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added quant mass property to masscenter #714

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Merged
YukiMatsuzawa merged 2 commits into from
Mar 11, 2026
+9 −3
Merged

added quant mass property to masscenter #714

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c1d0c10
added quant mass property to masscenter
htsugawa Mar 11, 2026
58a153f
Add ContinueOnError to DownloadFile task
YukiMatsuzawa Mar 11, 2026
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4 changes: 2 additions & 2 deletions src/MSDIAL4/MsDial/MSDIAL.csproj
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Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,7 @@
<ItemGroup>
<_DeployToItem Include="$(TargetDir)\*.lbm*" />
</ItemGroup>
<DownloadFile SourceUrl="$(Lbm2Url)" DestinationFolder="$(TargetDir)" Condition="!Exists('%(_DeployToItem.FullPath)')" />
<DownloadFile SourceUrl="$(Lbm2Url)" DestinationFolder="$(TargetDir)" Condition="!Exists('%(_DeployToItem.FullPath)')" ContinueOnError="true"/>
<Exec Command="xcopy &quot;$(ProjectDir)CytoscapeLocalBrowser&quot; &quot;$(TargetDir)CytoscapeLocalBrowser&quot; /D/E/C/I/H/Y" />
</Target>
</Project>
</Project>
4 changes: 4 additions & 0 deletions src/MSDIAL5/MsdialCore/Utility/DataObjConverter.cs
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Expand Up @@ -174,6 +174,10 @@ public static void SetRepresentativeProperty(AlignmentSpotProperty spot) {
Mz = new MzValue(spot.MassCenter, representative.ChromXsTop.Mz.Unit),
Drift = new DriftTime(alignedPeaks.Average(peak => peak.ChromXsTop.Drift.Value), representative.ChromXsTop.Drift.Unit),
};

if (spot.QuantMass > 0) {
spot.MassCenter = spot.QuantMass;
}
Comment on lines +178 to +180
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Copilot AI Mar 11, 2026

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SetRepresentativeProperty builds spot.TimesCenter (including Mz) using the current spot.MassCenter, but then conditionally overwrites spot.MassCenter with spot.QuantMass. This can leave TimesCenter.Mz inconsistent with MassCenter (and with the value later used as the spot's m/z). Consider moving the QuantMass→MassCenter assignment before constructing TimesCenter, or also updating spot.TimesCenter.Mz when MassCenter is overwritten (and ensure any dependent mass fields stay consistent).

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}

public static AlignmentChromPeakFeature? GetRepresentativePeak(IReadOnlyList<AlignmentChromPeakFeature> alignment) {
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4 changes: 3 additions & 1 deletion src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
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Expand Up @@ -76,6 +76,7 @@ private List<AlignmentSpotProperty> ResetQuantMasses(List<AlignmentSpotProperty>
var reference = _refer.Refer(spot.MatchResults.Representative);
if (reference is not null && _parameter.PeakPickBaseParam.IsInMassRange(reference.QuantMass)) {
spot.MassCenter = reference.QuantMass;
spot.QuantMass = reference.QuantMass;
results.Add(spot);
continue;
}
Expand All @@ -90,6 +91,7 @@ private List<AlignmentSpotProperty> ResetQuantMasses(List<AlignmentSpotProperty>

if (_parameter.IsRepresentativeQuantMassBasedOnBasePeakMz) {
spot.QuantMass = msdec.Spectrum.Argmax(s => s.Intensity).Mass;
spot.MassCenter = spot.QuantMass;
results.Add(spot);
continue;
}
Expand All @@ -110,7 +112,7 @@ private List<AlignmentSpotProperty> ResetQuantMasses(List<AlignmentSpotProperty>
else {
spot.QuantMass = msdec.Spectrum.Argmax(s => s.Intensity).Mass;
}

spot.MassCenter = spot.QuantMass;
results.Add(spot);
}
var counter = 0;
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