public CompactPeptideWithModifiedMass(CompactPeptideBase cp, double monoisotopicMassIncludingFixedMods) { CTerminalMasses = cp.CTerminalMasses; NTerminalMasses = cp.NTerminalMasses; MonoisotopicMassIncludingFixedMods = cp.MonoisotopicMassIncludingFixedMods; ModifiedMass = monoisotopicMassIncludingFixedMods; }
public void AddOrReplace(CompactPeptideBase compactPeptide, double score, int notch, bool reportAllAmbiguity) { if (score - Score > tolForScoreDifferentiation) //if new score beat the old score, overwrite it { compactPeptides = new Dictionary <CompactPeptideBase, Tuple <int, HashSet <PeptideWithSetModifications> > > { { compactPeptide, new Tuple <int, HashSet <PeptideWithSetModifications> >(notch, null) } }; Score = score; } else if (score - Score > -tolForScoreDifferentiation && reportAllAmbiguity) //else if the same score and ambiguity is allowed { compactPeptides[compactPeptide] = new Tuple <int, HashSet <PeptideWithSetModifications> >(notch, null); } }
public PeptideSpectralMatch(CompactPeptideBase peptide, int notch, double score, int scanIndex, IScan scan) { this.ScanIndex = scanIndex; this.FullFilePath = scan.FullFilePath; this.ScanNumber = scan.OneBasedScanNumber; this.PrecursorScanNumber = scan.OneBasedPrecursorScanNumber; this.ScanRetentionTime = scan.RetentionTime; this.ScanExperimentalPeaks = scan.NumPeaks; this.TotalIonCurrent = scan.TotalIonCurrent; this.ScanPrecursorCharge = scan.PrecursorCharge; this.ScanPrecursorMonoisotopicPeakMz = scan.PrecursorMonoisotopicPeakMz; this.ScanPrecursorMass = scan.PrecursorMass; AddOrReplace(peptide, score, notch, true); this.AllScores = new List <int>(new int[(int)Math.Floor(score) + 1]); this.AllScores[AllScores.Count - 1]++; MatchedIonDictOnlyMatches = new Dictionary <ProductType, double[]>(); ProductMassErrorDa = new Dictionary <ProductType, double[]>(); ProductMassErrorPpm = new Dictionary <ProductType, double[]>(); }
public PeptideSpectralMatch(CompactPeptideBase peptide, int notch, double score, int scanIndex, IScan scan, DigestionParams digestionParams) { ScanIndex = scanIndex; FullFilePath = scan.FullFilePath; ScanNumber = scan.OneBasedScanNumber; PrecursorScanNumber = scan.OneBasedPrecursorScanNumber; ScanRetentionTime = scan.RetentionTime; ScanExperimentalPeaks = scan.NumPeaks; TotalIonCurrent = scan.TotalIonCurrent; ScanPrecursorCharge = scan.PrecursorCharge; ScanPrecursorMonoisotopicPeakMz = scan.PrecursorMonoisotopicPeakMz; ScanPrecursorMass = scan.PrecursorMass; AddOrReplace(peptide, score, notch, true); AllScores = new List <double>(); DigestionParams = digestionParams; MatchedIonSeriesDict = new Dictionary <ProductType, int[]>(); MatchedIonMassToChargeRatioDict = new Dictionary <ProductType, double[]>(); MatchedIonIntensitiesDict = new Dictionary <ProductType, double[]>(); ProductMassErrorDa = new Dictionary <ProductType, double[]>(); ProductMassErrorPpm = new Dictionary <ProductType, double[]>(); MatchedFragmentIons = new List <MatchedFragmentIon>(); }