‎RawFileParser.cs‎

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@@ -1,7 +1,9 @@
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using System;
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using System.IO;
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using System.Linq;
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using System.Reflection;
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using System.Runtime.InteropServices;
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using log4net;
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using ThermoFisher.CommonCore.Data;
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using ThermoFisher.CommonCore.Data.Business;
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using ThermoFisher.CommonCore.Data.Interfaces;
@@ -12,8 +14,8 @@ namespace ThermoRawFileParser
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{
1315
public static class RawFileParser
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{
15-
private static readonly log4net.ILog Log =
16-
log4net.LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
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private static readonly ILog Log =
18+
LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
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/// <summary>
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/// Process and extract the RAW file(s).

‎ThermoRawFileParser.csproj‎

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@@ -3,7 +3,7 @@
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<PropertyGroup>
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<OutputType>Exe</OutputType>
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<TargetFramework>net8.0</TargetFramework>
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<ImplicitUsings>enable</ImplicitUsings>
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<ImplicitUsings>disable</ImplicitUsings>
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<Nullable>enable</Nullable>
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<StartupObject>ThermoRawFileParser.MainClass</StartupObject>
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<PlatformTarget>x64</PlatformTarget>

‎Writer/MzMlSpectrumWriter.cs‎

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@@ -653,7 +653,8 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
653653
Writer.Flush();
654654
Writer.Close();
655655

656-
if (_doIndexing)
656+
//This section is not necessary?
657+
/*if (_doIndexing)
657658
{
658659
try
659660
{
@@ -665,7 +666,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
665666
// Cannot access a closed file. CryptoStream was already closed when closing _writer
666667
Log.Warn($"Warning: {e.Message}");
667668
}
668-
}
669+
}*/
669670
}
670671

671672
// In case of indexed mzML, change the extension from xml to mzML and check for the gzip option
@@ -2450,7 +2451,7 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
24502451
reactionCount++;
24512452
}
24522453
}
2453-
catch (ArgumentOutOfRangeException)
2454+
catch (IndexOutOfRangeException)
24542455
{
24552456
// If we failed do nothing
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}

‎XIC/XicExecutor.cs‎

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@@ -1,5 +1,4 @@
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using System;
2-
using System.Data;
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using System.IO;
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using System.Text;
54
using System.Reflection;

‎XIC/XicReader.cs‎

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@@ -1,4 +1,7 @@
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using System;
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using System.IO;
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using System.Reflection;
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using System.Collections.Generic;
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using System.Runtime.InteropServices;
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using log4net;
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using ThermoFisher.CommonCore.Data;

‎log4net.config‎

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This file was deleted.

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