}
}
writer.Flush();
startNum += 1;
}
writer.Close();
}
public static void getMSdataFromRT(double startRT, int endRT, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
if (highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
int startNum = plus.ScanNumberFromRetentionTime(startRT);
int endNum = plus.ScanNumberFromRetentionTime(endRT);
int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter");
while (startNum <= endNum)
{
Scan scan = Scan.FromFile(plus, startNum);
string filter = plus.GetFilterForScanNumber(startNum).ToString();
int cnt = 0;
while (cnt < scan.PreferredMasses.Length)
{
if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
//writer.WriteLine("{0},{1},{2},{3},{4},{5},{6}", startNum.ToString(), rt.ToString(), msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(), filter.ToString());
writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
public static void getSRMIacdMZ(string filePath, double valMS,int recVal)
private void InitializeChromatogramPlot()
{
chromatogram = new PlotModel();
chromatogram.Axes.Add(new LinearAxis {
Position = AxisPosition.Left, AbsoluteMinimum = 0
});
chromatogram.Axes.Add(new LinearAxis {
Position = AxisPosition.Bottom, AbsoluteMinimum = 0, AbsoluteMaximum = TotalTime
});
chromatogram.Axes[x].MajorGridlineStyle = LineStyle.Solid;
chromatogram.Axes[y].MajorGridlineStyle = LineStyle.Solid;
//chromatogram.Axes[y].IsZoomEnabled = false;
var currentScanLine = new LineAnnotation()
{
Type = LineAnnotationType.Vertical,
X = 0,
Color = OxyColors.Black
};
var mouseLocationLine = new LineAnnotation()
{
Type = LineAnnotationType.Vertical,
X = 0,
Color = OxyColors.DimGray
};
var chroSeries = new AreaSeries();
chroSeries.Color = Colors.ColorBrewer8ClassSet2(255).Last();
for (int i = 0; i < ChromatogramData.PositionsArray[0].Length; i++)
{
chroSeries.Points.Add(new DataPoint(ChromatogramData.PositionsArray[0][i], ChromatogramData.IntensitiesArray[0][i]));
}
chromatogram.Series.Add(chroSeries);
double max = (from i in ChromatogramData.IntensitiesArray[0] select i).Max() * 1.5;
if (max <= 0)
{
max = 1000;
}
chromatogram.Axes[y].AbsoluteMaximum = max;
chromatogram.Axes[y].Maximum = chromatogram.Axes[y].AbsoluteMaximum;
chromatogram.Axes[y].MajorStep = chromatogram.Axes[y].Maximum / 3;
chromatogram.Axes[y].StringFormat = "0.00E00";
chromatogram.Axes[y].TransformChanged += (object sender, EventArgs e) =>
{
chromatogram.Axes[y].MajorStep = (chromatogram.Axes[y].ActualMaximum - chromatogram.Axes[y].ActualMinimum) / 3;
};
plotViewChromatogram.MouseEnter += (s, e) =>
{
plotViewChromatogram.Cursor = Cursors.Cross;
};
chromatogram.MouseDown += (s, e) =>
{
if (e.ChangedButton == OxyMouseButton.Left)
{
double rt = chromatogram.Axes[x].InverseTransform(e.Position.X, e.Position.Y, chromatogram.Axes[y]).X;
scanNumber.Text = RawData.ScanNumberFromRetentionTime(rt).ToString();
currentScanLine.X = RawData.RetentionTimeFromScanNumber(Convert.ToInt32(scanNumber.Text));
e.Handled = true;
chromatogram.InvalidatePlot(false);
}
};
chromatogram.MouseMove += (s, e) =>
{
try
{
mouseLocationLine.X = currentScanLine.InverseTransform(e.Position).X;
}
catch (Exception)
{
//do nothing
}
e.Handled = false;
chromatogram.InvalidatePlot(false);
};
chromatogram.MouseUp += (s, e) =>
{
plotViewChromatogram.Cursor = Cursors.Cross;
chromatogram.InvalidatePlot(true);
e.Handled = false;
};
chromatogram.MouseLeave += (s, e) =>
{
mouseLocationLine.X = 0;
chromatogram.InvalidatePlot(false);
e.Handled = true;
};
chromatogram.Annotations.Add(currentScanLine);
chromatogram.Annotations.Add(mouseLocationLine);
currentScanLine.MouseDown += (s, e) =>
{
if (e.ChangedButton != OxyMouseButton.Left)
{
return;
}
plotViewChromatogram.Cursor = Cursors.SizeWE;
chromatogram.InvalidatePlot(false);
e.Handled = true;
};
currentScanLine.MouseMove += (s, e) =>
{
double rt = currentScanLine.InverseTransform(e.Position).X;
currentScanLine.X = rt;
mouseLocationLine.X = rt;
scanNumber.Text = RawData.ScanNumberFromRetentionTime(rt).ToString();
chromatogram.InvalidatePlot(false);
e.Handled = true;
};
currentScanLine.MouseUp += (s, e) =>
{
plotViewChromatogram.Cursor = Cursors.Cross;
e.Handled = true;
};
chromatogram.InvalidatePlot(true);
}
//int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
LimitedSizeDictionary<string, int> precursorMs2ScanNumbers = new LimitedSizeDictionary<string, int>(40);
plus.SelectInstrument(Device.MS, 1);
if(highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
double maxMs = plus.RunHeaderEx.HighMass;
double minMs = plus.RunHeaderEx.LowMass;
lowMS = minMs;
highMS = maxMs;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter,MSLevel,collisionEnergy, precursorNum,precursorMS");
while (startNum <= endNum)
{
var levelInfo = "";
var spectrumRef = "";
Scan scan = Scan.FromFile(plus, startNum);
IScanFilter scanFilter = plus.GetFilterForScanNumber(startNum);
IScanEvent scanEvent = plus.GetScanEventForScanNumber(startNum);
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
// Keep track of scan number for precursor reference
precursorMs1ScanNumber = startNum;
reaction = scanEvent.GetReaction(0);
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
levelInfo = scanFilter.MSOrder.ToString() + "," + "" + "," + "" + "," + "";
break;
case MSOrderType.Ms2:
// Keep track of scan number and isolation m/z for precursor reference
var result = Regex.Match(scanEvent.ToString(), FilterStringIsolationMzPattern);
if (result.Success)
{
if (precursorMs2ScanNumbers.ContainsKey(result.Groups[1].Value))
{
precursorMs2ScanNumbers.Remove(result.Groups[1].Value);
}
precursorMs2ScanNumbers.Add(result.Groups[1].Value, startNum);
}
spectrumRef = precursorMs1ScanNumber.ToString();
reaction = scanEvent.GetReaction(0);
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
precursorMS = reaction.PrecursorMass;
levelInfo = scanFilter.MSOrder.ToString() + "," + value + "," + spectrumRef.ToString() + "," + precursorMS.ToString() ;
break;
case MSOrderType.Ms3:
var precursorMs2ScanNumber = precursorMs2ScanNumbers.Keys.FirstOrDefault(isolationMz => scanEvent.ToString().Contains(isolationMz));
spectrumRef = precursorMs2ScanNumbers[precursorMs2ScanNumber].ToString();
if (!precursorMs2ScanNumber.IsNullOrEmpty())
{
reaction = scanEvent.GetReaction(1);
}
else
{
throw new InvalidOperationException("Couldn't find a MS2 precursor scan for MS3 scan " + scanEvent);
}
precursorMS = reaction.PrecursorMass;
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
levelInfo = scanFilter.MSOrder.ToString() + "," + value + "," + spectrumRef.ToString() + "," + precursorMS.ToString();
break;
default:
throw new ArgumentOutOfRangeException();
}
//var scanStatistics = plus.GetScanStatsForScanNumber(startNum);
//// Get the segmented (low res and profile) scan data
//var segmentedScan = plus.GetSegmentedScanFromScanNumber(startNum, scanStatistics);
//var masses = segmentedScan.Positions;
//var intensitis = segmentedScan.Intensities;
//Console.WriteLine(masses.Length);
//Console.WriteLine(intensitis.Length);
//Console.WriteLine(filterObj.MSOrder);
int cnt = 0;
while(cnt < scan.PreferredMasses.Length)
{
if(lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS )
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
writer.WriteLine("{0},{1},{2},{3},{4},{5},{6},{7}", startNum.ToString(), rt.ToString(),
msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(),
scanFilter.ToString(), levelInfo);
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
public static void getMSdataFromRT(double startRT, int endRT, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
if (highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
int startNum = plus.ScanNumberFromRetentionTime(startRT);
int endNum = plus.ScanNumberFromRetentionTime(endRT);
int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter");
while (startNum <= endNum)
{
Scan scan = Scan.FromFile(plus, startNum);
string filter = plus.GetFilterForScanNumber(startNum).ToString();
int cnt = 0;
while (cnt < scan.PreferredMasses.Length)
{
if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
writer.WriteLine("{0},{1},{2},{3},{4},{5},{6}", startNum.ToString(), rt.ToString(), msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(), filter.ToString());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}