Ptm stoich#1
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… branch of mzlib. Code is untestested. Have seen some discrepancies with the quantity of quantified mods and their indexing.
…(uninitialized object). commit wip.
…iants can be written.
…upsOutput() was not consistent when run individually vs when run with all other tests. The ordering of the output was changing. Fixed to not look for the first data line but rather for the one with the right PG.
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… it to gui options. default will be to still write those mods out.
… into ptm_stoich
… into ptm_stoich
…t if exp design is no bueno) and meeting test expectations.
… iteration through collection without worrying about threading.
Resolve conflict in SpectralMatch.cs: - Keep ScanMetadata record approach from ptm_stoich branch - Add PrecursorScanDeconvolutionScore as separate property (not in ScanMetadata record)
Reverts the defensive default case that throws ArgumentOutOfRangeException for unhandled DeconvolutionType enum values (FromFile, Multiple). These values were added in mzLib 1.0.579 and are not yet supported by the GUI. Keeping the switch without a default allows unknown enum values to fall through silently, matching master behavior and fixing test failures in DeconHostViewModelTests and MetaDraw tests that transitively create a DeconHostViewModel. This is intentionally left as out-of-scope for this PR.
…ties and PeptideFdrInfo The protected SpectralMatch copy constructor (used by PeptideSpectralMatch.Clone for SILAC light/heavy conversion) was missing copies of: - IsobaricMassTagReporterIonIntensities (TMT/iTRAQ/diLeu reporter ions) - PeptideFdrInfo (peptide-level FDR stats) Both are now copied from the source PSM to the clone. Adds TestSilacClonePreservesQuantAndFdrData regression test.
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draft pr before opening pr upstream.