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>();
}