protected override MetaMorpheusEngineResults RunSpecific()
{
CrosslinkAnalysisResults myAnalysisResults = new CrosslinkAnalysisResults(this);
Status("Running analysis engine!");
//At this point have Spectrum-Sequence matching, without knowing which protein, and without know if target/decoy
//myAnalysisResults.AddText("Starting compactPeptideToProteinPeptideMatching count: " + compactPeptideToProteinPeptideMatching.Count);
Status("Adding observed peptides to dictionary...");
foreach (var psmpair in NewPsms)
{
if (psmpair != null)
{
var cp = psmpair.compactPeptide;
if (!CompactPeptideToProteinPeptideMatching.ContainsKey(cp))
{
CompactPeptideToProteinPeptideMatching.Add(cp, new HashSet <PeptideWithSetModifications>());
}
if (psmpair.BetaPsmCross != null)
{
var cp1 = psmpair.BetaPsmCross.compactPeptide;
if (!CompactPeptideToProteinPeptideMatching.ContainsKey(cp1))
{
CompactPeptideToProteinPeptideMatching.Add(cp1, new HashSet <PeptideWithSetModifications>());
}
}
}
}
int proteinsSeen = 0;
int old_progress = 0;
Status("Adding possible sources to peptide dictionary...");
Parallel.ForEach(Partitioner.Create(0, ProteinList.Count), new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (fff, loopState) =>
{
for (int i = fff.Item1; i < fff.Item2; i++)
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
loopState.Stop();
return;
}
foreach (var peptideWithSetModifications in ProteinList[i].Digest(commonParameters.DigestionParams, FixedModifications, VariableModifications))
{
var compactPeptide = peptideWithSetModifications.CompactPeptide(TerminusType);
if (CompactPeptideToProteinPeptideMatching.TryGetValue(compactPeptide, out HashSet <PeptideWithSetModifications> peptidesWithSetMods))
{
lock (peptidesWithSetMods)
peptidesWithSetMods.Add(peptideWithSetModifications);
}
}
proteinsSeen += fff.Item2 - fff.Item1;
var new_progress = (int)((double)proteinsSeen / (ProteinList.Count) * 100);
if (new_progress > old_progress)
{
ReportProgress(new ProgressEventArgs(new_progress, "In adding possible" +
" sources to peptide dictionary loop", nestedIds));
old_progress = new_progress;
}
}
});
Status("Computing info about actual peptides with modifications...");
for (int myScanWithMassIndex = 0; myScanWithMassIndex < NewPsms.Count; myScanWithMassIndex++)
{
if (NewPsms[myScanWithMassIndex] != null)
{
NewPsms[myScanWithMassIndex].MatchToProteinLinkedPeptides(CompactPeptideToProteinPeptideMatching);
if (NewPsms[myScanWithMassIndex].BetaPsmCross != null)
{
NewPsms[myScanWithMassIndex].BetaPsmCross.MatchToProteinLinkedPeptides(CompactPeptideToProteinPeptideMatching);
}
}
}
return(myAnalysisResults);
}
protected override MetaMorpheusEngineResults RunSpecific()
{
MassDiffAcceptor XLsearchMode = new OpenSearchMode();
CrosslinkAnalysisResults myAnalysisResults = new CrosslinkAnalysisResults(this);
Status("Running analysis engine!");
//At this point have Spectrum-Sequence matching, without knowing which protein, and without know if target/decoy
#region Match Seqeunces to PeptideWithSetModifications
//myAnalysisResults.AddText("Starting compactPeptideToProteinPeptideMatching count: " + compactPeptideToProteinPeptideMatching.Count);
Status("Adding observed peptides to dictionary...");
foreach (var psmpair in newPsms)
{
if (psmpair != null)
{
var cp = psmpair.compactPeptide;
if (!compactPeptideToProteinPeptideMatching.ContainsKey(cp))
{
compactPeptideToProteinPeptideMatching.Add(cp, new HashSet <PeptideWithSetModifications>());
}
if (psmpair.BetaPsmCross != null)
{
var cp1 = psmpair.BetaPsmCross.compactPeptide;
if (!compactPeptideToProteinPeptideMatching.ContainsKey(cp1))
{
compactPeptideToProteinPeptideMatching.Add(cp1, new HashSet <PeptideWithSetModifications>());
}
}
}
}
//myAnalysisResults.AddText("Ending compactPeptideToProteinPeptideMatching count: " + compactPeptideToProteinPeptideMatching.Count);
int totalProteins = proteinList.Count;
int proteinsSeen = 0;
int old_progress = 0;
var obj = new object();
Status("Adding possible sources to peptide dictionary...");
Parallel.ForEach(Partitioner.Create(0, totalProteins), fff =>
{
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > local = compactPeptideToProteinPeptideMatching.ToDictionary(b => b.Key, b => new HashSet <PeptideWithSetModifications>());
for (int i = fff.Item1; i < fff.Item2; i++)
{
foreach (var peptideWithSetModifications in proteinList[i].Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications))
{
if (local.TryGetValue(new CompactPeptide(peptideWithSetModifications, terminusType), out HashSet <PeptideWithSetModifications> v))
{
v.Add(peptideWithSetModifications);
}
}
}
lock (obj)
{
foreach (var ye in local)
{
if (compactPeptideToProteinPeptideMatching.TryGetValue(ye.Key, out HashSet <PeptideWithSetModifications> v))
{
foreach (var huh in ye.Value)
{
v.Add(huh);
}
}
}
proteinsSeen += fff.Item2 - fff.Item1;
var new_progress = (int)((double)proteinsSeen / (totalProteins) * 100);
if (new_progress > old_progress)
{
ReportProgress(new ProgressEventArgs(new_progress, "In adding possible" +
" sources to peptide dictionary loop", nestedIds));
old_progress = new_progress;
}
}
});
#endregion Match Seqeunces to PeptideWithSetModifications
Status("Computing info about actual peptides with modifications...");
for (int myScanWithMassIndex = 0; myScanWithMassIndex < newPsms.Count; myScanWithMassIndex++)
{
var huh = newPsms[myScanWithMassIndex];
if (huh != null)
{
huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
if (huh != null)
{
var huh1 = newPsms[myScanWithMassIndex].BetaPsmCross;
if (huh1 != null)
{
huh1.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
}
}
return(myAnalysisResults);
}