public void GetSICParam()
{
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
List <IGlycanPeak> glycans = builder.Build();
HashSet <double> mzList = new HashSet <double>();
foreach (IGlycanPeak g in glycans)
{
if (!mzList.Contains(g.HighestPeak()))
{
mzList.Add(g.HighestPeak());
}
}
using (StreamWriter file = new(@"C:\Users\iruiz\Downloads\SICParam.csv"))
{
file.WriteLine("MZ,MZToleranceDa");
foreach (double mz in mzList.OrderBy(p => p).ToList())
{
file.WriteLine(mz.ToString() + ",0.5");
}
}
}
public void AreaTest()
{
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
List <IGlycanPeak> glycans = builder.Build();
ISpectrumReader spectrumReader = new ThermoRawSpectrumReader();
spectrumReader.Init(@"C:\Users\iruiz\Downloads\GUI\compare\data\HBS1_dextrinspkd_C18_10252018.raw");
List <double> ions = new List <double>();
ions.Add(Calculator.proton);
Calculator.To.SetChargeIons(ions);
using (StreamWriter file = new(@"C:\Users\iruiz\Downloads\GUI\compare\data\WriteLines2.csv"))
{
file.WriteLine("glycan,mass,mz,charge,score,area");
//for (int scan = spectrumReader.GetFirstScan(); scan <= spectrumReader.GetLastScan(); scan++)
//{
int scan = 2931; // 3943;
if (spectrumReader.GetMSnOrder(scan) != 1)
{
return;
}
ISpectrum spectrum = spectrumReader.GetSpectrum(scan);
IResultFactory factory = new NGlycanResultFactory();
EnvelopeProcess envelopeProcess = new EnvelopeProcess(10, ToleranceBy.PPM);
MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory);
IProcess spectrumProcess = new LocalNeighborPicking();
ISpectrumSearch spectrumSearch = new NGlycanSpectrumSearch(glycans,
spectrumProcess, envelopeProcess, monoisotopicSearcher);
List <IResult> results = spectrumSearch.Search(spectrum);
//IAreaCalculator areaCalculator = new TrapezoidalRule();
IXIC xicer = new TIQ3XIC(spectrumReader, 0.01, ToleranceBy.Dalton);
//IXIC xicer = new PeakXIC(areaCalculator, spectrumReader, 0.01, ToleranceBy.Dalton);
foreach (IResult r in results)
{
double area = xicer.Area(r);
string output = r.Glycan().GetGlycan().Name() + "," +
r.Glycan().GetGlycan().Mass().ToString() + "," +
r.GetMZ().ToString() + "," +
r.GetCharge().ToString() + "," +
r.Score().ToString() + "," +
area.ToString();
file.WriteLine(output);
}
//}
}
Assert.Pass();
}
public void NGlycanSearch()
{
IResultFactory factory = new NGlycanResultFactory();
EnvelopeProcess envelopeProcess = new EnvelopeProcess(10, ToleranceBy.PPM);
MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory);
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
List <IGlycanPeak> glycans = builder.Build();
IProcess spectrumProcess = new LocalNeighborPicking();
ISpectrumSearch spectrumSearch = new NGlycanSpectrumSearch(glycans,
spectrumProcess, envelopeProcess, monoisotopicSearcher);
ISpectrumReader spectrumReader = new ThermoRawSpectrumReader();
spectrumReader.Init(@"C:\Users\iruiz\Downloads\Serum_dextrinspiked_C18_10162018_2.raw");
for (int scan = spectrumReader.GetFirstScan(); scan <= spectrumReader.GetLastScan(); scan++)
{
if (spectrumReader.GetMSnOrder(scan) != 1)
{
continue;
}
ISpectrum spectrum = spectrumReader.GetSpectrum(scan);
List <IResult> results = spectrumSearch.Search(spectrum);
foreach (IResult r in results)
{
Console.WriteLine(r.Glycan().GetGlycan().Name()
+ ": " + r.Glycan().GetGlycan().Mass().ToString());
List <double> mzList = Calculator.To.ComputeMZ(r.Glycan().HighestPeak(), 3);
Console.WriteLine(string.Join(",", mzList));
Console.WriteLine(r.Score());
foreach (IPeak pk in r.Matches())
{
Console.WriteLine(pk.GetMZ() + " " + pk.GetIntensity());
}
Console.WriteLine();
}
break;
}
Assert.Pass();
}
public void NGlycanTest()
{
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
List <IGlycanPeak> peaks = builder.Build();
foreach (var item in peaks)
{
Console.WriteLine(item.GetGlycan().Name());
Console.WriteLine(String.Join(",", item.GetDistrib().Select(d => Math.Round(d, 2).ToString())));
Console.WriteLine(item.GetGlycan().Mass().ToString()
+ " " + item.HighestPeak().ToString());
Console.WriteLine();
}
Assert.Pass();
}
public MainWindow()
{
InitializeComponent();
// build up searcher
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
glycans = builder.Build();
IResultFactory factory = new NGlycanResultFactory();
EnvelopeProcess envelopeProcess = new EnvelopeProcess(10, ToleranceBy.PPM);
MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory);
spectrumSearch = new NGlycanSpectrumSearch(glycans,
spectrumProcessor, envelopeProcess, monoisotopicSearcher);
}
static void Main(string[] args)
{
string dir = @"C:\Users\iruiz\Downloads\GUI\compare\data";
string[] files = Directory.GetFiles(dir);
List <double> ions = new List <double>();
ions.Add(Calculator.proton);
Calculator.To.SetChargeIons(ions);
foreach (string path in files)
{
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
List <IGlycanPeak> glycans = builder.Build();
IResultFactory factory = new NGlycanResultFactory();
EnvelopeProcess envelopeProcess = new EnvelopeProcess(10, ToleranceBy.PPM);
MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory);
IProcess spectrumProcess = new LocalNeighborPicking();
ISpectrumSearch spectrumSearch = new NGlycanSpectrumSearch(glycans,
spectrumProcess, envelopeProcess, monoisotopicSearcher);
ISpectrumReader spectrumReader = new ThermoRawSpectrumReader();
spectrumReader.Init(path);
ICurveFitting Fitter = new PolynomialFitting();
IResultSelect resultSelect = new ResultMaxSelect();
List <GUI> GuiPoints = Init(ref Fitter, spectrumReader);
List <IResult> final = new List <IResult>();
for (int scan = spectrumReader.GetFirstScan(); scan <= spectrumReader.GetLastScan(); scan++)
{
if (spectrumReader.GetMSnOrder(scan) != 1)
{
continue;
}
ISpectrum spectrum = spectrumReader.GetSpectrum(scan);
List <IResult> results = spectrumSearch.Search(spectrum);
resultSelect.Add(results);
final.AddRange(results);
}
// original
List <string> outputString = new List <string>();
foreach (IResult present in final)
{
int scan = present.GetScan();
double rt = present.GetRetention();
double index = Math.Round(Normalize(Fitter, rt), 2);
TIQ3XIC xicer = new TIQ3XIC(spectrumReader);
double area = xicer.OneArea(present);
List <string> output = new List <string>()
{
scan.ToString(), rt.ToString(),
index > 0? index.ToString():"0",
present.Glycan().GetGlycan().Name(),
present.GetMZ().ToString(),
area.ToString(),
};
outputString.Add(string.Join(",", output));
}
string outputPath = Path.Combine(Path.GetDirectoryName(path),
Path.GetFileNameWithoutExtension(path) + "_one_quant.csv");
using (FileStream ostrm = new FileStream(outputPath, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
writer.WriteLine("scan,time,GUI,glycan,mz,area");
foreach (string output in outputString)
{
writer.WriteLine(output);
}
writer.Flush();
}
}
// merged
List <string> outputStringMerge = new List <string>();
Dictionary <string, List <SelectResult> > resultContainer = resultSelect.Produce();
foreach (string name in resultContainer.Keys)
{
//if (name == "5-6-1-2-0")
// Console.WriteLine("here");
List <SelectResult> selectResults = resultContainer[name];
foreach (SelectResult select in selectResults)
{
if (select.Results.Count == 0)
{
continue;
}
IResult present = select.Present;
int scan = present.GetScan();
double rt = present.GetRetention();
double index = Math.Round(Normalize(Fitter, rt), 2);
IXIC xicer = new TIQ3XIC(spectrumReader);
double area = xicer.Area(select);
List <string> output = new List <string>()
{
scan.ToString(), rt.ToString(),
index > 0? index.ToString():"0",
name,
present.GetMZ().ToString(),
area.ToString()
};
outputStringMerge.Add(string.Join(",", output));
}
}
string outputPathMerge = Path.Combine(Path.GetDirectoryName(path),
Path.GetFileNameWithoutExtension(path) + "_quant.csv");
using (FileStream ostrm = new FileStream(outputPathMerge, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
writer.WriteLine("scan,time,GUI,glycan,mz,area");
foreach (string output in outputStringMerge)
{
writer.WriteLine(output);
}
writer.Flush();
}
}
stopWatch.Stop();
TimeSpan ts = stopWatch.Elapsed;
string elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}",
ts.Hours, ts.Minutes, ts.Seconds,
ts.Milliseconds / 10);
Console.WriteLine("RunTime " + elapsedTime);
}
}
public void Run(string path, Counter counter, ISpectrumReader spectrumReader, NormalizerEngine normalizer)
{
NGlycanTheoryPeaksBuilder builder = new NGlycanTheoryPeaksBuilder();
builder.SetBuildType(true, false, false);
List <IGlycanPeak> glycans = builder.Build();
spectrumReader.Init(path);
IResultSelect resultSelect = new ResultMaxSelect(SearchingParameters.Access.Threshold,
SearchingParameters.Access.PeakCutoff);
List <IResult> final = new List <IResult>();
int start = spectrumReader.GetFirstScan();
int end = spectrumReader.GetLastScan();
Parallel.For(start, end, (i) =>
{
if (spectrumReader.GetMSnOrder(i) < 2)
{
IResultFactory factory = new NGlycanResultFactory();
EnvelopeProcess envelopeProcess = new EnvelopeProcess(
SearchingParameters.Access.Tolerance,
SearchingParameters.Access.ToleranceBy);
MonoisotopicSearcher monoisotopicSearcher = new MonoisotopicSearcher(factory);
IProcess spectrumProcess = new LocalNeighborPicking();
ISpectrumSearch spectrumSearch = new NGlycanSpectrumSearch(glycans,
spectrumProcess, envelopeProcess, monoisotopicSearcher,
SearchingParameters.Access.MaxCharage, SearchingParameters.Access.Cutoff);
ISpectrum spectrum = spectrumReader.GetSpectrum(i);
List <IResult> results = spectrumSearch.Search(spectrum);
lock (resultLock)
{
resultSelect.Add(results);
final.AddRange(results);
}
}
counter.Add(end - start);
});
//original
string outputPath = Path.Combine(Path.GetDirectoryName(path),
Path.GetFileNameWithoutExtension(path) + "_one_quant.csv");
List <string> outputString = new List <string>();
foreach (IResult present in final.OrderBy(r => r.GetRetention()))
{
int scan = present.GetScan();
double rt = present.GetRetention();
double index = Math.Round(normalizer.Normalize(rt), 2);
TIQ3XIC xicer = new TIQ3XIC(spectrumReader);
double area = xicer.OneArea(present);
List <string> output;
if (!normalizer.Initialized())
{
output = new List <string>()
{
scan.ToString(), rt.ToString(),
present.Glycan().GetGlycan().Name(),
present.GetMZ().ToString(),
area.ToString(),
};
}
else
{
output = new List <string>()
{
scan.ToString(), rt.ToString(),
index > 0? index.ToString():"0",
present.Glycan().GetGlycan().Name(),
present.GetMZ().ToString(),
area.ToString(),
};
}
outputString.Add(string.Join(",", output));
}
using (FileStream ostrm = new FileStream(outputPath, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
if (!normalizer.Initialized())
{
writer.WriteLine("scan,time,glycan,mz,area");
}
else
{
writer.WriteLine("scan,time,GUI,glycan,mz,area");
}
foreach (string output in outputString)
{
writer.WriteLine(output);
}
writer.Flush();
}
}
// merged
string outputPathMerge = Path.Combine(Path.GetDirectoryName(path),
Path.GetFileNameWithoutExtension(path) + "_quant.csv");
List <string> outputStringMerge = new List <string>();
Dictionary <string, List <SelectResult> > resultContainer = resultSelect.Produce();
foreach (string name in resultContainer.Keys)
{
List <SelectResult> selectResults = resultContainer[name];
foreach (SelectResult select in selectResults)
{
IResult present = select.Present;
int scan = present.GetScan();
double rt = present.GetRetention();
double index = Math.Round(normalizer.Normalize(rt), 2);
IXIC xicer = new TIQ3XIC(spectrumReader);
double area = xicer.Area(select);
List <string> output;
if (!normalizer.Initialized())
{
output = new List <string>()
{
scan.ToString(), rt.ToString(),
name,
present.GetMZ().ToString(),
area.ToString(),
};
}
else
{
output = new List <string>()
{
scan.ToString(), rt.ToString(),
index.ToString(),
name,
present.GetMZ().ToString(),
area.ToString(),
};
}
outputStringMerge.Add(string.Join(",", output));
}
}
using (FileStream ostrm = new FileStream(outputPathMerge, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
if (!normalizer.Initialized())
{
writer.WriteLine("scan,time,glycan,mz,area");
}
else
{
writer.WriteLine("scan,time,GUI,glycan,mz,area");
}
foreach (string output in outputStringMerge)
{
writer.WriteLine(output);
}
writer.Flush();
}
}
}
