public double[][] Data()
{
double[][] data = new double[2][];
// next make a request for the filtered chromatogram.
// Define settings for XIC
ChromatogramTraceSettings traceSettings =
new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = filterMS,
MassRanges = new[] { new Range(mass, mass) }
};
// create the array of chromatogram settings
IChromatogramSettings[] allSettings = { traceSettings };
// set tolerance of +/- whatever ppm
MassOptions tolerance = new MassOptions()
{
Tolerance = ppm, ToleranceUnits = ToleranceUnits.ppm
};
// read the chromatogram
var chroData = rawFile.GetChromatogramData(allSettings, -1, -1, tolerance);
data[0] = chroData.PositionsArray.ToArray()[0];
data[1] = chroData.IntensitiesArray.ToArray()[0];
return(data);
}
/// <summary>
/// Get and set chromatogram data from the raw file
/// </summary>
/// <param name="inputRawFile"></param>
private void GetChromatogramData(IRawDataPlus inputRawFile)
{
try
{
//Get mass resolution for the run from the header
MassResolution = inputRawFile.RunHeaderEx.MassResolution;
// Find startScan and endScan
int startScan = inputRawFile.RunHeader.FirstSpectrum;
int endScan = inputRawFile.RunHeader.LastSpectrum;
//Set up settings to extract the data
ChromatogramTraceSettings traceSettings =
new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = FILTER_MS,
MassRanges = new[] { new Range(LowMass, HighMass) }
};
IChromatogramSettings[] allSettings = { traceSettings };
MassOptions massOptions = new MassOptions()
{
Tolerance = Tolerance, ToleranceUnits = ToleranceUnits
};
var chromatogramData = inputRawFile.GetChromatogramData(allSettings, startScan, endScan, massOptions); //get all chromatogram data
// Get data from the chromatogram
ScanNumList = chromatogramData.ScanNumbersArray[0];
ExactMassList = chromatogramData.PositionsArray[0]; //get positions of each scan
MassIntensityList = chromatogramData.IntensitiesArray[0]; //get list of intensities for scan numbers
}
catch (Exception ex)
{
Console.Write("Error in accessing chromatogram data: " + ex);
}
}
private void UpdateChromatogramData()
{
ChromatogramTraceSettings traceSettings;
MassOptions tolerance = null;
string msFilter;
if (ChroMsLevelComboBox.Text == "MS1" | ChroMsLevelComboBox.SelectedIndex == -1)
{
msFilter = "ms";
}
else if (ChroMsLevelComboBox.Text == "MS2")
{
msFilter = "ms2";
}
else if (ChroMsLevelComboBox.Text == "MS3")
{
msFilter = "ms3";
}
else
{
msFilter = String.Empty;
}
if (ChroTICRadioButton.Checked)
{
traceSettings = new ChromatogramTraceSettings(TraceType.TIC);
}
else if (ChroBPRadioButton.Checked)
{
traceSettings = new ChromatogramTraceSettings(TraceType.BasePeak);
}
else
{
if (ChroXICmzTextBox.Text.IsNullOrEmpty() || ChroXICmzTextBox.BackColor == Color.Red || ChroXICmzTextBox.Text == "")
{
traceSettings = new ChromatogramTraceSettings(TraceType.TIC);
}
else
{
double da = Convert.ToDouble(ChroXICmzTextBox.Text);
traceSettings = new ChromatogramTraceSettings(TraceType.MassRange)
{
MassRanges = new[] { new Range(da, da) },
};
if (!chroXICToleranceTextBox.Text.IsNullOrEmpty() && !(chroXICToleranceTextBox.BackColor == Color.Red) && !(chroXICToleranceTextBox.Text == ""))
{
tolerance = new MassOptions()
{
Tolerance = Convert.ToDouble(chroXICToleranceTextBox.Text)
};
if (chroMassTolPPM.Checked)
{
tolerance.ToleranceUnits = ToleranceUnits.ppm;
}
else if (chroMassTolDa.Checked)
{
tolerance.ToleranceUnits = ToleranceUnits.amu;
}
else
{
tolerance.ToleranceUnits = ToleranceUnits.mmu;
}
}
}
}
traceSettings.Filter = msFilter;
IChromatogramSettingsEx[] allSettings = { traceSettings };
ChromatogramData = RawData.GetChromatogramDataEx(allSettings, -1, -1, tolerance);
}
