private void RunTagBasedSearch(SortedSet <DatabaseSequenceSpectrumMatch>[] matches, FastaDatabase db,
CancellationToken?cancellationToken = null, IProgress <ProgressData> progress = null)
{
_tagSearchEngine.SetDatabase(db);
//var ms2ScanNums = _run.GetScanNumbers(2);
var progData = new ProgressData(progress)
{
Status = "Tag-based Searching for matches"
};
var sw = new Stopwatch();
long estimatedProteins = _tagMs2ScanNum.Length;
Console.WriteLine(@"Number of spectra containing sequence tags: " + estimatedProteins);
var numProteins = 0;
var lastUpdate = DateTime.MinValue; // Force original update of 0%
sw.Reset();
sw.Start();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
Parallel.ForEach(_tagMs2ScanNum, pfeOptions, ms2ScanNum =>
{
var tagSeqMatches = _tagSearchEngine.RunSearch(ms2ScanNum);
foreach (var tagSequenceMatch in tagSeqMatches)
{
var offset = _tagSearchEngine.FastaDatabase.GetOffset(tagSequenceMatch.ProteinName);
if (offset == null)
{
continue;
}
var sequence = tagSequenceMatch.Sequence;
var numNTermCleavages = tagSequenceMatch.TagMatch.StartIndex;
var seqObj = Sequence.CreateSequence(sequence, tagSequenceMatch.TagMatch.ModificationText, AminoAcidSet);
var precursorIon = new Ion(seqObj.Composition + Composition.H2O, tagSequenceMatch.TagMatch.Charge);
var prsm = new DatabaseSequenceSpectrumMatch(sequence, tagSequenceMatch.Pre, tagSequenceMatch.Post,
ms2ScanNum, (long)offset, numNTermCleavages,
tagSequenceMatch.TagMatch.Modifications,
precursorIon, tagSequenceMatch.TagMatch.Score, db.IsDecoy)
{
ModificationText = tagSequenceMatch.TagMatch.ModificationText,
};
AddMatch(matches, ms2ScanNum, prsm);
}
SearchProgressReport(ref numProteins, ref lastUpdate, estimatedProteins, sw, progData, "spectra");
});
Console.WriteLine(@"Collected candidate matches: {0}", GetNumberOfMatches(matches));
progData.StatusInternal = string.Empty;
progData.Report(100.0);
}