public void Run(string fileName)
{
spectrumReader.Init();
spectrumReader.Read(fileName);
firstScanNum = spectrumReader.GetFirstScan();
lastScanNum = spectrumReader.GetLastScan();
}
private void MSMSFileName_Click(object sender, RoutedEventArgs e)
{
OpenFileDialog fileNameDialog = new OpenFileDialog();
fileNameDialog.Filter = "Raw File|*.raw";
fileNameDialog.Title = "Open a MS2 File";
if (fileNameDialog.ShowDialog() == true)
{
Binding fileNameBinding = new Binding();
fileNameBinding.Path = new PropertyPath("FileName");
fileNameBinding.Source = fileNameDialog;
fileNameBinding.Mode = BindingMode.OneWay;
displayFileName.SetBinding(TextBox.TextProperty, fileNameBinding);
path = displayFileName.Text;
spectrumReader.Init(path);
int start = spectrumReader.GetFirstScan();
int end = spectrumReader.GetLastScan();
for (int i = start; i <= end; i++)
{
if (spectrumReader.GetMSnOrder(i) == 1)
{
validScan.Add(i);
}
}
ScanScroll.Minimum = 0;
ScanScroll.Maximum = validScan.Count - 1;
}
}
static List <GUI> Init(ref ICurveFitting Fitter, ISpectrumReader reader)
{
double ppm = 5;
object resultLock = new object();
List <double> Retention = new List <double>();
List <double> Guis = new List <double>();
IGUIFinder finder = new BinarySearchFinder(ppm);
IProcess picking = new LocalNeighborPicking();
Dictionary <int, List <GUI> > pointMaps = new Dictionary <int, List <GUI> >();
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
Parallel.For(start, end, (i) =>
{
if (reader.GetMSnOrder(i) < 2)
{
ISpectrum spectrum = picking.Process(reader.GetSpectrum(i));
lock (resultLock)
{
pointMaps[i] = finder.FindGlucoseUnits(spectrum);
}
}
});
List <List <GUI> > points =
pointMaps.OrderBy(p => p.Key).Select(p => p.Value).ToList();
IGUISequencer sequencer = new DynamicProgrammingSequencer();
List <GUI> GuiPoints = sequencer.Choose(points);
Fitter = new PolynomialFitting();
Dictionary <int, GUI> guiSelected = new Dictionary <int, GUI>();
foreach (GUI gui in GuiPoints)
{
if (guiSelected.ContainsKey(gui.Unit))
{
if (guiSelected[gui.Unit].Peak.GetIntensity() < gui.Peak.GetIntensity())
{
guiSelected[gui.Unit] = gui;
}
}
else
{
guiSelected[gui.Unit] = gui;
}
}
Retention.Clear();
Guis.Clear();
List <GUI> guiChoice = guiSelected.Values.OrderBy(g => g.Scan).ToList();
foreach (GUI gui in guiChoice)
{
int scan = gui.Scan;
double time = reader.GetRetentionTime(scan);
Retention.Add(time);
Guis.Add(gui.Unit);
}
Fitter.Fit(Retention, Guis);
return(GuiPoints);
}
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();
}
}
}
public int GetFirstScan()
{
return(reader.GetFirstScan());
}
public double Area(IResult glycan)
{
// search xic
double mz = glycan.GetMZ();
int scan = glycan.GetScan();
int charge = glycan.GetCharge();
// get neighbors
List <ISpectrum> neighbors = new List <ISpectrum>();
int nextScan = scan;
while (nextScan > spectrumReader.GetFirstScan())
{
if (spectrumReader.GetMSnOrder(nextScan) == 1)
{
ISpectrum spectrum = spectrumReader.GetSpectrum(nextScan);
int index = BinarySearch.Search(spectrum.GetPeaks(), mz, tol, by);
if (index < 0)
{
break;
}
neighbors.Add(spectrum);
}
nextScan--;
}
nextScan = scan + 1;
while (nextScan <= spectrumReader.GetLastScan())
{
if (spectrumReader.GetMSnOrder(nextScan) == 1)
{
ISpectrum spectrum = spectrumReader.GetSpectrum(nextScan);
int index = BinarySearch.Search(spectrum.GetPeaks(), mz, tol, by);
if (index < 0)
{
break;
}
neighbors.Add(spectrum);
}
nextScan++;
}
// each neighbor get top 3 peaks
List <double> topArea = new List <double>();
List <int> delta = new List <int>()
{
-2, -1, 0, 1, 2
};
foreach (ISpectrum spetrum in neighbors)
{
List <IPeak> top = new List <IPeak>();
foreach (int j in delta)
{
int index = BinarySearch.BestSearch(spetrum.GetPeaks(), mz + 1.0 / charge * j, tol, by);
if (index < 0)
{
continue;
}
top.Add(spetrum.GetPeaks()[index]);
}
topArea.Add(top.OrderByDescending(p => p.GetIntensity()).
Take(3).Select(p => p.GetIntensity()).Sum());
}
return(topArea.OrderByDescending(a => a).Take(3).Sum());
}
public void Run(string path, Counter counter, ISpectrumReader reader)
{
reader.Init(path);
IGUIFinder finder = new BinarySearchFinder(PPM);
IProcess picking = new LocalNeighborPicking();
Dictionary <int, List <GUI> > pointMaps = new Dictionary <int, List <GUI> >();
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
Parallel.For(start, end, (i) =>
{
if (reader.GetMSnOrder(i) < 2)
{
ISpectrum spectrum = picking.Process(reader.GetSpectrum(i));
lock (resultLock)
{
pointMaps[i] = finder.FindGlucoseUnits(spectrum);
}
}
counter.Add(end - start);
});
List <List <GUI> > points =
pointMaps.OrderBy(p => p.Key).Select(p => p.Value).ToList();
IGUISequencer sequencer = new DynamicProgrammingSequencer();
List <GUI> guiPoints = sequencer.Choose(points);
Dictionary <int, GUI> guiSelected = new Dictionary <int, GUI>();
foreach (GUI gui in guiPoints)
{
if (guiSelected.ContainsKey(gui.Unit))
{
if (guiSelected[gui.Unit].Peak.GetIntensity() < gui.Peak.GetIntensity())
{
guiSelected[gui.Unit] = gui;
}
}
else
{
guiSelected[gui.Unit] = gui;
}
}
Retention.Clear();
Guis.Clear();
List <GUI> looped = guiSelected.Values.OrderBy(g => g.Scan).ToList();
string output = Path.Combine(Path.GetDirectoryName(path),
Path.GetFileNameWithoutExtension(path) + ".csv");
using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
writer.WriteLine("scan,time,gui,peak,intensity");
foreach (GUI gui in looped)
{
int scan = gui.Scan;
double time = reader.GetRetentionTime(scan);
Retention.Add(time);
Guis.Add(gui.Unit);
writer.WriteLine(scan.ToString() + "," +
time.ToString() + "," +
gui.Unit.ToString() + "," +
gui.Peak.GetMZ().ToString() + "," +
gui.Peak.GetIntensity().ToString());
}
writer.Flush();
}
}
Fitter.Fit(Retention, Guis);
initialized = true;
}