[Ignore Coverage] #4 - Digestion params generalization

MetaMorpheus/EngineLayer/CommonParameters.cs

@@ -6,6 +6,7 @@
 using System.Collections.Generic;
 using System.Reflection;
 using Nett;
+using Omics.Digestion;
 using Omics.Fragmentation.Peptide;
 
 namespace EngineLayer
@@ -46,7 +47,7 @@ public CommonParameters(
  Tolerance precursorMassTolerance = null, 
  Tolerance deconvolutionMassTolerance = null,
  int maxThreadsToUsePerFile = -1, 
- DigestionParams digestionParams = null, 
+ IDigestionParams digestionParams = null, 
  IEnumerable<(string, string)> listOfModsVariable = null, 
  IEnumerable<(string, string)> listOfModsFixed = null,
  bool assumeOrphanPeaksAreZ1Fragments = true, 
@@ -155,7 +156,7 @@ public int DeconvolutionMaxAssumedChargeState
  /// </summary>
  public double PepQValueThreshold { get; private set; }
  public double ScoreCutoff { get; private set; }
- public DigestionParams DigestionParams { get; private set; }
+ public IDigestionParams DigestionParams { get; private set; }
  public bool ReportAllAmbiguity { get; private set; }
  public int? NumberOfPeaksToKeepPerWindow { get; private set; }
  public double? MinimumAllowedIntensityRatioToBasePeak { get; private set; }
@@ -233,17 +234,7 @@ public CommonParameters CloneWithNewTerminus(FragmentationTerminus? terminus = n
  PrecursorMassTolerance,
  DeconvolutionMassTolerance,
  MaxThreadsToUsePerFile,
- new DigestionParams(
- DigestionParams.Protease.Name,
- DigestionParams.MaxMissedCleavages,
- DigestionParams.MinPeptideLength,
- DigestionParams.MaxPeptideLength,
- DigestionParams.MaxModificationIsoforms,
- DigestionParams.InitiatorMethionineBehavior,
- DigestionParams.MaxModsForPeptide,
- DigestionParams.SearchModeType,
- terminus.Value //possibly changed
- ),
+ (DigestionParams)DigestionParams.Clone(terminus),
  ListOfModsVariable,
  ListOfModsFixed,
  AssumeOrphanPeaksAreZ1Fragments,

MetaMorpheus/EngineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs

@@ -320,9 +320,10 @@ private void FindCrosslinkedPeptide(Ms2ScanWithSpecificMass scan, List<(double,
  possibleMatches = new List<CrosslinkSpectralMatch>();
  }
 
+ var initiatorMethionine = ((DigestionParams)CommonParameters.DigestionParams).InitiatorMethionineBehavior;
  foreach (var id in idsOfPeptidesPossiblyObserved)
  {
- List<int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, PeptideIndex[id], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, PeptideIndex[id], initiatorMethionine, CleaveAtCrosslinkSite);
 
 
  foreach (var pre in precursors)
@@ -397,7 +398,7 @@ private void FindCrosslinkedPeptide(Ms2ScanWithSpecificMass scan, List<(double,
  }
  }
  }
- else if (pre.Item1 - PrecursorMassTable[id] >= (CommonParameters.DigestionParams.MinPeptideLength * 50))
+ else if (pre.Item1 - PrecursorMassTable[id] >= (CommonParameters.DigestionParams.MinLength * 50))
  {
  if (possibleCrosslinkLocations == null)
  {
@@ -419,14 +420,14 @@ private void FindCrosslinkedPeptide(Ms2ScanWithSpecificMass scan, List<(double,
  {
  seenPair.Add(key);
 
- List<int> possibleBetaCrosslinkSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, NextPeptideIndex[betaMassLowIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleBetaCrosslinkSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, NextPeptideIndex[betaMassLowIndex], initiatorMethionine, CleaveAtCrosslinkSite);
 
  if (possibleBetaCrosslinkSites == null)
  {
  continue;
  }
 
- CrosslinkSpectralMatch x = LocalizeCrosslinkSites(scan, id, betaMassLowIndex, Crosslinker, experimentFragmentMasses, intensityRanks);
+ CrosslinkSpectralMatch x = LocalizeCrosslinkSites(scan, id, betaMassLowIndex, Crosslinker, experimentFragmentMasses, intensityRanks, initiatorMethionine);
 
  if (x != null)
  {
@@ -459,7 +460,7 @@ private void FindCrosslinkedPeptide(Ms2ScanWithSpecificMass scan, List<(double,
  /// <summary>
  /// Localizes the crosslink position on the alpha and beta peptides
  /// </summary>
- private CrosslinkSpectralMatch LocalizeCrosslinkSites(Ms2ScanWithSpecificMass theScan, int alphaIndex, int betaIndex, Crosslinker crosslinker, double[] experimentFragmentMasses, int[] intensityRanks)
+ private CrosslinkSpectralMatch LocalizeCrosslinkSites(Ms2ScanWithSpecificMass theScan, int alphaIndex, int betaIndex, Crosslinker crosslinker, double[] experimentFragmentMasses, int[] intensityRanks, InitiatorMethionineBehavior initiatorMethionineBehavior)
  {
  CrosslinkSpectralMatch localizedCrosslinkedSpectralMatch = null;
 
@@ -468,20 +469,20 @@ private CrosslinkSpectralMatch LocalizeCrosslinkSites(Ms2ScanWithSpecificMass th
 
  if (crosslinker.CrosslinkerModSites.Equals(crosslinker.CrosslinkerModSites2))
  {
- List<int> possibleAlphaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), PeptideIndex[alphaIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
- List<int> possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), NextPeptideIndex[betaIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleAlphaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), PeptideIndex[alphaIndex], initiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), NextPeptideIndex[betaIndex], initiatorMethionineBehavior, CleaveAtCrosslinkSite);
 
  pairs.Add(new Tuple<List<int>, List<int>>(possibleAlphaXlSites, possibleBetaXlSites));
  }
  else
  {
- List<int> possibleAlphaXlSites =CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), PeptideIndex[alphaIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
- List<int> possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites2.ToCharArray(), NextPeptideIndex[betaIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleAlphaXlSites =CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), PeptideIndex[alphaIndex], initiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites2.ToCharArray(), NextPeptideIndex[betaIndex], initiatorMethionineBehavior, CleaveAtCrosslinkSite);
 
  pairs.Add(new Tuple<List<int>, List<int>>(possibleAlphaXlSites, possibleBetaXlSites));
 
- List<int> possibleAlphaXlSites2 = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites2.ToCharArray(), PeptideIndex[alphaIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
- List<int> possibleBetaXlSites2 = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), NextPeptideIndex[betaIndex], CommonParameters.DigestionParams.InitiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleAlphaXlSites2 = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites2.ToCharArray(), PeptideIndex[alphaIndex], initiatorMethionineBehavior, CleaveAtCrosslinkSite);
+ List<int> possibleBetaXlSites2 = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), NextPeptideIndex[betaIndex], initiatorMethionineBehavior, CleaveAtCrosslinkSite);
 
  pairs.Add(new Tuple<List<int>, List<int>>(possibleAlphaXlSites2, possibleBetaXlSites2));
  }

MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs

@@ -45,7 +45,7 @@ private void DoFalseDiscoveryRateAnalysis(FdrAnalysisResults myAnalysisResults)
  if (GlobalVariables.StopLoops) { return; }
 
  // calculate FDR on a per-protease basis (targets and decoys for a specific protease)
- var psmsGroupedByProtease = AllPsms.GroupBy(p => p.DigestionParams.Protease);
+ var psmsGroupedByProtease = AllPsms.GroupBy(p => p.DigestionParams.DigestionAgent);
 
  foreach (var proteasePsms in psmsGroupedByProtease)
  {
@@ -151,7 +151,7 @@ public void Compute_PEPValue(FdrAnalysisResults myAnalysisResults)
  if (AllPsms.Count > 100)
  {
  string searchType = "standard";
- if (AllPsms[0].DigestionParams.Protease.Name == "top-down")
+ if (AllPsms[0].DigestionParams.DigestionAgent.Name == "top-down")
  {
  searchType = "top-down";
  }

MetaMorpheus/EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs

@@ -745,7 +745,7 @@ public static PsmData CreateOnePsmDataEntry(string searchType, List<(string file
  hasSpectralAngle = 1;
  }
 
- if (psm.DigestionParams.Protease.Name != "top-down")
+ if (psm.DigestionParams.DigestionAgent.Name != "top-down")
  {
  missedCleavages = selectedPeptide.MissedCleavages;
  bool fileIsCzeSeparationType = fileSpecificParameters.Any(p => Path.GetFileName(p.fileName) == Path.GetFileName(psm.FullFilePath) && p.fileSpecificParameters.SeparationType == "CZE");

MetaMorpheus/EngineLayer/GlycoSearch/Node.cs

@@ -1,18 +1,8 @@
 
 namespace EngineLayer
 {
-
  public class Node
  {
- public Node(char v, Node l, Node r, Node m)
- {
- Value = v;
- LeftChild = l;
- RightChild = r;
- MiddleChild = m;
- Level = null;
- }
-
  public Node(char v)
  {
  Value = v;

MetaMorpheus/EngineLayer/Indexing/IndexingEngine.cs

@@ -9,6 +9,7 @@
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using Omics;
 using Omics.Fragmentation.Peptide;
 using Omics.Modifications;
 using UsefulProteomicsDatabases;
@@ -68,16 +69,18 @@
  sb.AppendLine("Dissociation Type: " + CommonParameters.DissociationType);
  sb.AppendLine("Contaminant Handling: " + TcAmbiguity);
 
- sb.AppendLine("protease: " + CommonParameters.DigestionParams.Protease);
- sb.AppendLine("initiatorMethionineBehavior: " + CommonParameters.DigestionParams.InitiatorMethionineBehavior);
+ sb.AppendLine("protease: " + CommonParameters.DigestionParams.DigestionAgent);
+ if (CommonParameters.DigestionParams is DigestionParams digestionParams)
+ sb.AppendLine("initiatorMethionineBehavior: " + digestionParams.InitiatorMethionineBehavior);
  sb.AppendLine("maximumMissedCleavages: " + CommonParameters.DigestionParams.MaxMissedCleavages);
- sb.AppendLine("minPeptideLength: " + CommonParameters.DigestionParams.MinPeptideLength);
- sb.AppendLine("maxPeptideLength: " + CommonParameters.DigestionParams.MaxPeptideLength);
+ sb.AppendLine("minPeptideLength: " + CommonParameters.DigestionParams.MinLength);
+ sb.AppendLine("maxPeptideLength: " + CommonParameters.DigestionParams.MaxLength);
  sb.AppendLine("maximumVariableModificationIsoforms: " + CommonParameters.DigestionParams.MaxModificationIsoforms);
  sb.AppendLine("digestionTerminus: " + CommonParameters.DigestionParams.FragmentationTerminus);
- sb.AppendLine("maxModsForEachPeptide: " + CommonParameters.DigestionParams.MaxModsForPeptide);
+ sb.AppendLine("maxModsForEachPeptide: " + CommonParameters.DigestionParams.MaxMods);
  sb.AppendLine("cleavageSpecificity: " + CommonParameters.DigestionParams.SearchModeType);
- sb.AppendLine("specificProtease: " + CommonParameters.DigestionParams.SpecificProtease);
+ if (CommonParameters.DigestionParams is DigestionParams digestionParam)
+ sb.AppendLine("specificProtease: " + digestionParam.SpecificProtease);
  sb.AppendLine("maximumFragmentSize" + (int)Math.Round(MaxFragmentSize));
 
  sb.Append("Localizeable mods: " + ProteinList.Select(b => b.OneBasedPossibleLocalizedModifications.Count).Sum());
@@ -92,6 +95,9 @@
  // digest database
  List<PeptideWithSetModifications> peptides = new List<PeptideWithSetModifications>();
 
+ if (CommonParameters.DigestionParams is not DigestionParams digestionParams)
+ throw new MetaMorpheusException("Digestion parameters must be of type DigestionParams. Not yet implemented for Rna Digestion");
+
  int maxThreadsPerFile = CommonParameters.MaxThreadsToUsePerFile;
  int[] threads = Enumerable.Range(0, maxThreadsPerFile).ToArray();
  Parallel.ForEach(threads, (i) =>
@@ -103,7 +109,7 @@
  // Stop loop if canceled
  if (GlobalVariables.StopLoops) { return; }
 
- localPeptides.AddRange(ProteinList[i].Digest(CommonParameters.DigestionParams, FixedModifications, VariableModifications, SilacLabels, TurnoverLabels));
+ localPeptides.AddRange(ProteinList[i].Digest(digestionParams, FixedModifications, VariableModifications, SilacLabels, TurnoverLabels));
 
  progress++;
  var percentProgress = (int)((progress / ProteinList.Count) * 100);
@@ -130,7 +136,7 @@
  {
  precursorIndex = CreateNewPrecursorIndex(peptides);
  }
- bool addInteriorTerminalModsToPrecursorIndex = GeneratePrecursorIndex && CommonParameters.DigestionParams.Protease.Name.Contains("single");
+ bool addInteriorTerminalModsToPrecursorIndex = GeneratePrecursorIndex && CommonParameters.DigestionParams.DigestionAgent.Name.Contains("single");
  List<Modification> terminalModifications = addInteriorTerminalModsToPrecursorIndex ?
  NonSpecificEnzymeSearchEngine.GetVariableTerminalMods(CommonParameters.DigestionParams.FragmentationTerminus, VariableModifications) :
  null;