private string FixFilterLine()
{
// split FilterLine by spaces. remove empty entries
var filterLineParts = FilterLine.Split(new[] { ' ' }, StringSplitOptions.RemoveEmptyEntries).ToList();
for (var i = 0; i < filterLineParts.Count; i++)
{
var item = filterLineParts[i];
if (item.Contains("cv="))
{
filterLineParts.RemoveAt(i);
i--;
}
}
return(string.Join(" ", filterLineParts.ToArray()));
}
private string GetScanType()
{
const string returnString = "Unknown";
foreach (var param in FilterLine.Split(new[] { ' ' }, StringSplitOptions.RemoveEmptyEntries))
{
if (param.Equals("Full"))
{
return("Full");
}
if (param.Equals("SIM"))
{
return("SIM");
}
}
return(returnString);
}
public void AddMs2ScanParameters(XRawFileIO reader)
{
// grab precursorMz from raw file
var success = reader.GetScanInfo(ScanNumber, out var scanInfo);
if (!success)
{
ConsoleMsgUtils.ShowWarning("Scan {0} not found by AddMs2ScanParameters", ScanNumber);
return;
}
var precursorMzValue = Math.Round(scanInfo.ParentIonMZ, 8);
var parentScanInfo = GetParentScan(reader, scanInfo);
var parentScanDataCount = reader.GetScanData(parentScanInfo.ScanNumber, out var mzList, out var intensityList);
double precursorIntensity = 0;
if (parentScanDataCount > 0)
{
const double PRECURSOR_TOLERANCE = 0.1;
var closestDifference = double.MaxValue;
for (var i = 0; i < mzList.Length; i++)
{
var mzDifference = Math.Abs(mzList[i] - precursorMzValue);
if (mzDifference > closestDifference)
{
continue;
}
closestDifference = mzDifference;
precursorIntensity = Math.Round(intensityList[i], 2);
}
if (closestDifference > PRECURSOR_TOLERANCE)
{
// couldn't find precursor mass in MS1. That's fine i guess.
precursorIntensity = 0;
}
}
var filterLineParts = FilterLine.Split(' ');
string activationType;
switch (scanInfo.ActivationType)
{
case ActivationTypeConstants.CID:
case ActivationTypeConstants.MPD:
case ActivationTypeConstants.ECD:
case ActivationTypeConstants.PQD:
case ActivationTypeConstants.ETD:
case ActivationTypeConstants.HCD:
case ActivationTypeConstants.SA:
case ActivationTypeConstants.PTR:
case ActivationTypeConstants.NETD:
case ActivationTypeConstants.NPTR:
case ActivationTypeConstants.UVPD:
activationType = scanInfo.ActivationType.ToString();
break;
default:
// Includes ActivationTypeConstants.AnyType
activationType = "CID";
break;
}
foreach (var param in filterLineParts)
{
if (param.Contains("@"))
{
// HCD25.00 -> [HCD, 25.00]
// RegEx alpha from numeric
var activationArray = Regex.Matches(param.Split('@')[1].Trim(), @"\D+|\d+").Cast <Match>().Select(m => m.Value).ToArray();
CollisionEnergy = Convert.ToInt32(double.Parse(activationArray[1]));
}
}
PrecursorMz = new PrecursorMz(precursorIntensity, activationType, precursorMzValue);
}