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();
}
void Search()
{
List <SearchResult> tempResults = new List <SearchResult>();
List <SearchResult> tempDecoyResults = new List <SearchResult>();
ISearch <string> oneSearcher = new BucketSearch <string>(
SearchingParameters.Access.MS1ToleranceBy, SearchingParameters.Access.MS1Tolerance);
PrecursorMatch precursorMatcher = new PrecursorMatch(oneSearcher);
precursorMatcher.Init(peptides, glycanBuilder.GlycanMaps());
ISearch <string> twoSearcher = new BucketSearch <string>(
SearchingParameters.Access.MS1ToleranceBy, SearchingParameters.Access.MS1Tolerance);
PrecursorMatch decoyPrecursorMatcher = new PrecursorMatch(twoSearcher);
decoyPrecursorMatcher.Init(decoyPeptides, glycanBuilder.GlycanMaps());
ISearch <string> moreSearcher = new BucketSearch <string>(
SearchingParameters.Access.MS2ToleranceBy, SearchingParameters.Access.MSMSTolerance);
SequenceSearch sequenceSearcher = new SequenceSearch(moreSearcher);
ISearch <int> extraSearcher = new BucketSearch <int>(
SearchingParameters.Access.MS2ToleranceBy, SearchingParameters.Access.MSMSTolerance);
GlycanSearch glycanSearcher = new GlycanSearch(extraSearcher, glycanBuilder.GlycanMaps(),
SearchingParameters.Access.ComplexInclude,
SearchingParameters.Access.HybridInclude,
SearchingParameters.Access.MannoseInclude);
SearchAnalyzer searchAnalyzer = new SearchAnalyzer();
SearchTask task;
while ((task = TryGetTask()) != null)
{
ISpectrum spectrum = task.Spectrum;
//precursor match
var pre_results = precursorMatcher.Match(task.PrecursorMZ, task.Charge);
if (pre_results.Count > 0)
{
// spectrum search
var peptide_results = sequenceSearcher.Search(spectrum.GetPeaks(), task.Charge, pre_results);
if (peptide_results.Count > 0)
{
var glycan_results = glycanSearcher.Search(spectrum.GetPeaks(), task.Charge, pre_results);
if (glycan_results.Count > 0)
{
var targets = searchAnalyzer.Analyze(spectrum.GetScanNum(), spectrum.GetPeaks(), peptide_results, glycan_results);
targets = searchAnalyzer.Filter(targets, glycanBuilder.GlycanMaps(),
task.PrecursorMZ, task.Charge);
tempResults.AddRange(targets);
}
}
}
var decoy_results = decoyPrecursorMatcher.Match(task.PrecursorMZ, task.Charge);
if (decoy_results.Count > 0)
{
// spectrum search
var peptide_results = sequenceSearcher.Search(spectrum.GetPeaks(), task.Charge, decoy_results);
if (peptide_results.Count > 0)
{
var glycan_results = glycanSearcher.Search(spectrum.GetPeaks(), task.Charge, decoy_results);
if (glycan_results.Count > 0)
{
var decoys = searchAnalyzer.Analyze(spectrum.GetScanNum(), spectrum.GetPeaks(), peptide_results, glycan_results);
decoys = searchAnalyzer.Filter(decoys, glycanBuilder.GlycanMaps(),
task.PrecursorMZ, task.Charge);
tempDecoyResults.AddRange(decoys);
}
}
}
searchCounter.Add(taskSize);
}
UpdateTask(tempResults, tempDecoyResults);
}
public void Test1()
{
string path = @"C:\Users\Rui Zhang\Downloads\ZC_20171218_C16_R1.raw";
string fasta = @"C:\Users\Rui Zhang\Downloads\haptoglobin.fasta";
// peptides
IProteinReader proteinReader = new FastaReader();
List <IProtein> proteins = proteinReader.Read(fasta);
List <IProtein> decoyProteins = new List <IProtein>();
foreach (IProtein protein in proteins)
{
IProtein p = new BaseProtein();
p.SetSequence(Reverse(protein.Sequence()));
decoyProteins.Add(p);
}
List <Proteases> proteases = new List <Proteases>()
{
Proteases.Trypsin, Proteases.GluC
};
HashSet <string> peptides = new HashSet <string>();
ProteinDigest proteinDigest = new ProteinDigest(2, 5, proteases[0]);
foreach (IProtein protein in decoyProteins)
{
peptides.UnionWith(proteinDigest.Sequences(protein.Sequence(),
ProteinPTM.ContainsNGlycanSite));
}
for (int i = 1; i < proteases.Count; i++)
{
proteinDigest.SetProtease(proteases[i]);
List <string> peptidesList = peptides.ToList();
foreach (string seq in peptidesList)
{
peptides.UnionWith(proteinDigest.Sequences(seq,
ProteinPTM.ContainsNGlycanSite));
}
}
Assert.True(peptides.Contains("KDNLTYVGDGETR"));
// build glycan
GlycanBuilder glycanBuilder = new GlycanBuilder();
glycanBuilder.Build();
// search
List <SearchResult> searchResults = new List <SearchResult>();
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking();
IProcess process = new LocalNeighborPicking();
reader.Init(path);
double searchRange = 2;
ISpectrum ms1 = null;
List <IPeak> majorPeaks = new List <IPeak>();
ISearch <string> oneSearcher = new BucketSearch <string>(ToleranceBy.PPM, 10);
PrecursorMatch precursorMatcher = new PrecursorMatch(oneSearcher);
precursorMatcher.Init(peptides.ToList(), glycanBuilder.GlycanMaps());
ISearch <string> moreSearcher = new BucketSearch <string>(ToleranceBy.Dalton, 0.01);
SequenceSearch sequenceSearcher = new SequenceSearch(moreSearcher);
ISearch <int> extraSearcher = new BucketSearch <int>(ToleranceBy.Dalton, 0.01);
GlycanSearch glycanSearcher = new GlycanSearch(extraSearcher, glycanBuilder.GlycanMaps());
SearchAnalyzer searchAnalyzer = new SearchAnalyzer();
for (int i = reader.GetFirstScan(); i < reader.GetLastScan(); i++)
{
if (reader.GetMSnOrder(i) < 2)
{
ms1 = reader.GetSpectrum(i);
majorPeaks = picking.Process(ms1.GetPeaks());
}
else
{
double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i));
if (ms1.GetPeaks()
.Where(p => p.GetMZ() > mz - searchRange && p.GetMZ() < mz + searchRange)
.Count() == 0)
{
continue;
}
Patterson charger = new Patterson();
int charge = charger.Charge(ms1.GetPeaks(), mz - searchRange, mz + searchRange);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
continue;
}
// find monopeak
Averagine averagine = new Averagine(AveragineType.GlycoPeptide);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
double precursorMZ = result.GetMZ();
// search
ISpectrum ms2 = reader.GetSpectrum(i);
ms2 = process.Process(ms2);
//precursor match
var pre_results = precursorMatcher.Match(precursorMZ, charge);
if (pre_results.Count == 0)
{
continue;
}
// spectrum search
var peptide_results = sequenceSearcher.Search(ms2.GetPeaks(), charge, pre_results);
if (peptide_results.Count == 0)
{
continue;
}
var glycan_results = glycanSearcher.Search(ms2.GetPeaks(), charge, pre_results);
if (glycan_results.Count == 0)
{
continue;
}
var temp_results = searchAnalyzer.Analyze(i, ms2.GetPeaks(), peptide_results, glycan_results);
break;
}
}
}
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();
}
