public ExperimentalSpectra GetExperimentalSpectra(int scanNumber, int scanCount, int chargeState)
{
if (!mzAccessor.GetSpectrumByScanNumber(scanNumber, out var specInfo))
{
return(null);
}
var entries = new List <ExperimentalSpectraEntry>();
var precursorMass = specInfo.ParentIonMZ;
var precursorChargeState = chargeState;
var mzList = specInfo.MZList;
var intensityList = specInfo.IntensityList;
for (var i = 0; i < mzList.Length; i++)
{
var mz = mzList[i];
double intensity = intensityList[i];
entries.Add(new ExperimentalSpectraEntry(mz, intensity));
}
var expSpec = new ExperimentalSpectra(scanNumber, chargeState, precursorMass, precursorChargeState, entries, mPeptideMassCalculator);
return(expSpec);
}
// Note that Centroid is ignored by this class
public override bool GetRawData(out List <double> mzs, out List <double> intensities, int scan_num, bool centroid, int num_pts)
{
if (scan_num > mint_num_scans)
{
var mesg = "File only has " + mint_num_scans + " scans. Cannot read to scan number: " + scan_num;
throw new Exception(mesg);
}
mint_current_scan = scan_num;
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan_num, out mobj_CurrentScanData);
mzs = new List <double>();
intensities = new List <double>();
var scanData = new clsSpectrumInfo();
mobj_MzXmlFile.GetSpectrumByScanNumber(scan_num, out scanData);
var num_points = scanData.DataCount;
if (num_pts > 0 && num_pts < num_points)
{
num_points = num_pts;
}
mzs.Capacity = num_points;
intensities.Capacity = num_points;
double fMass;
double fInten;
var max_intensity = -1 * double.MaxValue;
var min_intensity = double.MaxValue;
for (var i = 0; i < scanData.DataCount; i++)
{
fMass = scanData.MZList[i];
fInten = scanData.IntensityList[i];
if (fInten > max_intensity)
{
max_intensity = fInten;
}
if (fInten < min_intensity) //Anoop Jan 08: was > before
{
min_intensity = fInten;
}
mzs.Add(fMass);
intensities.Add(fInten);
}
mdbl_signal_level = max_intensity - min_intensity;
return(true);
}