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nielshulstaertnielshulstaert
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thermo libraries upgrade from 5.0.0.6 to 5.0.0.38
centroiding of scan segmented data
1 parent 182e958 commit 3145547

17 files changed

+909
-53
lines changed

‎Query/ProxiSpectrumReader.cs‎

Lines changed: 3 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -176,12 +176,9 @@ public List<ProxiSpectrum> Retrieve()
176176
// Otherwise take the profile data
177177
else
178178
{
179-
// Get the scan statistics from the RAW file for this scan number
180-
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
181-
182-
// Get the segmented (low res and profile) scan data
183-
var segmentedScan =
184-
rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
179+
// centroid the profile data by default
180+
var segmentedScan = !queryParameters.noPeakPicking ? Scan.ToCentroid(scan).SegmentedScan : scan.SegmentedScan;
181+
185182
proxiSpectrum.AddMz(segmentedScan.Positions);
186183
proxiSpectrum.AddIntensities(segmentedScan.Intensities);
187184

‎ThermoRawFileParser.csproj‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -126,12 +126,11 @@
126126
<Reference Include="System.Data.DataSetExtensions" />
127127
<Reference Include="System.Data" />
128128
<Reference Include="System.Xml" />
129-
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
130-
<HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.6\lib\net471\ThermoFisher.CommonCore.Data.dll</HintPath>
131-
<Private>True</Private>
129+
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.38, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
130+
<HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.38\lib\net471\ThermoFisher.CommonCore.Data.dll</HintPath>
132131
</Reference>
133-
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
134-
<HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.6\lib\net471\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
132+
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.38, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
133+
<HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.38\lib\net471\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
135134
<Private>True</Private>
136135
</Reference>
137136
<Reference Include="zlib.net, Version=1.0.3.0, Culture=neutral, PublicKeyToken=47d7877cb3620160">

‎ThermoRawFileParserTest/ThermoRawFileParserTest.csproj‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -136,16 +136,16 @@
136136
<HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoFisher.CommonCore.BackgroundSubtraction.dll</HintPath>
137137
<Private>True</Private>
138138
</Reference>
139-
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
140-
<HintPath>..\packages\ThermoFisher.CommonCore.Data.5.0.0.6\lib\net471\ThermoFisher.CommonCore.Data.dll</HintPath>
139+
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.38, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
140+
<HintPath>../packages/ThermoFisher.CommonCore.Data.5.0.0.38/lib/net471/ThermoFisher.CommonCore.Data.dll</HintPath>
141141
<Private>True</Private>
142142
</Reference>
143143
<Reference Include="ThermoFisher.CommonCore.MassPrecisionEstimator, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
144144
<HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoFisher.CommonCore.MassPrecisionEstimator.dll</HintPath>
145145
<Private>True</Private>
146146
</Reference>
147-
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
148-
<HintPath>..\packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.6\lib\net471\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
147+
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.38, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
148+
<HintPath>../packages/ThermoFisher.CommonCore.RawFileReader.5.0.0.38/lib/net471/ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
149149
<Private>True</Private>
150150
</Reference>
151151
<Reference Include="ThermoRawFileReader, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">

‎ThermoRawFileParserTest/packages.config‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
<package id="NJsonSchema" version="10.1.5" targetFramework="net472" />
1414
<package id="NUnit" version="3.12.0" targetFramework="net472" />
1515
<package id="PSI_Interface" version="2.2.1" targetFramework="net472" />
16-
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.6" targetFramework="net472" />
17-
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.6" targetFramework="net472" />
16+
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.38" targetFramework="net472" />
17+
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.38" targetFramework="net472" />
1818
<package id="zlib.net" version="1.0.4.0" targetFramework="net471" />
1919
</packages>

‎Writer/MgfSpectrumWriter.cs‎

Lines changed: 2 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -145,12 +145,9 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
145145
// Otherwise take the profile data
146146
else
147147
{
148-
// Get the scan statistics from the RAW file for this scan number
149-
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
148+
// centroid the profile data by default
149+
var segmentedScan = !ParseInput.NoPeakPicking ? Scan.ToCentroid(scan).SegmentedScan : scan.SegmentedScan;
150150

151-
// Get the segmented (low res and profile) scan data
152-
var segmentedScan =
153-
rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
154151
for (var i = 0; i < segmentedScan.Positions.Length; i++)
155152
{
156153
Writer.WriteLine(

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 4 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -994,14 +994,11 @@ private SpectrumType ConstructSpectrum(int scanNumber)
994994
}
995995
else
996996
{
997-
// Get the scan statistics from the RAW file for this scan number
998-
var scanStatistics = _rawFile.GetScanStatsForScanNumber(scanNumber);
997+
basePeakMass = scan.ScanStatistics.BasePeakMass;
998+
basePeakIntensity = scan.ScanStatistics.BasePeakIntensity;
999999

1000-
basePeakMass = scanStatistics.BasePeakMass;
1001-
basePeakIntensity = scanStatistics.BasePeakIntensity;
1002-
1003-
// Get the segmented (low res and profile) scan data
1004-
var segmentedScan = _rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
1000+
// centroid the profile data by default
1001+
var segmentedScan = !ParseInput.NoPeakPicking ? Scan.ToCentroid(scan).SegmentedScan : scan.SegmentedScan;
10051002
if (segmentedScan.Positions.Length > 0)
10061003
{
10071004
switch (scanEvent.ScanData)

‎packages.config‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@
1515
<package id="System.Runtime.CompilerServices.Unsafe" version="4.5.2" targetFramework="net472" />
1616
<package id="System.Text.Encoding.CodePages" version="4.5.1" targetFramework="net472" />
1717
<package id="System.ValueTuple" version="4.5.0" targetFramework="net472" />
18-
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.6" targetFramework="net471" />
19-
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.6" targetFramework="net471" />
18+
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.38" targetFramework="net471" />
19+
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.38" targetFramework="net472" />
2020
<package id="zlib.net" version="1.0.4.0" targetFramework="net471" />
2121
</packages>

‎packages/ThermoFisher.CommonCore.Data.5.0.0.38/ThermoFisher.CommonCore.Data.5.0.0.38.nupkg‎

312 KB
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‎packages/ThermoFisher.CommonCore.Data.5.0.0.38/lib/net471/ThermoFisher.CommonCore.Data.dll‎

374 KB
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