public override ResultItems Analyze(RawFileName rawfile, SettingsForAnalysis settingName, UIsettings fixedSettings)
{
//Stopwatch stopwatch = new Stopwatch();
//stopwatch.Start();
ResultItems results = GetResultItems(fixedSettings);
//MsScanParameters msScanParameters = new MsScanParameters(settingName);
//progress.Report("[" + rawfile.FullName + "] Start at " + stopwatch.Elapsed.TotalMinutes.ToString("0.00") + " minutes");
results.SetValue("RawFile", rawfile.BaseName);
results.SetValue("User", rawfile.User);
results.SetValue("MS instrument", rawfile.MsInstrument);
results.SetValue("MS instrument number", rawfile.MsInstrumentDetails);
results.SetValue("LC instrument", rawfile.LcInstrument);
results.SetValue("LC instrument number", rawfile.LcInstrumentDetails);
results.SetValue("Sample type", rawfile.SampleType);
results.SetValue("Sample type details", rawfile.SampleTypeDetails);
results.SetValue("File name convention followed", (!rawfile.SomethingWrongWithFileName).ToString()); // shitty hack, should be bool
results.SetValue("File size (MiB)", rawfile.FileSizeMiB, 1);
results.SetValue("Storage space left (GiB)", rawfile.SpaceLeftGiB, 1);
if (settingName.UseBaseAnalysis)
{
StatusLog statusLog;
using (RawFileProcessing rawfileResults = new RawFileProcessing(raw, rawfile.FullName, settingName))
{
rawfile.SetDates(rawfileResults._filecreation, rawfileResults._msStart, rawfileResults._msEnd);
statusLog = rawfileResults.statusLog;
results.SetValue("Warning log", rawfileResults.WarningMessage);
results.SetValue("MS count", rawfileResults.MsCount, 0);
results.SetValue("MS TIC", rawfileResults.MsTic, 0);
results.SetValue("MS TIC (high percentile)", rawfileResults.MsTicHigh, 0);
results.SetValue("MS signal to noise", rawfileResults.MsS2N, 2);
results.SetValue("MS ion count", rawfileResults.MsIonCount, 0);
results.SetValue("CTCD or PrOSA minimum", rawfileResults.CtcdMin, 3);
results.SetValue("CTCD or PrOSA maximum", rawfileResults.CtcdMax, 3);
results.SetValue("Lock mass correction maximum absolute (ppm)", rawfileResults.LockMassCorrectionMaxAbsolute, 2);
results.SetValue("Large injection time fluctuations", rawfileResults.LargeFluctuations, 1); //set as parameter from usrcontrol
results.SetValue("Polymer01", rawfileResults.Polymer1, 1);
results.SetValue("Polymer02", rawfileResults.Polymer2, 1);
results.SetValue("Polymer03", rawfileResults.Polymer3, 1);
results.SetValue("Polymer04", rawfileResults.Polymer4, 1);
results.SetValue("Polymer05", rawfileResults.Polymer5, 1);
results.SetValue("AdductNa", rawfileResults.AdductNa, 1);
results.SetValue("AdductCa", rawfileResults.AdductCa, 1);
results.SetValue("AdductFe", rawfileResults.AdductFe, 1);
results.SetValue("AdductK", rawfileResults.AdductK, 1);
results.SetValue("AdductFA", rawfileResults.AdductFA, 1);
results.SetValue("AdductNH3", rawfileResults.AdductNH3, 1);
results.SetValue("AdductACN", rawfileResults.AdductACN, 1);
results.SetValue("Precursor 5 percent mass quantile", rawfileResults.PrecursorMass5percent, 1);
results.SetValue("Precursor 95 percent mass quantile", rawfileResults.PrecursorMass95percent, 1);
results.SetValue("MS2 topN", rawfileResults.TopN, 2);
results.SetValue("MS2 count", rawfileResults.Ms2Count, 0);
results.SetValue("MS2 TIC", rawfileResults.Ms2Tic, 0);
results.SetValue("MS2 signal to noise", rawfileResults.Ms2S2N, 2);
results.SetValue("MS2 ion count", rawfileResults.Ms2IonCount, 0);
results.SetValue("MS2 precursor isolation width TIC", rawfileResults.Ms2IsolationWindowTic, 0);
results.SetValue("MS2TIC / MS2 precursor isolation width TIC", rawfileResults.Ms2IsolationWindowTicRelative, 3);
results.SetValue("MS2 count above ion threshold", rawfileResults.Ms2ScansAboveIonThreshold, 0);
results.SetValue("MS2 with charge 2 in percent", rawfileResults.Ms2charge2, 2);
results.SetValue("MS2 with charge 3 in percent", rawfileResults.Ms2charge3, 2);
results.SetValue("MS2 with charge 4 or higher in percent", rawfileResults.Ms2charge4orMore, 2);
results.SetValue("MS2 scans XIC above precursor percentage", rawfileResults.Ms2ScansAbovePrecursorPercent, 2);
results.SetValue("MS2 count above ion threshold percentage", rawfileResults.Ms2ScansAboveIonThresholdPercent, 1);
results.SetValue("MS2 scans with precursor as BP percentage", rawfileResults.Ms2ScansWithPrecursorBasePeakPercent, 2);
}
results.SetValue("LCMS start", rawfile.GetDates(0));
results.SetValue("MS start", rawfile.GetDates(1));
results.SetValue("LCMS end", rawfile.GetDates(2));
results.SetValue("MS time in minutes", rawfile.MsTime, 2);
results.SetValue("LC time in minutes", rawfile.LcTime, 2);
Dictionary <int, Tuple <double, double, double> > usage = rawfile.GetUsagePercent();
foreach (int day in usage.Keys)
{
results.SetValue("Last " + day.ToString() + " day(s) LCMS usage percent", usage[day].Item1, 1);
results.SetValue("Last " + day.ToString() + " day(s) MS usage percent", usage[day].Item2, 1);
results.SetValue("Last " + day.ToString() + " day(s) MS excl QC usage percent", usage[day].Item3, 1);
}
//status log entries
foreach (StatusLogItem item in fixedSettings.statusLogItems)
{
if (item.CalculateMedian)
{
results.SetValue(item.Name, statusLog.GetMedianOf(item.Name));
}
if (item.CalculateMin)
{
results.SetValue(item.Name + " min", statusLog.GetMinOf(item.Name));
}
if (item.CalculateMax)
{
results.SetValue(item.Name + " max", statusLog.GetMaxOf(item.Name));
}
if (item.CalculateIQR)
{
results.SetValue(item.Name + " IQR", statusLog.GetIqrOf(item.Name));
}
}
}
results.SetValue("Analysis tool version", "0.0.1.21");
return(results);
}
public override ResultItems Analyze(RawFileName rawfile, SettingsForAnalysis settingName, UIsettings fixedSettings)
{
ResultItems results = GetResultItems(fixedSettings);
List <double> resultlist = new List <double>();
if (settingName.UseExternal1Analysis)
{
Log.Information("Started external1");
string filename = rawfile.FullName;//"f:/temp2/20190114_QE99_Evo1_DBJ_E7_LFQprot_QC4_HELA_PAC_250ng_7500_01.raw";
//get list of files and column/row names
List <string> resultfiles = new List <string>();
List <string> resultnames = new List <string>();
foreach (ExternalResultParseSetting settings in fixedSettings.ExternalResults)
{
string resultfile = settings.ResultFile;
resultfile = resultfile.Replace("{FILE}", rawfile.FullName);
resultfiles.Add(resultfile);
resultnames.Add(settings.Resultname);
}
//maybe add option to delete resultfile?
try
{
string arguments = fixedSettings.Arguments;
arguments = arguments.Replace("{FILE}", rawfile.FullName);
resultlist = ExecuteProgram.GetResultsFromExternalProgram(
fixedSettings.Executable, //raw.exe
arguments, //"parse -x -f " + filename
resultfiles.ToArray(),
resultnames.ToArray(),
fixedSettings.Timeout,
fixedSettings.ExternalToolSepChar,
!fixedSettings.AsRow);
if (resultlist.Count != fixedSettings.ExternalResults.Count)
{
resultlist.Clear();
for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
{
resultlist.Add(0.0);
}
Log.Error("External1 result was not parsed correctly (are headers correct?)");
}
Log.Information("Finished external1");
}
catch
{
//something went wrong, adding 0s as filler and reporting error
Log.Error("External1 failed");
for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
{
resultlist.Add(0.0);
}
}
}
else
{
//no analysis requested, adding 0s as filler
for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
{
resultlist.Add(0.0);
}
}
//set results
for (int i = 0; i < fixedSettings.ExternalResults.Count; i++)
{
results.SetValue(fixedSettings.ExternalResults[i].Resultname, resultlist[i]);
}
return(results);
}