public void ProduceResult(IDataPoints data, ISpectrum spectrum, IGlycoPeptide glycoPeptide)
{
ITableNGlycan glycan = glycoPeptide.GetGlycan() as ITableNGlycan;
Dictionary <string, IPeak> peaks = new Dictionary <string, IPeak>();
List <IAnnotatedPeak> annotatedPeaks = new List <IAnnotatedPeak>();
foreach (PeakPoint pt in data.GetPoints())
{
if (!peaks.ContainsKey(pt.GetID()))
{
double mass = Double.Parse(pt.GetID());
peaks[pt.GetID()] = new GeneralPeak(mass, pt.GetIntensity());
}
List <IGlycoPeptide> glycoPeptides = new List <IGlycoPeptide>();
foreach (NGlycoPeptideNode node in pt.GetMaxNode())
{
if (IsGlycanMatch(node.GetNGlycan(), glycan))
{
glycoPeptides.Add(new GeneralGlycoPeptide(node.GetPeptide(), node.GetNGlycan(), -1));
}
}
if (glycoPeptides.Count > 0)
{
IAnnotatedPeak p = new GeneralAnnotatedSpectrumPeak(peaks[pt.GetID()], glycoPeptides);
annotatedPeaks.Add(p);
}
}
result = new GeneralAnnotatedSpectrumPeakResultProduct(spectrum,
annotatedPeaks.OrderBy(x => x.GetMZ()).ToList());
}
public void Annotate(ISpectrum spectrum, IGlycoPeptide glycoPeptide)
{
InitMatcher(glycoPeptide);
List <IAnnotatedPeak> peaks = GenerateMatcherResult(spectrum);
result = new GeneralAnnotatedSpectrumPeakResultProduct(spectrum, peaks);
}
public override void Analyze(int scan)
{
if (resultTable[scan] != null)
{
foreach (IGlycoPeptideScore r in resultTable[scan].GetResults())
{
annotator.Annotate(spectrumTable[scan], r);
product = annotator.GetResult();
(analyzer as IAnnotatedPeakResultAnalyzer).SetResultProduct(product);
analyzer.Analyze();
}
}
}
public void SetResultProduct(IAnnotatedPeakResultProduct product)
{
this.product = product;
}
public override void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
FastaSearchRunPeptides pepRunner = new FastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new GeneralPeptideCreator()));
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\ms_fasta.fasta");
//List<IPeptide> peptides = pepRunner.Run(@"C:\Users\rz20\Downloads\ms_fasta.fasta");
Console.WriteLine(peptides.Count);
IAccumulatedMSNGlycanCreator glyRunner = new AccumulatedMSBruteForceNGlycanCreator();
List <IAccumulatedGlycanMassProxy> glycans = glyRunner.GenerateSpecific();
IAccumulatedStructNGlycanCreator glyRunner2 = new AccumulatedStructBruteForceNGlycanCreator();
List <IAccumulatedGlycanStructureProxy> glycans2 = glyRunner2.GenerateSpecific();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(@"C:\Users\iruiz\Downloads\1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\1.raw");
//for (int i = 1; i < specRunner.GetLastScan(); i++)
//{
ISpectrum spectrum = specRunner.GetSpectrum(3361);
//if (spectrum.GetMSnOrder() == 1) continue;
//if ((spectrum as ISpectrumMSn).GetActivation() != TypeOfMSActivation.ETD) continue;
List <IGlycan> glycanSet = new List <IGlycan>();
glycanSet.AddRange(glycans);
ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
processor.Process(spectrum);
double pretol = 20;
IAccumulatedPrecursorMatcher precursorMatcher = new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycanSet, pretol);
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum);
IGlycoPeptideScoreFactory searchRunner = new BinSearchSpectrumEThcD();
searchRunner.Search(spectrum, glycoPeptides);
IGlycoPeptideScoreResultProduct result = searchRunner.GetResult();
List <IGlycoPeptideScore> results = result.GetResults();
IAnnotatedPeakFactory annotator = new BinSearchAnnotatedSpectrumEThcD(glycans2, 20);
foreach (IGlycoPeptideScore r in results)
{
annotator.Annotate(spectrum, r);
IAnnotatedPeakResultProduct peaks = annotator.GetResult();
peaks.Report("test.txt");
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
}
