protected override void Load(ContainerBuilder builder)
{
builder.Register(c =>
{
List <IPeptideSequencesGenerator> generatorList = new List <IPeptideSequencesGenerator>();
foreach (string enzyme in Enzymes)
{
IPeptideSequencesGeneratorParameter parameter = new GeneralPeptideGeneratorParameter();
parameter.SetMissCleavage(MissCleavage);
parameter.SetMiniLength(MiniLength);
switch (enzyme)
{
case "GluC":
parameter.SetProtease(Proteases.GluC);
break;
case "Chymotrypsin":
parameter.SetProtease(Proteases.Chymotrypsin);
break;
case "Pepsin":
parameter.SetProtease(Proteases.Pepsin);
break;
case "Trypsin":
parameter.SetProtease(Proteases.Trypsin);
break;
default:
parameter.SetProtease(Proteases.Trypsin);
break;
}
NGlycosylatedPeptideSequencesGenerator generator = new NGlycosylatedPeptideSequencesGenerator(parameter);
generatorList.Add(generator);
}
IPeptideSequencesGenerator peptideSequencesGenerator = new DoubleDigestionPeptideSequencesGeneratorProxy(generatorList);
return(new GeneralPeptideCreator(peptideSequencesGenerator));
}).As <IPeptideCreator>();
}
public void Run()
{
IPeptideSequencesGeneratorParameter parameter = new GeneralPeptideGeneratorParameter(Proteases.Trypsin);
List <IPeptideSequencesGenerator> generator = new List <IPeptideSequencesGenerator>();
generator.Add(new NGlycosylatedPeptideSequencesGenerator(parameter));
IPeptideSequencesGeneratorParameter parameter2 = new GeneralPeptideGeneratorParameter(Proteases.GluC);
generator.Add(new NGlycosylatedPeptideSequencesGenerator(parameter2));
IPeptideSequencesGenerator generators = new DoubleDigestionPeptideSequencesGeneratorProxy(generator);
List <string> sequences = generators.Generate("ILGGHLDAKGSFPWQAKMVSHHNLTTGATLINEQWLLTTAK");
IPeptideCreator creator = new GeneralPeptideCreator(generators);
List <IPeptide> peptidese = creator.Create(new GeneralProtein("this", "ILGGHLDAKGSFPWQAKMVSHHNLTTGATLINEQWLLTTAK"));
foreach (IPeptide s in peptidese)
{
Console.WriteLine(s.GetSequence());
}
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();
}
