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Fix "--reintegrate-model-name=Default" #3648

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Merged
merged 2 commits into from
Oct 17, 2025
Merged

Fix "--reintegrate-model-name=Default" #3648

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cd5640d
Fix "--reintegrate-model-name=Default"
nickshulman Oct 17, 2025
0088202
Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Sk…
nickshulman Oct 17, 2025
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5 changes: 5 additions & 0 deletions pwiz_tools/Skyline/CommandLine.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -2643,6 +2643,11 @@ private bool ReintegratePeaks(CommandArgs commandArgs)
_out.WriteLine(SkylineResources.CommandLine_ReintegratePeaks_Error__Unknown_peak_scoring_model___0__);
return false;
}
if (Equals(scoringModel, LegacyScoringModel.DEFAULT_UNTRAINED_MODEL))
{
scoringModel = LegacyScoringModel.DEFAULT_MODEL;
}

modelAndFeatures = new ModelAndFeatures(scoringModel, null);
}

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12 changes: 3 additions & 9 deletions pwiz_tools/Skyline/Model/SrmDocument.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -1154,15 +1154,9 @@ private SrmSettings UpdateHasHeavyModifications(SrmSettings settings)
.Any(mods => mods.Modifications.Count > 0);
if (!hasHeavyModifications && HasSmallMolecules)
{
foreach (var molecule in Molecules)
{
if (molecule.TransitionGroups.Any(group =>
!ReferenceEquals(group.TransitionGroup.LabelType, IsotopeLabelType.light)))
{
hasHeavyModifications = true;
break;
}
}
hasHeavyModifications = Molecules
.SelectMany(mol => mol?.TransitionGroups ?? Array.Empty<TransitionGroupDocNode>())
.Any(group => !ReferenceEquals(group.TransitionGroup.LabelType, IsotopeLabelType.light));
}
if (hasHeavyModifications == settings.PeptideSettings.Modifications.HasHeavyModifications)
{
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