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* mzlib * Retention time prediction contract change * revised protease and rnase custom loading * fix tests * more tests
…ttings button, and settings re-render
Updates the mzLib PackageReference from 1.0.578 to 1.0.579 across CMD, EngineLayer, GUI, GuiFunctions, TaskLayer, and Test. 1.0.579 ships mzLib PR smith-chem-wisc#1046 (unified IRetentionTimePredictor with a batch method and Koina RetentionTimeModel implementation); the legacy single-input methods remain on the interface as obsolete, so no MetaMorpheus call sites are affected. Solution builds cleanly. Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…th-chem-wisc#2661) * feat(pep): add PrecursorDeconvolutionScore feature for bottom-up Wires mzLib's method-agnostic envelope-quality score (PR smith-chem-wisc#1054, shipped in mzLib 1.0.579 -- IsotopicEnvelope.GenericScore) into the PEP analysis pipeline as a new PsmData feature. Bottom-up search type only in this PR; once approved, the same wiring will be extended to top-down, crosslink, and RNA using bottom-up as the template. Data path GetMs2Scans (MetaMorpheusTask.cs:274) computes envelope.GetOrComputeGenericScore(commonParameters.PrecursorDeconvolutionParameters) for each yielded precursor envelope. The score is stashed on the new Precursor.DeconvolutionScore field, threaded into the new Ms2ScanWithSpecificMass.PrecursorDeconvolutionScore constructor parameter, copied onto SpectralMatch.PrecursorScanDeconvolutionScore (mirroring the existing PrecursorScanIntensity/PrecursorFractionalIntensity pattern), and finally read by PEPAnalysisEngine.CreateOnePsmDataEntry to populate the new PsmData.PrecursorDeconvolutionScore field. [LoadColumn(29), direction +1 in assumedAttributeDirection -- higher score = better Averagine match = more likely target.] Added to trainingInfos["standard"] only. Sentinel handling Default value is 0 when the precursor was constructed from scan-header data alone (the UseProvidedPrecursorInfo path) and no envelope was deconvoluted. mzLib's scorer also returns near-zero for a maximally-bad envelope, so the model cannot strictly distinguish these two cases -- an accepted limitation for now per scope discussion. Test baseline updates FdrTest.TestPsmData -- trainingInfo["standard"] gains "PrecursorDeconvolutionScore"; assumedAttributeDirection gains PrecursorDeconvolutionScore=1; standardToString gains "\t28". PostSearchAnalysisTaskTests.AllResultsAndResultsTxtContainsCorrectValues_PepQValue_BottomUp -- counts shift modestly because the model has a new feature: All target PSMs: 382 -> 384 All target protein groups: 145 -> 144 Per-file PSMs: 190 -> 191 Per-file protein groups: 145 -> 144 Peptide counts unchanged. Verification Full Test.csproj suite: 1446 passed, 0 failed, 1 skipped, 7m 27s. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Fix comment formatting in MetaMorpheusTask.cs --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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