11using MassSpectrometry ;
2+ using MzLibUtil ;
23using Proteomics ;
34using Spectra ;
45using System ;
@@ -21,12 +22,12 @@ public class AnalysisEngine : MyEngine
2122 private readonly int maxModIsoforms ;
2223 private readonly PsmParent [ ] [ ] newPsms ;
2324 private readonly List < Protein > proteinList ;
24- private readonly List < MetaMorpheusModification > variableModifications ;
25- private readonly List < MetaMorpheusModification > fixedModifications ;
26- private readonly List < MetaMorpheusModification > localizeableModifications ;
25+ private readonly List < ModificationWithMass > variableModifications ;
26+ private readonly List < ModificationWithMass > fixedModifications ;
27+ private readonly List < ModificationWithMass > localizeableModifications ;
2728 private readonly Protease protease ;
2829 private readonly List < SearchMode > searchModes ;
29- private readonly IMsDataFile < IMzSpectrum < MzPeak > > myMsDataFile ;
30+ private readonly IMsDataFile < IMsDataScan < IMzSpectrum < IMzPeak > > > myMsDataFile ;
3031 private readonly Tolerance fragmentTolerance ;
3132 private readonly Action < BinTreeStructure , string > writeHistogramPeaksAction ;
3233 private readonly Action < List < NewPsmWithFdr > , string > writePsmsAction ;
@@ -40,7 +41,7 @@ public class AnalysisEngine : MyEngine
4041
4142 #region Public Constructors
4243
43- public AnalysisEngine ( PsmParent [ ] [ ] newPsms , Dictionary < CompactPeptide , HashSet < PeptideWithSetModifications > > compactPeptideToProteinPeptideMatching , List < Protein > proteinList , List < MetaMorpheusModification > variableModifications , List < MetaMorpheusModification > fixedModifications , List < MetaMorpheusModification > localizeableModifications , Protease protease , List < SearchMode > searchModes , IMsDataFile < IMzSpectrum < MzPeak > > myMSDataFile , Tolerance fragmentTolerance , Action < BinTreeStructure , string > action1 , Action < List < NewPsmWithFdr > , string > action2 , Action < List < ProteinGroup > , string > action3 , bool doParsimony , int maximumMissedCleavages , int maxModIsoforms , bool doHistogramAnalysis , List < ProductType > lp , double binTol ) : base ( 2 )
44+ public AnalysisEngine ( PsmParent [ ] [ ] newPsms , Dictionary < CompactPeptide , HashSet < PeptideWithSetModifications > > compactPeptideToProteinPeptideMatching , List < Protein > proteinList , List < ModificationWithMass > variableModifications , List < ModificationWithMass > fixedModifications , List < ModificationWithMass > localizeableModifications , Protease protease , List < SearchMode > searchModes , IMsDataFile < IMsDataScan < IMzSpectrum < IMzPeak > > > myMSDataFile , Tolerance fragmentTolerance , Action < BinTreeStructure , string > action1 , Action < List < NewPsmWithFdr > , string > action2 , Action < List < ProteinGroup > , string > action3 , bool doParsimony , int maximumMissedCleavages , int maxModIsoforms , bool doHistogramAnalysis , List < ProductType > lp , double binTol ) : base ( 2 )
4445 {
4546 this . doParsimony = doParsimony ;
4647 this . doHistogramAnalysis = doHistogramAnalysis ;
@@ -203,8 +204,8 @@ public Dictionary<CompactPeptide, HashSet<PeptideWithSetModifications>> ApplyPro
203204 {
204205 HashSet < Protein > proteinsWithThisBaseSeq ;
205206 peptideBaseSeqProteinListMatch . TryGetValue ( newBaseSeq , out proteinsWithThisBaseSeq ) ;
206-
207- foreach ( var protein in proteinsWithThisBaseSeq )
207+
208+ foreach ( var protein in proteinsWithThisBaseSeq )
208209 {
209210 HashSet < CompactPeptide > t ;
210211 proteinToPeptidesMatching . TryGetValue ( protein , out t ) ;
@@ -728,12 +729,13 @@ private static void IdentifyUnimodBins(BinTreeStructure myTreeStructure, double
728729 {
729730 var ok = new HashSet < string > ( ) ;
730731 var okformula = new HashSet < string > ( ) ;
731- foreach ( var hm in UnimodDeserialized . modifications )
732+ foreach ( var hm in UnimodDeserialized )
732733 {
733- if ( Math . Abs ( hm . mono_mass - bin . MassShift ) <= v )
734+ var theMod = hm as ModificationWithMassAndCf ;
735+ if ( Math . Abs ( theMod . monoisotopicMass - bin . MassShift ) <= v )
734736 {
735- ok . Add ( hm . full_name ) ;
736- okformula . Add ( hm . composition ) ;
737+ ok . Add ( hm . id ) ;
738+ okformula . Add ( theMod . chemicalFormula . Formula ) ;
737739 }
738740 }
739741 bin . UnimodId = string . Join ( " or " , ok ) ;
@@ -748,10 +750,12 @@ private static void IdentifyUniprotBins(BinTreeStructure myTreeStructure, double
748750 var ok = new HashSet < string > ( ) ;
749751 foreach ( var hm in UniprotDeseralized )
750752 {
751- if ( Math . Abs ( hm . Value . MonoisotopicMass - bin . MassShift ) <= v )
752- {
753- ok . Add ( hm . Value . NameAndSites ) ;
754- }
753+ var theMod = hm as ModificationWithMass ;
754+ if ( theMod != null )
755+ if ( Math . Abs ( theMod . monoisotopicMass - bin . MassShift ) <= v )
756+ {
757+ ok . Add ( hm . id ) ;
758+ }
755759 }
756760 bin . uniprotID = string . Join ( " or " , ok ) ;
757761 }
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