public void test2()
{
string path = @"C:\Users\Rui Zhang\Downloads\Serum_1_C18_03292019_Ali.raw";
ISpectrumReader reader = new ThermoRawSpectrumReader();
reader.Init(path);
RidgeLineFinder coeffMatrix = new RidgeLineFinder(1.0, 2, 1, 2);
IProcess processer = new PeakPickingCWT(coeffMatrix);
//for (int i = reader.GetFirstScan(); i < reader.GetLastScan(); i++)
int i = 347;
{
if (reader.GetMSnOrder(i) < 2)
{
ISpectrum spectrum = reader.GetSpectrum(i);
List <IPeak> peaks = spectrum.GetPeaks();
spectrum = processer.Process(spectrum);
IAreaCalculator calculator = new TrapezoidalRule();
IBounder bounder = new PerpendicularDrop();
PeakAreaCalculator areaCalculator = new PeakAreaCalculator(calculator, bounder);
areaCalculator.Init(peaks);
foreach (IPeak peak in spectrum.GetPeaks())
{
Console.WriteLine(peak.GetMZ() + " : " + areaCalculator.Area(peak).ToString());
}
}
}
}
public ISpectrum Process(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks();
double[] signal = peaks.Select(p => p.GetIntensity()).ToArray();
SortedDictionary <double, List <double> > matrix =
new SortedDictionary <double, List <double> >();
for (double a = 1.0; a <= maxScale; a += steps)
{
double[] processed = Algorithm.CWT.Transform(signal, a);
matrix[a] = processed.ToList();
}
List <RidgeLine> lines = finder.Find(
spectrum.GetPeaks().Select(p => p.GetMZ()).ToList(),
matrix);
HashSet <double> mz = new HashSet <double>(lines.Select(p => p.Pos).ToList());
List <IPeak> processedPeaks = peaks.Where(p => mz.Contains(p.GetMZ())).ToList();
ISpectrum newSpectrum = spectrum.Clone();
newSpectrum.SetPeaks(processedPeaks);
return(newSpectrum);
}
public ISpectrum Process(ISpectrum spectrum)
{
if (spectrum.GetPeaks().Count == 0)
{
return(spectrum);
}
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double mz = spectrum.GetPeaks().First().GetMZ();
peaks.Add(new GeneralPeak(mz - precision, 0));
foreach (IPeak peak in spectrum.GetPeaks())
{
if (peak.GetMZ() - mz > precision)
{
double middle = (mz + peak.GetMZ()) / 2;
peaks.Add(new GeneralPeak(middle, 0));
}
peaks.Add(peak);
mz = peak.GetMZ();
}
peaks.Add(new GeneralPeak(mz + precision, 0));
List <IPeak> processedPeaks = new List <IPeak>();
int index = 1;
int end = peaks.Count - 1;
int head = index + 1;
while (index < end)
{
if (peaks[index - 1].GetIntensity() < peaks[index].GetIntensity())
{
head = index + 1;
}
while (head < end &&
peaks[head].GetIntensity() == peaks[index].GetIntensity())
{
head++;
}
if (peaks[head].GetIntensity() < peaks[index].GetIntensity())
{
processedPeaks.Add(peaks[index]);
index = head;
}
index++;
}
ISpectrum newSpectrum = spectrum.Clone();
newSpectrum.SetPeaks(processedPeaks);
return(newSpectrum);
}
public List <IGlycoPeptideScore> MatchSpectrum(ISpectrum spectrum,
List <IGlycoPeptide> glycoPeptides)
{
List <IGlycoPeptideScore> results = new List <IGlycoPeptideScore>();
foreach (IAccumulatedGlycoPeptideMassProxy glyco in glycoPeptides)
{
double score = 0.0;
List <double> massList = glyco.GetMass();
foreach (IPeak peak in spectrum.GetPeaks())
{
if (MatchPeakGlycoPeptideMass(peak,
(spectrum as ISpectrumMSn).GetParentCharge(), massList))
{
score += (alpha * peak.GetIntensity() + beta) * 1000.0;
}
}
if (score > 0)
{
results.Add(new GeneralGlycoPeptideScore(glyco, score));
}
}
return(results);
}
public List <GUI> FindGlucoseUnits(ISpectrum spectrum)
{
List <GUI> units = new List <GUI>();
List <IPeak> peaks = spectrum.GetPeaks();
int scan = spectrum.GetScanNum();
for (int i = 0; i < Glucose.Length; i++)
{
double mass = Glucose[i];
double bestIntensity = 0;
IPeak bestPeak = null;
List <double> mzCandidates = Calculator.To.ComputeMZ(mass, maxCharge);
foreach (double mz in mzCandidates)
{
int idx = BinarySearchPoints(peaks, mz);
if (idx > 0 && peaks[idx].GetIntensity() > bestIntensity)
{
bestIntensity = peaks[idx].GetIntensity();
bestPeak = peaks[idx];
}
}
if (bestPeak is null)
{
continue;
}
units.Add(new GUI(i + 2, scan, bestPeak));
}
return(units);
}
public List <IPeptide> PeptidesFilter(ISpectrum spectrum)
{
List <IPeptide> peptides = new List <IPeptide>();
List <double> massList = new List <double>();
int parentCharge = (spectrum as ISpectrumMSn).GetParentCharge();
for (int i = 1; i <= parentCharge; i++)
{
foreach (IPeak peak in spectrum.GetPeaks())
{
massList.Add(calcualtor.CalcChargeMass(peak.GetMZ(), i, option));
}
}
if (massList.Count > 0)
{
massList.Sort();
}
foreach (IPeptide peptide in peptideDB)
{
double mass = calcualtor.CalcPeptideMass(peptide, option) + UtilMass.HexNAc;
if (MassBinarySearch.FindPPM(mass, massList, matcher.GetTolerance()))
{
peptides.Add(peptide);
}
}
return(peptides);
}
public void test1()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
string path = @"C:\Users\Rui Zhang\Downloads\Serum_1_C18_03292019_Ali.raw";
ISpectrumReader reader = new ThermoRawSpectrumReader();
reader.Init(path);
//for (int i = reader.GetFirstScan(); i < reader.GetLastScan(); i++)
int i = 342;
RidgeLineFinder coeffMatrix = new RidgeLineFinder(1.0, 2, 1, 2);
{
if (reader.GetMSnOrder(i) < 2)
{
ISpectrum spectrum = reader.GetSpectrum(i);
List <IPeak> peaks = spectrum.GetPeaks();
double[] signal = peaks.Select(p => p.GetIntensity()).ToArray();
SortedDictionary <double, List <double> > matrix =
new SortedDictionary <double, List <double> >();
for (double a = 1; a <= 120; a += 6)
{
double[] processed = CWT.Transform(signal, a);
matrix[a] = processed.ToList();
}
List <RidgeLine> lines = coeffMatrix.Find(spectrum.GetPeaks().Select(p => p.GetMZ()).ToList(),
matrix);
Console.WriteLine(lines.Count);
Console.WriteLine(peaks.Count);
foreach (RidgeLine line in lines)
{
Console.WriteLine(line.Pos);
}
}
//break;
}
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
//Console.Read();
}
public static Spectrum GetMS1Spectrum(ref ThermoRawSpectrumReader reader,
int scan, ref ISpectrum ms1)
{
// scan header
Spectrum spectrum = new Spectrum
{
id = "scan=" + scan.ToString()
};
double dLowMass = 0;
double dHighMass = 0;
double dTIC = 0;
double dBasePeakMass = 0;
double dBasePeakIntensity = 0;
reader.GetScanHeaderInfoForScanNum(scan, ref dLowMass, ref dHighMass,
ref dTIC, ref dBasePeakMass, ref dBasePeakIntensity);
SetScanHeader(spectrum, dLowMass, dHighMass, dTIC,
dBasePeakMass, dBasePeakIntensity);
// binary data
spectrum.binaryDataArrayList = new BinaryDataArrayList();
SetBinaryDataArrayHeader(spectrum.binaryDataArrayList);
ms1 = reader.GetSpectrum(scan);
//majorPeaks = picking.Process(ms1.GetPeaks());
spectrum.cvParam[0] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000511",
name = "ms level",
value = "1",
};
spectrum.binaryDataArrayList.binaryDataArray[0].binary =
ms1.GetPeaks().SelectMany(p => BitConverter.GetBytes(p.GetMZ())).ToArray();
spectrum.binaryDataArrayList.binaryDataArray[1].binary =
ms1.GetPeaks().SelectMany(p => BitConverter.GetBytes(p.GetIntensity())).ToArray();
spectrum.defaultArrayLength = ms1.GetPeaks().Count.ToString();
spectrum.binaryDataArrayList.binaryDataArray[0].encodedLength =
Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[0].binary).Length.ToString();
spectrum.binaryDataArrayList.binaryDataArray[1].encodedLength =
Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[1].binary).Length.ToString();
return(spectrum);
}
public ISpectrum Process(ISpectrum spectrum)
{
List <IPeak> peaks = peakpick(spectrum.GetPeaks(), maxPeaks);
peaks.Sort();
NormalizePeaks(peaks, factor);
spectrum.SetPeaks(peaks);
return(spectrum);
}
public void Process(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks()
.OrderByDescending(pk => pk.GetIntensity())
.Take(maxPeaks)
.OrderBy(pk => pk.GetMZ()).ToList();;
spectrum.SetPeaks(peaks);
}
private void SetMatcher(ISpectrum spectrum)
{
List <IPoint> points = new List <IPoint>();
foreach (IPeak peaks in spectrum.GetPeaks())
{
points.Add(new GeneralPoint(peaks.GetMZ()));
}
matcher.setData(points);
}
public ISpectrum Process(ISpectrum spectrum)
{
ISpectrum filtered = peakPicking.Process(spectrum);
List <IPeak> peaks = new List <IPeak>();
double minIntensity = filtered.GetPeaks().Min(p => p.GetIntensity());
filtered.SetPeaks(
peaks.Where(p => p.GetIntensity() > ratio * minIntensity).ToList());
return(filtered);
}
protected virtual List <IPeak> InsertPeaks(ISpectrum spectrum)
{
List <IPeak> peaks = new List <IPeak>();
double mz = spectrum.GetPeaks().First().GetMZ();
peaks.Add(new GeneralPeak(mz - precision, 0));
foreach (IPeak peak in spectrum.GetPeaks())
{
if (peak.GetMZ() - mz > precision)
{
double middle = (mz + peak.GetMZ()) / 2;
peaks.Add(new GeneralPeak(middle, 0));
}
peaks.Add(peak);
mz = peak.GetMZ();
}
peaks.Add(new GeneralPeak(mz + precision, 0));
return(peaks);
}
public DrawingVisual CreateDrawingVisual(ISpectrum spectrum, List <IResult> results,
double x1 = 40, double y1 = 40, double x2 = 660, int y2 = 300)
{
DrawingVisual drawingVisual = new DrawingVisual();
// Create a drawing and draw it in the DrawingContext.
using (DrawingContext drawingContext = drawingVisual.RenderOpen())
{
double delta = 10;
Pen pen = new Pen(Brushes.Black, 1);
Rect rect =
new Rect(new Point(x1 - delta, y1 - delta),
new Point(x2 + delta, y2 + delta)); // range of (600, 260)
drawingContext.DrawRectangle(Brushes.Transparent, pen, rect);
// process peaks
List <IPeak> peaks = spectrum.GetPeaks();
double deltaX = x2 - x1;
double deltaY = y2 - y1;
double minX = peaks.Min(p => p.GetMZ());
double maxX = peaks.Max(p => p.GetMZ());
List <double> x = peaks.Select(p => (p.GetMZ() - minX) / (maxX - minX) * deltaX + x1).ToList();
double maxY = peaks.Max(p => p.GetIntensity());
List <double> y = peaks.Select(p => y2 - p.GetIntensity() / maxY * deltaY).ToList();
// draw curve
List <Point> points = new List <Point>();
for (int i = 0; i < x.Count; i++)
{
points.Add(new Point(x[i], y[i]));
}
Pen curve = new Pen(Brushes.Blue, 1);
for (int i = 0; i < points.Count - 1; i++)
{
drawingContext.DrawLine(curve, points[i], points[i + 1]);
}
// draw points
Pen p = new Pen(Brushes.Red, 3);
List <double> mzList = results.Select(r => r.GetMZ()).ToList();
for (int i = 0; i < mzList.Count; i++)
{
double xi = (mzList[i] - minX) / (maxX - minX) * deltaX + x1;
double yi = y[BinarySearchPoints(mzList, xi)];
Point point = new Point(xi, yi);
drawingContext.DrawEllipse(Brushes.Red, p, point, 0.5, 0.5);
}
}
return(drawingVisual);
}
public void Process(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks();
//double sumsIntensity = Math.Log10(peaks.Sum(x => x.GetIntensity()));
for (int i = 0; i < peaks.Count; i++)
{
peaks[i].SetIntensity(Math.Log10(peaks[i].GetIntensity()) * scale);
}
spectrum.SetPeaks(peaks);
}
public void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
var builder = new ContainerBuilder();
builder.RegisterModule(new TopPeakPickingDelegatorModule()
{
MaxPeaks = 100
});
builder.RegisterModule(new SpectrumProcessingModule()
{
ScaleFactor = 1.0
});
builder.RegisterModule(new ThermoRawSpectrumModule());
IContainer Container = builder.Build();
List <IPeak> peakA = new List <IPeak>();
List <IPeak> peakB = new List <IPeak>();
using (var scope = Container.BeginLifetimeScope())
{
var spectrumFacotry = scope.Resolve <ISpectrumFactory>();
spectrumFacotry.Init(@"C:\Users\Rui Zhang\Downloads\ZC_20171218_H95_R1.raw");
ISpectrum spectrum = spectrumFacotry.GetSpectrum(8140);
peakA.AddRange(spectrum.GetPeaks());
}
using (var scope = Container.BeginLifetimeScope())
{
var spectrumFacotry = scope.Resolve <ISpectrumFactory>();
spectrumFacotry.Init(@"C:\Users\Rui Zhang\Downloads\ZC_20171218_H68_R1.raw");
ISpectrum spectrum = spectrumFacotry.GetSpectrum(8081);
peakB.AddRange(spectrum.GetPeaks());
}
double cons = computeCos(peakA, peakB, 0.01);
if (cons < 0.3)
{
Console.WriteLine("spectrum: " + cons.ToString());
Console.WriteLine(cons);
}
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
public ISpectrum Process(ISpectrum spectrum)
{
ISpectrum centroid = peakPicking.Process(spectrum);
List <IPeak> peaks = new List <IPeak>();
foreach (IPeak cPeak in centroid.GetPeaks())
{
List <IPeak> neighbors = NeighborPeaks(cPeak, spectrum.GetPeaks());
peaks.Add(Average(cPeak, neighbors));
}
centroid.SetPeaks(peaks);
return(centroid);
}
public double computeCos(ISpectrum spectrumA, ISpectrum spectrumB, double tol)
{
List <IPeak> p1 = spectrumA.GetPeaks();
List <IPeak> p2 = spectrumB.GetPeaks();
double lowerBound = Math.Min(p1.Min(x => x.GetMZ()), p2.Min(x => x.GetMZ()));
double upperBound = Math.Max(p1.Max(x => x.GetMZ()), p2.Max(x => x.GetMZ()));
int bucketNums = (int)Math.Ceiling((upperBound - lowerBound + 1) / tol);
List <IPeak>[] q1 = new List <IPeak> [bucketNums];
List <IPeak>[] q2 = new List <IPeak> [bucketNums];
for (int i = 0; i < bucketNums; i++)
{
q1[i] = new List <IPeak>();
q2[i] = new List <IPeak>();
}
foreach (IPeak pk in p1)
{
int index = (int)Math.Ceiling((pk.GetMZ() - lowerBound) / tol);
q1[index].Add(pk);
}
foreach (IPeak pk in p2)
{
int index = (int)Math.Ceiling((pk.GetMZ() - lowerBound) / tol);
q2[index].Add(pk);
}
double numerator = 0;
for (int i = 0; i < bucketNums; i++)
{
numerator += computeDot(q1[i], q2[i]);
}
double denominator1 = 0;
foreach (IPeak pk in p1)
{
denominator1 += pk.GetIntensity() * pk.GetIntensity();
}
double denominator2 = 0;
foreach (IPeak pk in p2)
{
denominator2 += pk.GetIntensity() * pk.GetIntensity();
}
double denominator = Math.Sqrt(denominator1) * Math.Sqrt(denominator2);
return(numerator / denominator);
}
protected List <IAnnotatedPeak> GenerateMatcherResult(ISpectrum spectrum)
{
List <IAnnotatedPeak> peaks = new List <IAnnotatedPeak>();
foreach (IPeak peak in spectrum.GetPeaks())
{
List <IGlycoPeptide> g = MatchPoints(peak, (spectrum as ISpectrumMSn).GetParentCharge());
if (g.Count > 0)
{
peaks.Add(new GeneralAnnotatedSpectrumPeak(peak, g));
}
}
return(peaks);
}
private void Visualize_Click(object sender, RoutedEventArgs e)
{
if (path.Length == 0)
{
MessageBox.Show("Please input the spectrum file (*.Raw) path!");
return;
}
int scan;
int.TryParse(ScanNumber.Text, out scan);
if (scan > 0 && scan < spectrumReader.GetLastScan() &&
spectrumReader.GetMSnOrder(scan) == 1)
{
ISpectrum spectrum = spectrumProcessor.Process(spectrumReader.GetSpectrum(scan));
double rt = spectrumReader.GetRetentionTime(scan);
double index = Math.Round(engine.Normalize(rt), 2);
string output = "Retention time: " + Math.Round(rt, 2).ToString() + " (min) ";
if (index > 0)
{
output += "GUI index " + index.ToString();
}
RTtime.Text = output;
// search
List <IResult> results = spectrumSearch.Search(spectrum);
//// draw curve
canvas.Children.Clear();
if (spectrum.GetPeaks().Count > 0)
{
canvas.Children.Add(new VisualHost
{
Visual = visualizer.CreateDrawingVisual(spectrum, results)
});
}
PeakArea.Visibility = Visibility.Visible;
}
else
{
MessageBox.Show("Please input a valid scan number!");
canvas.Children.Clear();
PeakArea.Visibility = Visibility.Collapsed;
return;
}
}
protected IDataPoints InitSpectrum(ISpectrum spectrum)
{
BucketSpectrumDataPoints data = new BucketSpectrumDataPoints(
(parameter as DPSpectrumCIDParameter).GetBucketSize(),
(parameter as DPSpectrumCIDParameter).GetMinRange());
int charge = (spectrum as ISpectrumMSn).GetParentCharge();
for (int i = 1; i <= charge; i++)
{
foreach (IPeak peak in spectrum.GetPeaks())
{
PeakPoint pt = new PeakPoint(peak.GetIntensity(), peak.GetMZ(), i, peak.GetMZ().ToString());
data.Add(pt);
}
}
return(data);
}
// assume the spectrum read sequentially
public double GetMonoMass(ISpectrum spectrum)
{
if (spectrum.GetMSnOrder() == 1)
{
List <IPoint> points = new List <IPoint>();
foreach (IPeak pk in spectrum.GetPeaks())
{
points.Add(new PeakPoint(pk));
}
matcher.setData(points);
return(0);
}
ISpectrumMSn spectrumMSn = spectrum as ISpectrumMSn;
double mz = spectrumMSn.GetParentMZ();
double monoMass = mz;
// search isotopic point on full MS spectrum
int charge = spectrumMSn.GetParentCharge();
int isotopic = 0;
while (isotopic < maxIsotopic)
{
double target = mz - Proton / charge * (isotopic + 1);
if (!matcher.Found(new GeneralPoint(target)))
{
break;
}
isotopic++;
}
// get max intensity peak
if (isotopic == 0)
{
return(monoMass);
}
double isoMZ = mz - Proton / charge * isotopic;
List <IPoint> matched = matcher.Search(new GeneralPoint(isoMZ));
return(matched.OrderBy(x => Math.Abs((x as PeakPoint).MZ - isoMZ)).First().GetValue());
}
public ISpectrum Process(ISpectrum spectrum)
{
if (spectrum.GetPeaks().Count == 0)
{
return(spectrum);
}
// insert pseudo peaks for large gap
List <IPeak> peaks = InsertPeaks(spectrum);
List <IPeak> processedPeaks = new List <IPeak>();
int index = 1;
int end = peaks.Count - 1;
int head = index + 1;
while (index < end)
{
if (peaks[index - 1].GetIntensity() < peaks[index].GetIntensity())
{
head = index + 1;
}
while (head < end &&
peaks[head].GetIntensity() == peaks[index].GetIntensity())
{
head++;
}
if (peaks[head].GetIntensity() < peaks[index].GetIntensity())
{
processedPeaks.Add(peaks[index]);
index = head;
}
index++;
}
ISpectrum newSpectrum = spectrum.Clone();
newSpectrum.SetPeaks(processedPeaks);
return(newSpectrum);
}
public void test1()
{
string path = @"C:\Users\Rui Zhang\Downloads\ZC_20171218_C16_R1.raw";
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
reader.Init(path);
ISpectrum ms2 = reader.GetSpectrum(7638);
//IProcess processer = new LocalNeighborPicking();
IProcess processer = new WeightedAveraging(new LocalNeighborPicking());
//RidgeLineFinder coeffMatrix = new RidgeLineFinder(1.0, 2, 1, 2);
//IProcess processer = new PeakPickingCWT(coeffMatrix);
ms2 = processer.Process(ms2);
using (StreamWriter outputFile = new StreamWriter(@"C:\Users\Rui Zhang\Downloads\peak.csv"))
{
outputFile.WriteLine("mz,intensity");
foreach (IPeak pk in ms2.GetPeaks())
{
outputFile.WriteLine(pk.GetMZ().ToString() + "," + pk.GetIntensity().ToString());
}
}
}
public int FindGlucoseUnits(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks();
double bestIntensity = 0;
int units = 0;
for (int i = 0; i < Glucose.Length; i++)
{
double mass = Glucose[i];
List <double> mzCandidates = IonMassCalc.Instance.ComputeMZ(mass);
foreach (double mz in mzCandidates)
{
int idx = BinarySearchPoints(peaks, mz);
if (idx > 0 && peaks[idx].GetIntensity() > bestIntensity)
{
bestIntensity = peaks[idx].GetIntensity();
units = i + 2;
}
}
}
return(units);
}
public void test2()
{
string path = @"C:\Users\Rui Zhang\Downloads\Serum_1_C18_03292019_Ali.raw";
ISpectrumReader reader = new ThermoRawSpectrumReader();
reader.Init(path);
RidgeLineFinder coeffMatrix = new RidgeLineFinder(1.0, 2, 1, 2);
IProcess processer = new PeakPickingCWT(coeffMatrix);
//for (int i = reader.GetFirstScan(); i < reader.GetLastScan(); i++)
int i = 342;
{
if (reader.GetMSnOrder(i) < 2)
{
ISpectrum spectrum = reader.GetSpectrum(i);
spectrum = processer.Process(spectrum);
foreach (var peak in spectrum.GetPeaks())
{
Console.WriteLine(peak.GetMZ().ToString() + ": " + peak.GetIntensity().ToString());
}
}
}
}
public void ParallelRun(string path, string outputDir, AveragineType type, ChargerType chargerType)
{
string file = Path.GetFileNameWithoutExtension(path) + ".mgf";
string output = Path.Combine(outputDir, file);
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM);
reader.Init(path);
Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >();
int current = -1;
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
scanGroup[i] = new List <int>();
}
else if (reader.GetMSnOrder(i) == 2)
{
scanGroup[current].Add(i);
}
}
List <MS2Info> ms2Infos = new List <MS2Info>();
Parallel.ForEach(scanGroup, (scanPair) =>
{
if (scanPair.Value.Count > 0)
{
ISpectrum ms1 = reader.GetSpectrum(scanPair.Key);
foreach (int i in scanPair.Value)
{
double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
continue;
}
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
ICharger charger = new Patterson();
if (chargerType == ChargerType.Fourier)
{
charger = new Fourier();
}
else if (chargerType == ChargerType.Combined)
{
charger = new PattersonFourierCombine();
}
int charge = charger.Charge(peaks, 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(type);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
double precursorMZ = result.GetMZ();
// write mgf
ISpectrum ms2 = reader.GetSpectrum(i);
IProcess processer = new WeightedAveraging(new LocalNeighborPicking());
ms2 = processer.Process(ms2);
MS2Info ms2Info = new MS2Info
{
PrecursorMZ = result.GetMZ(),
PrecursorCharge = charge,
Scan = ms2.GetScanNum(),
Retention = ms2.GetRetention(),
Peaks = ms2.GetPeaks()
};
lock (resultLock)
{
ms2Infos.Add(ms2Info);
}
}
}
readingProgress.Add(scanGroup.Count);
});
ms2Infos = ms2Infos.OrderBy(m => m.Scan).ToList();
using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
foreach (MS2Info ms2 in ms2Infos)
{
WriteMGF(writer, path + ",SCANS=" + ms2.Scan.ToString() + ",PRECURSOR=" + ms2.PrecursorMZ, ms2.PrecursorMZ, ms2.PrecursorCharge,
ms2.Scan, ms2.Retention * 60, reader.GetActivation(ms2.Scan), ms2.Peaks);
writer.Flush();
}
}
}
// update progress
progress.Add();
}
public void Init(ISpectrum spectrum)
{
searcher.Init(spectrum.GetPeaks()
.Select(p => new Point <IPeak>(p.GetMZ(), p)).ToList());
}
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 Test1()
{
string path = @"D:\Raw\ZC_20171218_N14_R2.raw";
ISpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking(10);
reader.Init(path);
Dictionary <int, int> scanMap = new Dictionary <int, int>();
int current = -1;
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
}
else if (reader.GetMSnOrder(i) == 2)
{
scanMap[i] = current;
}
}
double searchRange = 1;
int scan_num = 6223;
if (scanMap.ContainsKey(scan_num))
{
int paranet_scan = scanMap[scan_num];
ISpectrum ms1 = reader.GetSpectrum(paranet_scan);
double mz = reader.GetPrecursorMass(scan_num, reader.GetMSnOrder(scan_num));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
return;
}
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
//Console.WriteLine("mz,intensity");
//foreach (IPeak pk in peaks)
//{
// Console.WriteLine(pk.GetMZ().ToString() + "," + pk.GetIntensity().ToString());
//}
Fourier charger = new Fourier();
int charge = charger.Charge(peaks, mz - searchRange, mz + searchRange);
Patterson charger2 = new Patterson();
PattersonFourierCombine charger3 = new PattersonFourierCombine();
Console.WriteLine(charge.ToString() + " "
+ charger2.Charge(peaks, mz - searchRange, mz + searchRange).ToString() + " "
+ charger3.Charge(peaks, mz - searchRange, mz + searchRange).ToString());
}
}