private void Area_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 = spectrumReader.GetSpectrum(scan);
List <IResult> results = spectrumSearch.Search(spectrum);
double rt = spectrumReader.GetRetentionTime(scan);
double index = Math.Round(engine.Normalize(rt), 2);
ConcurrentDictionary <IResult, double> quant = new ConcurrentDictionary <IResult, double>();
Parallel.ForEach(results, (r) =>
{
IXIC xicer = new TIQ3XIC(spectrumReader, 0.01, ToleranceBy.Dalton);
double area = xicer.Area(r);
quant[r] = area;
});
string outputPath = System.IO.Path.Combine(System.IO.Path.GetDirectoryName(path),
System.IO.Path.GetFileNameWithoutExtension(path) + ".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,factor");
foreach (IResult r in quant.Keys)
{
List <string> output = new List <string>()
{
scan.ToString(), rt.ToString(),
index > 0? index.ToString():"0",
r.Glycan().GetGlycan().Name(), r.GetMZ().ToString(),
quant[r].ToString()
};
writer.WriteLine(string.Join(",", output));
}
writer.Flush();
}
}
}
else
{
MessageBox.Show("Please input a valid scan number!");
return;
}
}
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();
}
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();
}
}
}
