private static void WritePScans(string fileName,
IRawDataPlus raw,
List <PScan> scans)
{
var enumerator = raw.GetFilteredScanEnumerator(" ");
foreach (var scanNumber in enumerator) // note in my tests serial is faster than Parallel.Foreach() (this involves disk access, so it makes sense)
{
//trailer iinformation is extracted via index
var trailers = raw.GetTrailerExtraValues(scanNumber);
var trailerLabels = raw.GetTrailerExtraInformation(scanNumber);
object chargeState = 0;
for (int i = 0; i < trailerLabels.Labels.Length; i++)
{
if (trailerLabels.Labels[i] == "Charge State:")
{
chargeState = raw.GetTrailerExtraValue(scanNumber, i);
break;
}
}
var scanFilter = raw.GetFilterForScanNumber(scanNumber);
var scanStats = raw.GetScanStatsForScanNumber(scanNumber);
CentroidStream centroidStream = new CentroidStream();
//check for FT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
centroidStream = raw.GetCentroidStream(scanNumber, false);
}
//check for IT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerITMS)
{
var scanData = raw.GetSimplifiedScan(scanNumber);
centroidStream.Masses = scanData.Masses;
centroidStream.Intensities = scanData.Intensities;
}
var msOrder = raw.GetScanEventForScanNumber(scanNumber).MSOrder;
if (msOrder == MSOrderType.Ms)
{
var pscan = GetPScan(scanStats, centroidStream, 1, fileName, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
if (msOrder == MSOrderType.Ms2)
{
var precursorMz = raw.GetScanEventForScanNumber(scanNumber).GetReaction(0).PrecursorMass;
var pscan = GetPScan(scanStats, centroidStream, 2, fileName, precursorMz, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
var t = raw.GetTrailerExtraValues(scanNumber);
}
WriteScans(scans, fileName);
}
private static TrailerExtraData ExtractOneTrailerExtra(IRawDataPlus rawFile, int scan, TrailerExtraIndices indices)
{
TrailerExtraData trailerExtra = new TrailerExtraData();
Double[] spsMasses;
if (indices.InjectionTime != -1)
{
trailerExtra.InjectionTime = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.InjectionTime));
}
if (indices.ChargeState != -1)
{
trailerExtra.ChargeState = Convert.ToInt32(rawFile.GetTrailerExtraValue(scan, indices.ChargeState));
}
if (indices.MonoisotopicMZ != -1)
{
trailerExtra.MonoisotopicMZ = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.MonoisotopicMZ));
}
if (indices.MasterScan != -1)
{
try
{
trailerExtra.MasterScan = Convert.ToInt32(rawFile.GetTrailerExtraValue(scan, indices.MasterScan));
}
// if that doesn't work the master scan is (hopefully) not applicable, we can leave it at the defaule value of -1
catch (FormatException)
{
}
}
if (indices.HCDEnergy != -1)
{
var hcd = rawFile.GetTrailerExtraValue(scan, indices.HCDEnergy).ToString();
if (hcd != "N/A" & hcd != "" & !hcd.All(x => x == ' '))
{
try
{
trailerExtra.HCDEnergy = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.HCDEnergy));
}
catch (FormatException)
{
}
}
}
if (indices.SPSMasses.Count > 2) // if so, this means with have all SPS masses listed individually
{
spsMasses = new double[indices.SPSMasses.Count];
for (int i = 0; i < indices.SPSMasses.Count; i++)
{
spsMasses[i] = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.SPSMasses[i]));
}
}
if (indices.SPSMasses.Count == 0) // there are no SPS masses
{
spsMasses = new double[0];
}
else // they are broken into two lists of strings, comma delimited
{
char[] delimiter = { ' ', ',' };
string[] stringsps1 = rawFile.GetTrailerExtraValue(scan, indices.SPSMasses[0]).ToString().Split(delimiter, StringSplitOptions.RemoveEmptyEntries);
string[] stringsps2 = rawFile.GetTrailerExtraValue(scan, indices.SPSMasses[1]).ToString().Split(delimiter, StringSplitOptions.RemoveEmptyEntries);
double[] sps1 = Array.ConvertAll(stringsps1, Convert.ToDouble);
double[] sps2 = Array.ConvertAll(stringsps2, Convert.ToDouble);
spsMasses = new double[sps1.Length + sps2.Length];
sps1.CopyTo(spsMasses, 0);
sps2.CopyTo(spsMasses, sps1.Length);
}
trailerExtra.SPSMasses = spsMasses;
return(trailerExtra);
}
