public void Run()
{
List <IPoint> points = new List <IPoint>();
for (int i = 0; i < 1200; i++)
{
points.Add(new MassPoint(i));
}
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
IComparer <IPoint> comparer = new ToleranceComparer(1.1);
Console.WriteLine(comparer.Compare(new MassPoint(122), new MassPoint(123)));
BinarySearch bins = new BinarySearch(comparer);
bins.setData(points);
List <IPoint> found = new List <IPoint>();
for (int j = 122; j < 123; j += 10)
{
found.AddRange(bins.Search(new MassPoint(j)));
}
//BucketSearch bucket = new BucketSearch(points, 1.1);
//List<IPoint> result = bucket.Search(new MassPoint(3));
watch.Stop();
Console.WriteLine(found.Count);
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
found.Clear();
watch = new System.Diagnostics.Stopwatch();
watch.Start();
//BinarySearch bins = new BinarySearch(points, 1.1);
//List<IPoint> result = bins.Search(new MassPoint(3));
BucketSearch bucket = new BucketSearch(comparer, 1.1);
bucket.setData(points);
for (int j = 122; j < 123; j += 10)
{
found.AddRange(bucket.Search(new MassPoint(j)));
}
watch.Stop();
Console.WriteLine(found.Count);
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
//foreach (IPoint p in result)
//{
// Console.WriteLine(p.GetValue());
//}
Console.ReadLine();
}
protected override void Load(ContainerBuilder builder)
{
builder.Register(c =>
{
IComparer <IPoint> comparer = new ToleranceComparer(Tolerance);
ISearch matcher = new BinarySearch(comparer);
return(new OxoniumSpectrumFilter(matcher));
}).As <ISpectrumFilter>();
}
protected override void Load(ContainerBuilder builder)
{
builder.Register(c =>
{
IComparer <IPoint> comparer = new ToleranceComparer(Tolerance);
ISearch matcherPeaks = new BinarySearch(comparer);
Dictionary <MassType, double> weights = new Dictionary <MassType, double>();
weights.Add(MassType.Core, coreGlycanWeight);
weights.Add(MassType.Branch, branchGlycanWeight);
weights.Add(MassType.Glycan, glycanWeight);
weights.Add(MassType.Peptide, peptideWeight);
IScoreFactory scoreFactory = new VectorScoreFactory(alpha, beta, weights);
IGlycoPeptidePointsCreator glycoPeptidePointsCreator = new GeneralGlycoPeptideMassProxyPointsCreator();
return(new GeneralSearchEThcD(matcherPeaks, scoreFactory, glycoPeptidePointsCreator));
}).As <ISearchEThcD>();
}
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();
}
