public IEnumerable <Tuple <Peptide, int> > DigestProteomeOnTheFlyFast(List <Protein> proteins, bool allowSNP, Queries AllQueries)
{
foreach (Peptide peptide in ProteinSearcher.ProteinDigest(options, proteins, allowSNP))
{
//int firstIndex = AllQueries.BinarySearch(MassTolerance.MzFloor(peptide.MonoisotopicMass, options.precursorMassTolerance));
//if (firstIndex >= 0 && firstIndex < AllQueries.Count)
// yield return new Tuple<Peptide, int>(peptide, firstIndex);
//foreach (Peptide peptide in ProteinSearcher.ProteinDigestNoEnzyme(dbOptions, proteins, AllQueries))
//if (!TargetPeptides.Contains(peptide.BaseSequence))
//{
foreach (Peptide modPeptide in peptide.GetVariablyModifiedPeptides(options.variableModifications, options.maximumVariableModificationIsoforms))
{
modPeptide.SetFixedModifications(options.fixedModifications);
int firstIndex = AllQueries.BinarySearch(MassTolerance.MzFloor(modPeptide.MonoisotopicMass, options.precursorMassTolerance));
if (firstIndex >= 0 && firstIndex < AllQueries.Count)
{
yield return(new Tuple <Peptide, int>(modPeptide, firstIndex));
}
}
//TODO check if this favors targets over decoys since proteins are sorted target->deco
// TargetPeptides.Add(peptide.BaseSequence);
//}
}
}
public IEnumerable <Tuple <Peptide, int> > DigestProteomeOnTheFly(List <Protein> proteins, bool allowSNP, Queries AllQueries)
{
//HashSet<string> TargetPeptides = new HashSet<string>();
//Dictionary<string, int> TargetPeptides = new Dictionary<string, int>();
//Digest proteins and store peptides in a Dictionnary
//Does not fit in memory -> 360 Go ....
//dicOfPeptideSequences = new Dictionary<string, List<Protein>>();
//double minimumMonoisotopicPeakOffset = dbOptions.precursorMonoisotopicPeakCorrection ? dbOptions.minimumPrecursorMonoisotopicPeakOffset : 0;
//double maximumMonoisotopicPeakOffset = dbOptions.precursorMonoisotopicPeakCorrection ? dbOptions.maximumPrecursorMonoisotopicPeakOffset : 0;
foreach (Peptide peptide in ProteinSearcher.ProteinDigest(options, proteins, allowSNP))
{
//int firstIndex = AllQueries.BinarySearch(MassTolerance.MzFloor(peptide.MonoisotopicMass, options.precursorMassTolerance));
//if (firstIndex >= 0 && firstIndex < AllQueries.Count)
// yield return new Tuple<Peptide, int>(peptide, firstIndex);
//foreach (Peptide peptide in ProteinSearcher.ProteinDigestNoEnzyme(dbOptions, proteins, AllQueries))
//if (!TargetPeptides.Contains(peptide.BaseSequence))
//{
foreach (Peptide modPeptide in peptide.GetVariablyModifiedPeptides(options.variableModifications, options.maximumVariableModificationIsoforms))
{
modPeptide.SetFixedModifications(options.fixedModifications);
int firstIndex = AllQueries.BinarySearch(MassTolerance.MzFloor(modPeptide.MonoisotopicMass, options.precursorMassTolerance));
if (firstIndex >= 0 && firstIndex < AllQueries.Count)
{
yield return(new Tuple <Peptide, int>(modPeptide, firstIndex));
}
}
//TODO check if this favors targets over decoys since proteins are sorted target->deco
// TargetPeptides.Add(peptide.BaseSequence);
//}
}
}