public static void RefineMonoIsoMassChargeValues(WorkFlows.WorkflowParameters parameters, CentroidStreamCollection centroids, PrecursorMassCollection precursorMasses, TrailerExtraCollection trailerExtras, PrecursorPeakCollection precursorPeaks, PrecursorScanCollection precursorScans)
{
int ms2Scan, ms1Scan, refinedCharge;
double refinedMass;
ProgressIndicator P = new ProgressIndicator(precursorPeaks.Count(), "Refining precursor charge and monoisotopic mass");
P.Start();
foreach (var peak in precursorPeaks)
{
ms2Scan = peak.Value.Ms2Scan;
if (peak.Value.PeakFound)
{
ms1Scan = peak.Value.MaxScan;
}
else
{
ms1Scan = precursorScans[ms2Scan].MasterScan;
}
(refinedCharge, refinedMass) = GetMonoIsotopicMassCharge(centroids[ms1Scan], precursorMasses[ms2Scan].ParentMZ,
trailerExtras[ms2Scan].ChargeState, parameters.ConsideredChargeStates.Min, parameters.ConsideredChargeStates.Max);
precursorMasses[ms2Scan].MonoisotopicMZ = refinedMass;
trailerExtras[ms2Scan].MonoisotopicMZ = refinedMass;
trailerExtras[ms2Scan].ChargeState = refinedCharge;
P.Update();
}
P.Done();
}
public static void WriteToDisk(WorkFlows.WorkflowParameters opts)
{
List <string> files = new List <string>();
Console.WriteLine();
Console.WriteLine("Writing log files");
foreach (var file in files)
{
Console.WriteLine(Path.GetFileName(file));
Console.WriteLine("----------------------------------------");
using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(file))
{
rawFile.SelectMsData();
var numberOfLogs = rawFile.GetStatusLogEntriesCount();
var logInfo = rawFile.GetStatusLogHeaderInformation();
string logName = file + ".INST_LOG.txt";
Dictionary <int, ISingleValueStatusLog> log = new Dictionary <int, ISingleValueStatusLog>();
ProgressIndicator P = new ProgressIndicator(logInfo.Count(), "Preparing log data");
P.Start();
for (int i = 0; i < logInfo.Count(); i++)
{
log.Add(i, rawFile.GetStatusLogAtPosition(i));
P.Update();
}
P.Done();
using (StreamWriter f = new StreamWriter(logName))
{
P = new ProgressIndicator(numberOfLogs, $"Writing log");
P.Start();
f.Write("Time\t");
foreach (var x in logInfo)
{
f.Write(x.Label + "\t");
}
f.Write("\n");
for (int i = 0; i < numberOfLogs; i++)
{
f.Write($"{log[0].Times[i]}\t");
for (int j = 0; j < logInfo.Length; j++)
{
try
{
f.Write("{0}\t", log[j].Values[i]);
}
catch (Exception)
{
f.Write("\t");
}
}
f.Write("\n");
P.Update();
}
P.Done();
}
}
Console.WriteLine("\n");
}
}
