From 06ca65de5e24cd1527a8c9e41c37b0c5a0264645 Mon Sep 17 00:00:00 2001 From: Alex Date: Fri, 13 Sep 2024 16:44:31 -0500 Subject: [PATCH] Removed unintended changes --- .../EngineLayer/PeptideSpectralMatch.cs | 4 -- MetaMorpheus/EngineLayer/SpectralMatch.cs | 40 ------------------- .../SearchTask/PostSearchAnalysisTask.cs | 1 + 3 files changed, 1 insertion(+), 44 deletions(-) diff --git a/MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs b/MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs index ee14f5770..1e23205e0 100644 --- a/MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs +++ b/MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs @@ -47,10 +47,6 @@ protected PeptideSpectralMatch(SpectralMatch psm, List<(int Notch, IBioPolymerWi : base(psm, bestMatchingPeptides) { } - - public PeptideSpectralMatch(SpectralMatch psm) : base(psm) - { - } #endregion diff --git a/MetaMorpheus/EngineLayer/SpectralMatch.cs b/MetaMorpheus/EngineLayer/SpectralMatch.cs index ee540d81c..299f13b00 100644 --- a/MetaMorpheus/EngineLayer/SpectralMatch.cs +++ b/MetaMorpheus/EngineLayer/SpectralMatch.cs @@ -379,46 +379,6 @@ protected SpectralMatch(SpectralMatch psm, List<(int Notch, IBioPolymerWithSetMo SpectralAngle = psm.SpectralAngle; } - public SpectralMatch(SpectralMatch psm) - { - _BestMatchingBioPolymersWithSetMods = psm._BestMatchingBioPolymersWithSetMods; - BaseSequence = PsmTsvWriter.Resolve(_BestMatchingBioPolymersWithSetMods.Select(b => b.Pwsm.BaseSequence)).ResolvedValue; - FullSequence = PsmTsvWriter.Resolve(_BestMatchingBioPolymersWithSetMods.Select(b => b.Pwsm.FullSequence)).ResolvedValue; - - ModsChemicalFormula = psm.ModsChemicalFormula; - Notch = psm.Notch; - BioPolymerWithSetModsLength = psm.BioPolymerWithSetModsLength; - OneBasedStartResidue = psm.OneBasedStartResidue; - OneBasedEndResidue = psm.OneBasedEndResidue; - BioPolymerWithSetModsMonoisotopicMass = psm.BioPolymerWithSetModsMonoisotopicMass; - ParentLength = psm.ParentLength; - Accession = psm.Accession; - Organism = psm.Organism; - MatchedFragmentIons = psm.MatchedFragmentIons; - PsmCount = psm.PsmCount; - ModsIdentified = psm.ModsIdentified; - LocalizedScores = psm.LocalizedScores; - ScanNumber = psm.ScanNumber; - PrecursorScanNumber = psm.PrecursorScanNumber; - ScanRetentionTime = psm.ScanRetentionTime; - ScanExperimentalPeaks = psm.ScanExperimentalPeaks; - TotalIonCurrent = psm.TotalIonCurrent; - ScanPrecursorCharge = psm.ScanPrecursorCharge; - ScanPrecursorMonoisotopicPeakMz = psm.ScanPrecursorMonoisotopicPeakMz; - ScanPrecursorMass = psm.ScanPrecursorMass; - FullFilePath = psm.FullFilePath; - ScanIndex = psm.ScanIndex; - FdrInfo = psm.FdrInfo; - Score = psm.Score; - Xcorr = psm.Xcorr; - RunnerUpScore = psm.RunnerUpScore; - IsDecoy = psm.IsDecoy; - IsContaminant = psm.IsContaminant; - DigestionParams = psm.DigestionParams; - BioPolymersWithSetModsToMatchingFragments = psm.BioPolymersWithSetModsToMatchingFragments; - SpectralAngle = psm.SpectralAngle; - } - #endregion #region FDR diff --git a/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs b/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs index 529ee8b0e..e30b4549a 100644 --- a/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs +++ b/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs @@ -139,6 +139,7 @@ private void CalculatePsmAndPeptideFdr(List psms, string analysis Status("Estimating PSM FDR...", Parameters.SearchTaskId); new FdrAnalysisEngine(psms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters, new List { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run(); + Status("Done estimating PSM FDR!", Parameters.SearchTaskId); }