public IEnumerable <Peptide> GenerateAllModificationCombinations()
{
// Get all the modifications that are isotopologues
var isotopologues = GetUniqueModifications <ModificationWithMultiplePossibilitiesCollection>().ToArray();
// Base condition, no more isotopologues to make, so just return
if (isotopologues.Length < 1)
{
yield break;
}
// Grab the the first isotopologue
ModificationWithMultiplePossibilitiesCollection isotopologue = isotopologues[0];
// Loop over each modification in the isotopologue
foreach (OldSchoolModification mod in isotopologue)
{
// Create a clone of the peptide, cloning modifications as well.
Peptide peptide = new Peptide(this);
// Replace the base isotopologue mod with the specific version
peptide.ReplaceModification(isotopologue, mod);
// There were more than one isotopologue, so we must go deeper
if (isotopologues.Length > 1)
{
// Call the same rotuine on the newly generate peptide that has one less isotopologue
foreach (var subpeptide in peptide.GenerateAllModificationCombinations())
{
yield return(subpeptide);
}
}
else
{
// Return this peptide
yield return(peptide);
}
}
}
protected override MetaMorpheusEngineResults RunSpecific()
{
Status("Extracting data points:");
// The final training point list
int numMs1MassChargeCombinationsConsidered = 0;
int numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks = 0;
int numMs2MassChargeCombinationsConsidered = 0;
int numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks = 0;
List <LabeledDataPoint> Ms1List = new List <LabeledDataPoint>();
List <LabeledDataPoint> Ms2List = new List <LabeledDataPoint>();
int numIdentifications = GoodIdentifications.Count;
// Loop over identifications
HashSet <string> sequences = new HashSet <string>();
object lockObj = new object();
object lockObj2 = new object();
Parallel.ForEach(Partitioner.Create(0, numIdentifications), new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (fff, loopState) =>
{
for (int matchIndex = fff.Item1; matchIndex < fff.Item2; matchIndex++)
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
loopState.Stop();
return;
}
PeptideSpectralMatch identification = GoodIdentifications[matchIndex];
// Each identification has an MS2 spectrum attached to it.
int ms2scanNumber = identification.ScanNumber;
int peptideCharge = identification.ScanPrecursorCharge;
if (identification.FullSequence == null)
{
continue;
}
var representativeSinglePeptide = identification.CompactPeptides.First().Value.Item2.First();
// Get the peptide, don't forget to add the modifications!!!!
var SequenceWithChemicalFormulas = representativeSinglePeptide.SequenceWithChemicalFormulas;
if (SequenceWithChemicalFormulas == null || representativeSinglePeptide.AllModsOneIsNterminus.Any(b => b.Value.neutralLosses.Count != 1 || b.Value.neutralLosses.First() != 0))
{
continue;
}
Proteomics.AminoAcidPolymer.Peptide coolPeptide = new Proteomics.AminoAcidPolymer.Peptide(SequenceWithChemicalFormulas);
var ms2tuple = SearchMS2Spectrum(MyMsDataFile.GetOneBasedScan(ms2scanNumber), identification);
lock (lockObj2)
{
Ms2List.AddRange(ms2tuple);
}
// Calculate isotopic distribution of the full peptide
var dist = IsotopicDistribution.GetDistribution(coolPeptide.GetChemicalFormula(), FineResolutionForIsotopeDistCalculation, 0.001);
double[] theoreticalMasses = dist.Masses.ToArray();
double[] theoreticalIntensities = dist.Intensities.ToArray();
Array.Sort(theoreticalIntensities, theoreticalMasses, Comparer <double> .Create((x, y) => y.CompareTo(x)));
var ms1tupleBack = SearchMS1Spectra(theoreticalMasses, theoreticalIntensities, ms2scanNumber, -1, peptideCharge, identification);
var ms1tupleForward = SearchMS1Spectra(theoreticalMasses, theoreticalIntensities, ms2scanNumber, 1, peptideCharge, identification);
lock (lockObj)
{
Ms1List.AddRange(ms1tupleBack.Item1);
numMs1MassChargeCombinationsConsidered += ms1tupleBack.Item2;
numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks += ms1tupleBack.Item3;
Ms1List.AddRange(ms1tupleForward.Item1);
numMs1MassChargeCombinationsConsidered += ms1tupleForward.Item2;
numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks += ms1tupleForward.Item3;
}
}
});
// datapoints are ordered because they were acquired in a parallized search and we want repeatable results
return(new DataPointAquisitionResults(this,
GoodIdentifications,
Ms1List.OrderBy(p => p.RetentionTime).ThenBy(p => p.ExperimentalMz).ToList(),
Ms2List.OrderBy(p => p.RetentionTime).ThenBy(p => p.ExperimentalMz).ToList(),
numMs1MassChargeCombinationsConsidered,
numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks,
numMs2MassChargeCombinationsConsidered,
numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks
));
}
