public void Run()
{
ISpectrumReader reader = new ThermoRawSpectrumReader();
reader.Init(@"C:\Users\iruiz\Desktop\app\ZC_20171218_H95_R1.raw");
ISpectrumFactory creator = new GeneralSpectrumFactory(reader);
Console.WriteLine(creator.GetFirstScan());
Console.WriteLine(creator.GetLastScan());
for (int i = creator.GetFirstScan(); i < creator.GetLastScan(); i++)
{
if (creator.GetMSnOrder(i) == 2)
{
Console.WriteLine(creator.GetActivation(i).ToString());
List <IPeak> peaks = creator.GetSpectrum(i).GetPeaks();
}
}
Console.Read();
}
public void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
// protein
IProteinDataBuilder proteinBuilder = new GeneralFastaDataBuilder();
IProteinCreator proteinCreator = new GeneralProteinCreator(proteinBuilder);
List <IProtein> proteins = proteinCreator.Create(@"C:\Users\iruiz\Desktop\app\HP.fasta");
// peptides
List <IPeptideSequencesGenerator> generatorList = new List <IPeptideSequencesGenerator>();
IPeptideSequencesGeneratorParameter parameter = new GeneralPeptideGeneratorParameter();
parameter.SetProtease(Proteases.GluC);
NGlycosylatedPeptideSequencesGenerator generatorGluc = new NGlycosylatedPeptideSequencesGenerator(parameter);
generatorList.Add(generatorGluc);
parameter = new GeneralPeptideGeneratorParameter();
parameter.SetProtease(Proteases.Trypsin);
NGlycosylatedPeptideSequencesGenerator generatorTrypsin = new NGlycosylatedPeptideSequencesGenerator(parameter);
generatorList.Add(generatorTrypsin);
IPeptideSequencesGenerator peptideSequencesGenerator = new DoubleDigestionPeptideSequencesGeneratorProxy(generatorList);
IPeptideCreator peptideCreator = new GeneralPeptideCreator(peptideSequencesGenerator);
List <IPeptide> peptides = new List <IPeptide>();
HashSet <string> seen = new HashSet <string>();
foreach (IProtein protein in proteins)
{
foreach (IPeptide peptide in peptideCreator.Create(protein))
{
if (!seen.Contains(peptide.GetSequence()))
{
seen.Add(peptide.GetSequence());
peptides.Add(peptide);
}
}
}
// glycans
ITableNGlycanProxyGenerator tableNGlycanProxyGenerator = new GeneralTableNGlycanMassProxyGenerator(12, 12, 5, 4, 0);
int[] structTable = new int[24];
structTable[0] = 1;
ITableNGlycanProxy root = new GeneralTableNGlycanMassProxy(new ComplexNGlycan(structTable));
IGlycanCreator glycanCreator = new GeneralTableNGlycanCreator(tableNGlycanProxyGenerator, root);
List <IGlycan> glycans = glycanCreator.Create();
// precursor
List <IPoint> points = new List <IPoint>();
foreach (IGlycan glycan in glycans)
{
points.Add(new GlycanPoint(glycan));
}
IComparer <IPoint> comparer = new ToleranceComparer(0.01);
ISearch matcher = new BucketSearch(comparer, 0.01);
matcher.setData(points);
IGlycoPeptideProxyGenerator glycoPeptideProxyGenerator = new GeneralTableNGlycoPeptideMassProxyGenerator();
IGlycoPeptideCreator glycoPeptideCreator = new GeneralNGlycoPeptideSingleSiteCreator(glycoPeptideProxyGenerator);
IPrecursorMatcher precursorMatcher = new GeneralPrecursorMatcher(matcher, glycoPeptideCreator);
precursorMatcher.SetGlycans(glycans);
precursorMatcher.SetPeptides(peptides);
// spectrum
ISpectrumReader spectrumReader = new ThermoRawSpectrumReader();
spectrumReader.Init(@"C:\Users\iruiz\Desktop\app\ZC_20171218_H95_R1.raw");
ISpectrumFactory spectrumFactory = new GeneralSpectrumFactory(spectrumReader);
ISpectrum spectrum = spectrumFactory.GetSpectrum(7039);
List <IGlycoPeptide> glycoPeptides = precursorMatcher.Match(spectrum);
watch.Stop();
Console.WriteLine(glycoPeptides.Count);
foreach (IGlycoPeptide glycoPeptide in glycoPeptides)
{
Console.WriteLine(glycoPeptide.GetType());
}
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
