public static TrailerExtraCollection TrailerExtras(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting trailer extras");
TrailerExtraCollection trailerExtras = new TrailerExtraCollection();
TrailerExtraIndices trailerIndices = new TrailerExtraIndices(rawFile);
Double[] spsMasses;
var scans = index.ScanEnumerators[MSOrderType.Any];
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting trailer extras");
P.Start();
foreach (int scan in scans)
{
trailerExtras[scan] = ExtractOneTrailerExtra(rawFile, scan, trailerIndices);
P.Update();
}
P.Done();
return(trailerExtras);
}
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);
}
