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nbollis wants to merge 20 commits into master from KeepMoreResultsAround

MetaMorpheus/EngineLayer/BioPolymerNotchFragmentIonComparer.cs

This file was deleted.

MetaMorpheus/EngineLayer/Calibration/DataPointAcquisitionEngine.cs

            
                      Original file line number
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    @@ -71,10 +71,10 @@ protected override MetaMorpheusEngineResults RunSpecific()
  
                        int ms2scanNumber = identification.ScanNumber;

                        int peptideCharge = identification.ScanPrecursorCharge;

                        //skip if ambiguous

                        if (identification.FullSequence == null || identification.BestMatchingBioPolymersWithSetMods.Any(p => p.Peptide.AllModsOneIsNterminus.Any(m => m.Value.ChemicalFormula == null)))

                        if (identification.FullSequence == null || identification.BestMatchingBioPolymersWithSetMods.Any(p => p.WithSetMods.AllModsOneIsNterminus.Any(m => m.Value.ChemicalFormula == null)))

                            continue;

                        var representativeSinglePeptide = identification.BestMatchingBioPolymersWithSetMods.First().Peptide;

                        var representativeSinglePeptide = identification.BestMatchingBioPolymersWithSetMods.First().WithSetMods;

                        // Get the peptide, don't forget to add the modifications!!!!

                        var SequenceWithChemicalFormulas = representativeSinglePeptide.SequenceWithChemicalFormulas;

MetaMorpheus/EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs

            
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    @@ -3,7 +3,6 @@
  
    using MzLibUtil;

    using Omics;

    using Omics.Fragmentation;

    using Proteomics.ProteolyticDigestion;

    using System;

    using System.Collections.Generic;

    using System.Linq;

    @@ -129,18 +128,16 @@ public static void CalculateSpectralAngles(SpectralLibrary spectralLibrary, Spec
  
                            if (psms[i] != null)

                            {

                                Ms2ScanWithSpecificMass scan = arrayOfSortedMs2Scans[psms[i].ScanIndex];

                                List<(int, IBioPolymerWithSetMods)> pwsms = new();

                                List<double> pwsmSpectralAngles = new();

                                foreach (var (Notch, Peptide) in psms[i].BestMatchingBioPolymersWithSetMods)

                                foreach (var bestMatch in psms[i].BestMatchingBioPolymersWithSetMods)

                                {

                                    //if peptide is target, directly look for the target's spectrum in the spectral library

                                    if (!Peptide.Parent.IsDecoy && spectralLibrary.TryGetSpectrum(Peptide.FullSequence, scan.PrecursorCharge, out var librarySpectrum))

                                    if (!bestMatch.IsDecoy && spectralLibrary.TryGetSpectrum(bestMatch.FullSequence, scan.PrecursorCharge, out var librarySpectrum))

                                    {

                                        SpectralSimilarity s = new SpectralSimilarity(scan.TheScan.MassSpectrum, librarySpectrum.XArray, librarySpectrum.YArray,

                                            SpectralSimilarity.SpectrumNormalizationScheme.SquareRootSpectrumSum, fileSpecificParameters.ProductMassTolerance.Value, false);

                                        if (s.SpectralContrastAngle().HasValue)

                                        {

                                            pwsms.Add((Notch, Peptide));

                                            pwsmSpectralAngles.Add((double)s.SpectralContrastAngle());

                                        }

                                    }

MetaMorpheus/EngineLayer/CrosslinkSearch/CrosslinkSpectralMatch.cs

            
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    @@ -25,7 +25,7 @@ public CrosslinkSpectralMatch(
  
                XLTotalScore = score;

                _BestMatchingBioPolymersWithSetMods.Clear();

                _BestMatchingBioPolymersWithSetMods.Add((0, theBestPeptide));

                _BestMatchingBioPolymersWithSetMods.Add(new SpectrumMatch.TentativeSpectralMatch(0, theBestPeptide, matchedFragmentIons));

            }

    @@ -127,8 +127,8 @@ public static bool IsIntraCsm(CrosslinkSpectralMatch csm)
  
                if (csm.Accession == null)

                {

                    var alphaProteins = csm.BestMatchingBioPolymersWithSetMods.Select(p => p.Peptide.Parent.Accession).ToList();

                    var betaProteins = csm.BetaPeptide.BestMatchingBioPolymersWithSetMods.Select(p => p.Peptide.Parent.Accession).ToList();

                    var alphaProteins = csm.BestMatchingBioPolymersWithSetMods.Select(p => p.WithSetMods.Parent.Accession).ToList();

                    var betaProteins = csm.BetaPeptide.BestMatchingBioPolymersWithSetMods.Select(p => p.WithSetMods.Parent.Accession).ToList();

                    foreach (var alpha in alphaProteins)

                    {

    @@ -373,7 +373,7 @@ public override string ToString()
  
                }

                sb.Append("\t"); //Intentionally left empty for readability in the tsv file.

                List<PeptideWithSetModifications> pepsWithMods = BestMatchingBioPolymersWithSetMods.Select(p => p.Peptide as PeptideWithSetModifications).ToList();

                List<PeptideWithSetModifications> pepsWithMods = BestMatchingBioPolymersWithSetMods.Select(p => p.WithSetMods as PeptideWithSetModifications).ToList();

                var proteinAccessionString = Accession ?? PsmTsvWriter.Resolve(pepsWithMods.Select(b => b.Protein.Accession), FullSequence).ResolvedString;

                sb.Append(proteinAccessionString + "\t");

                sb.Append(XlProteinPos + (XlProteinPosLoop.HasValue ? "~" + XlProteinPosLoop.Value : null) + "\t");

    @@ -422,7 +422,7 @@ public override string ToString()
  
                if (BetaPeptide != null)

                {

                    sb.Append("\t"); //Intentionally left empty for readability in the tsv file.

                    List<PeptideWithSetModifications> betaPepsWithMods = BetaPeptide.BestMatchingBioPolymersWithSetMods.Select(p => p.Peptide as PeptideWithSetModifications).ToList();

                    List<PeptideWithSetModifications> betaPepsWithMods = BetaPeptide.BestMatchingBioPolymersWithSetMods.Select(p => p.WithSetMods as PeptideWithSetModifications).ToList();

                    var betaProteinAccessionString = BetaPeptide.Accession ?? PsmTsvWriter.Resolve(betaPepsWithMods.Select(b => b.Protein.Accession), FullSequence).ResolvedString;

                    sb.Append(betaProteinAccessionString + "\t");

                    sb.Append(BetaPeptide.XlProteinPos + "\t");

MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs

-Original file line number
+Diff line change
@@ Expand Up @@
                         // e.g. if the PSM matched to 1 target and 2 decoys, it counts as 2/3 decoy
                         double decoyHits = 0;
                         double totalHits = 0;
-                        var hits = psm.BestMatchingBioPolymersWithSetMods.GroupBy(p => p.Peptide.FullSequence);
+                        var hits = psm.BestMatchingBioPolymersWithSetMods.GroupBy(p => p.FullSequence);
                         foreach (var hit in hits)
                         {
-                            if (hit.First().Peptide.Parent.IsDecoy)
+                            if (hit.First().IsDecoy)
                             {
                                 decoyHits++;
                             }
@@ Expand Down @@

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