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Fix MS-DIAL Console lcimms crash in alignment export (drift spots had no deconvolution result) - #838
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The lcimms command crashed with ArgumentOutOfRangeException in AlignmentCSVExporter.Export once alignment finished. The exporter (and MztabFormatExporter) index the deconvolution results by MasterAlignmentID for the drift spots as well as the RT spots, but the console loaded one result per RT spot only, so the first drift spot overflowed the list. Read each RT spot followed by its drift spots, the order LcimmsAlignmentRefiner numbers them in and the GUI's AlignmentFileBeanModel.LoadMSDecResultsFromEachFiles reads them in, through RepresentativeDeconvolutionReader as LcmsProcess does. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Problem
MSDIALCUI lcimmscrashed withArgumentOutOfRangeExceptioninAlignmentCSVExporter.Exportafter peak picking and alignment had finished, so no.mdalign/.mdmsp/.mzTabwas written. This was already broken in console release 5.5.260820. It is not a regression from the release/msdial-5.5 merge.Cause
LcimmsProcess.LoadRepresentativeDeconvolutionsloaded oneMSDecResultper top-level (RT) alignment spot.LcimmsAlignmentRefinernumbersMasterAlignmentIDacross each RT spot followed by its drift spots.AlignmentCSVExporterandMztabFormatExporterindex the results bydriftSpot.MasterAlignmentID, so the list ran out at the first drift spot.AlignmentMspExporter.BatchExportonly indexes RT spots byMasterAlignmentID, so it works once the list is complete.Fix (console only)
The loader now returns each RT spot followed by its drift spots, in the order the refiner numbers them. The GUI's
AlignmentFileBeanModel.LoadMSDecResultsFromEachFilesreads them in the same order. Results are read throughRepresentativeDeconvolutionReader, asLcmsProcessalready does. The shared exporters are not changed.Verification
LcimmsProcessTests.EveryRtAndDriftSpotHasItsResultAtItsMasterAlignmentId. It passes, together with the existingRepresentativeDeconvolutionReaderTests(13/13).4D-Lipidmics_pos_5times_2uL-inj(kidney1_5tims_pos_P2-E-2_1_15262.d and plasma1_5tims_pos_P2-F-2_1_15252.d). The method came fromMSDIALCUI template lcimms, withTarget omics: Lipidomicsand 8 threads.MSDIALCUI lcimms -i … -o … -m method.txt -pexits 0 and writes:.mdalign: 14,673 rows (6,174 RT spots and 8,499 drift spots).mdmsp: 6,174 spectra.mzTab: 14,673 SML rows.mdpeak/.mdmsp🤖 Generated with Claude Code