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Allowed reading of scan descriptions from Raw Files #736

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Nov 27, 2023
Merged

Allowed reading of scan descriptions from Raw Files #736

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f530c29
Allowed reading of scan descriptions from Raw Files
nbollis Oct 25, 2023
03c27a6
Merge branch 'master' into MsDataScanScanDescription
trishorts Nov 24, 2023
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5 changes: 4 additions & 1 deletion mzLib/MassSpectrometry/MsDataScan.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
using System;
using System.Collections;
using System.Collections.Generic;
using System.ComponentModel;
using System.Linq;

namespace MassSpectrometry
Expand All @@ -28,7 +29,7 @@ public class MsDataScan
{
public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer,
double totalIonCurrent, double? injectionTime, double[,] noiseData, string nativeId, double? selectedIonMz = null, int? selectedIonChargeStateGuess = null, double? selectedIonIntensity = null, double? isolationMZ = null,
double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null)
double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null, string scanDescription = null)
{
OneBasedScanNumber = oneBasedScanNumber;
MsnOrder = msnOrder;
Expand All @@ -52,6 +53,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
SelectedIonChargeStateGuess = selectedIonChargeStateGuess;
SelectedIonMonoisotopicGuessMz = selectedIonMonoisotopicGuessMz;
HcdEnergy = hcdEnergy;
ScanDescription = scanDescription;
}

/// <summary>
Expand Down Expand Up @@ -84,6 +86,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
public double? SelectedIonMonoisotopicGuessIntensity { get; private set; } // May be refined
public double? SelectedIonMonoisotopicGuessMz { get; private set; } // May be refined
public string HcdEnergy { get; private set; }
public string ScanDescription { get; private set; }

private MzRange isolationRange;

Expand Down
9 changes: 8 additions & 1 deletion mzLib/Readers/Thermo/ThermoRawFileReader.cs
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Expand Up @@ -252,6 +252,7 @@ private static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams
int? precursorScanNumber = null;
double? isolationMz = null;
string HcdEnergy = null;
string scanDescript = null;
ActivationType activationType = ActivationType.Any; // thermo enum
DissociationType dissociationType = DissociationType.Unknown; // mzLib enum

Expand Down Expand Up @@ -306,6 +307,11 @@ private static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams
{
HcdEnergy = values[i];
}

if (labels[i].StartsWith("Scan Description", StringComparison.Ordinal))
{
scanDescript = values[i].TrimEnd();
}
}

if (msOrder > 1)
Expand Down Expand Up @@ -397,7 +403,8 @@ private static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams
dissociationType: dissociationType,
oneBasedPrecursorScanNumber: precursorScanNumber,
selectedIonMonoisotopicGuessMz: precursorSelectedMonoisotopicIonMz,
hcdEnergy: HcdEnergy);
hcdEnergy: HcdEnergy,
scanDescription: scanDescript);
}

private static MzSpectrum GetSpectrum(IRawDataPlus rawFile, IFilteringParams filterParams,
Expand Down
Binary file added mzLib/Test/DataFiles/ScanDescriptionTestData.raw
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13 changes: 13 additions & 0 deletions mzLib/Test/FileReadingTests/TestRawFileReader.cs
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
using System;
using System.Collections.Generic;
using System.Collections.Specialized;
using System.Diagnostics;
using System.IO;
using System.Linq;
Expand Down Expand Up @@ -40,6 +41,18 @@ public void TestRawFileReaderFileNotFoundException()
#endregion


[Test]
public void TestScanDescription()
{
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "ScanDescriptionTestData.raw");
var scans = MsDataFileReader.GetDataFile(filePath).GetAllScansList();
var ms1Scans = scans.Where(x => x.MsnOrder == 1).ToList();
var ms2Scans = scans.Where(x => x.MsnOrder == 2).ToList();

ms1Scans.ForEach(x => Assert.That(x.ScanDescription, Is.EqualTo(null)));
ms2Scans.ForEach(x => Assert.That(x.ScanDescription, Is.EqualTo("Testing2")));
}

/// <summary>
/// Tests LoadAllStaticData for ThermoRawFileReader
/// </summary>
Expand Down
3 changes: 3 additions & 0 deletions mzLib/Test/Test.csproj
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Expand Up @@ -288,6 +288,9 @@
<None Update="DataFiles\GUACUG_NegativeMode_Sliced.mzML">
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
</None>
<None Update="DataFiles\ScanDescriptionTestData.raw">
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
</None>
<None Update="FileReadingTests\ExternalFileTypes\Ms1Feature_FlashDeconvOpenMs3.0.0_ms1.feature">
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
</None>
Expand Down