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Merge pull request #170 from compomics/1.4.3
Release of v1.4.3
2 parents 45ed3df + 34656a8 commit 5e38f34

26 files changed

+975
-914
lines changed

‎MainClass.cs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ public static class MainClass
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private static readonly ILog Log =
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LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
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23-
public const string Version = "1.4.2";
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public const string Version = "1.4.3";
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public static void Main(string[] args)
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{
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// Set Invariant culture as default for all further processing

‎README.md‎

Lines changed: 12 additions & 1 deletion
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@@ -192,7 +192,8 @@ Provide one of the following filters:
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* M/Z start and end
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* sequence and tolerance (tolerance unit optional, defaults to `ppm`)
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optionally one can define starting and ending retention times and thermo filter string (defaults to `ms`)
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optionally one can define starting and ending retention times, provide filter string (defaults to `ms`, i.e. only MS1 scans), and a comment (free text) field; any valid filter string is supported,
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however only basic validation is performed, see [issue #158](https://github.com/compomics/ThermoRawFileParser/issues/158) for details. Comment can contain any text and will be preserved in the output.
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An example input JSON file:
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@@ -219,7 +220,17 @@ An example input JSON file:
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{
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"sequence":"TRANNEL",
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"tolerance":10
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},
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{
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"mz":1014.5099732499732,
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"rt_start":14.0600881872,
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"rt_end":14.4167198290667,
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"tolerance":5,
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"tolerance_unit":"ppm",
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"comment":"Only ion trap scans"
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"scan_filter":"ITMS"
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}
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}
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]
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```

‎RawFileParser.cs‎

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@@ -136,18 +136,23 @@ private static void ProcessFile(ParseInput parseInput)
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// Get the number of instruments (controllers) present in the RAW file and set the
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// selected instrument to the MS instrument, first instance of it
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rawFile.SelectInstrument(Device.MS, 1);
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var firstScanNumber = -1;
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var lastScanNumber = -1;
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141-
rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;
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if (rawFile.GetInstrumentCountOfType(Device.MS) != 0)
143+
{
144+
rawFile.SelectInstrument(Device.MS, 1);
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rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;
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143-
// Get the first and last scan from the RAW file
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var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
145-
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
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// Get the first and last scan from the RAW file
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firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
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lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
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// Check for empty file
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if (lastScanNumber < 1)
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{
150-
throw new RawFileParserException("Empty RAW file, no output will be produced");
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// Check for empty file
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if (lastScanNumber < 1)
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{
154+
throw new RawFileParserException("Empty RAW file, no output will be produced");
155+
}
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}
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if (parseInput.MetadataFormat != MetadataFormat.NONE)

‎ThermoRawFileParser.csproj‎

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@@ -176,11 +176,11 @@
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<Reference Include="System.Data.DataSetExtensions" />
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<Reference Include="System.Data" />
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<Reference Include="System.Xml" />
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<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
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<HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.88\lib\ThermoFisher.CommonCore.Data.dll</HintPath>
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<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
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<HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.Data.dll</HintPath>
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</Reference>
182-
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
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<HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.88\lib\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
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<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
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<HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
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</Reference>
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<Reference Include="zlib.net, Version=1.0.3.0, Culture=neutral, PublicKeyToken=47d7877cb3620160">
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<HintPath>packages\zlib.net.1.0.4.0\lib\zlib.net.dll</HintPath>
@@ -199,6 +199,7 @@
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<Compile Include="Query\ProxiSpectrumReader.cs" />
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<Compile Include="RawFileParserException.cs" />
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<Compile Include="RawFileParser.cs" />
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<Compile Include="Util\CVHelpers.cs" />
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<Compile Include="Util\LimitedSizeDictionary.cs" />
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<Compile Include="Util\MZArray.cs" />
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<Compile Include="Util\NativeMethods.cs" />

‎ThermoRawFileParserTest/OntologyMappingTests.cs‎

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@@ -12,13 +12,13 @@ public class OntologyMappingTests
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public void TestGetInstrumentModel()
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{
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// exact match
15-
var match = OntologyMapping.getInstrumentModel("LTQ Orbitrap");
15+
var match = OntologyMapping.GetInstrumentModel("LTQ Orbitrap");
1616
Assert.AreEqual("MS:1000449", match.accession);
1717
// partial match, should return the longest partial match
18-
var partialMatch = OntologyMapping.getInstrumentModel("LTQ Orbitrap XXL");
18+
var partialMatch = OntologyMapping.GetInstrumentModel("LTQ Orbitrap XXL");
1919
Assert.AreEqual("MS:1000449", partialMatch.accession);
2020
// no match, should return the generic thermo instrument
21-
var noMatch = OntologyMapping.getInstrumentModel("non existing model");
21+
var noMatch = OntologyMapping.GetInstrumentModel("non existing model");
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Assert.AreEqual("MS:1000483", noMatch.accession);
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}
2424
}

‎ThermoRawFileParserTest/ThermoRawFileParserTest.csproj‎

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@@ -155,15 +155,15 @@
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<HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoFisher.CommonCore.BackgroundSubtraction.dll</HintPath>
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<Private>True</Private>
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</Reference>
158-
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
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<HintPath>..\packages\ThermoFisher.CommonCore.Data.5.0.0.88\lib\ThermoFisher.CommonCore.Data.dll</HintPath>
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<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
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<HintPath>..\packages\ThermoFisher.CommonCore.Data.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.Data.dll</HintPath>
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</Reference>
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<Reference Include="ThermoFisher.CommonCore.MassPrecisionEstimator, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
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<HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoFisher.CommonCore.MassPrecisionEstimator.dll</HintPath>
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<Private>True</Private>
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</Reference>
165-
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
166-
<HintPath>..\packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.88\lib\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
165+
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
166+
<HintPath>..\packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
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</Reference>
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<Reference Include="ThermoRawFileReader, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
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<HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoRawFileReader.dll</HintPath>

‎ThermoRawFileParserTest/app.config‎

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@@ -12,7 +12,7 @@
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="ThermoFisher.CommonCore.RawFileReader" publicKeyToken="1aef06afb5abd953" culture="neutral" />
15-
<bindingRedirect oldVersion="0.0.0.0-5.0.0.88" newVersion="5.0.0.88" />
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<bindingRedirect oldVersion="0.0.0.0-5.0.0.93" newVersion="5.0.0.93" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="System.Buffers" publicKeyToken="cc7b13ffcd2ddd51" culture="neutral" />
@@ -28,7 +28,7 @@
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="ThermoFisher.CommonCore.Data" publicKeyToken="1aef06afb5abd953" culture="neutral" />
31-
<bindingRedirect oldVersion="0.0.0.0-5.0.0.88" newVersion="5.0.0.88" />
31+
<bindingRedirect oldVersion="0.0.0.0-5.0.0.93" newVersion="5.0.0.93" />
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</dependentAssembly>
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<dependentAssembly>
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<assemblyIdentity name="System.IO.FileSystem.AccessControl" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />

‎ThermoRawFileParserTest/packages.config‎

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@@ -19,7 +19,7 @@
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<package id="System.IO.FileSystem.AccessControl" version="5.0.0" targetFramework="net472" />
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<package id="System.Security.AccessControl" version="5.0.0" targetFramework="net472" />
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<package id="System.Security.Principal.Windows" version="5.0.0" targetFramework="net472" />
22-
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.88" targetFramework="net472" />
23-
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.88" targetFramework="net472" />
22+
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.93" targetFramework="net472" />
23+
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.93" targetFramework="net472" />
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<package id="zlib.net" version="1.0.4.0" targetFramework="net471" />
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</packages>

‎Util/CVHelpers.cs‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
using ThermoRawFileParser.Writer.MzML;
2+
3+
namespace ThermoRawFileParser.Util
4+
{
5+
public static class CVHelpers
6+
{
7+
public static CVParamType Copy (this CVParamType old)
8+
{
9+
return new CVParamType
10+
{
11+
accession = old.accession,
12+
name = old.name,
13+
cvRef = old.cvRef,
14+
unitAccession = old.unitAccession,
15+
unitCvRef = old.unitCvRef,
16+
unitName = old.unitName,
17+
value = old.value
18+
};
19+
}
20+
}
21+
}

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