private static void HandleInput(String input)
{
if (input.Equals("0"))
{
Console.WriteLine("Setting output level to detailed");
DataProcessor.SetOutputLevel(0);
}
else if (input.Equals("1"))
{
Console.WriteLine("Setting output level to simple");
DataProcessor.SetOutputLevel(1);
}
else if (input.Equals("2"))
{
Console.WriteLine("Setting output level to peptide only");
DataProcessor.SetOutputLevel(2);
}
else if (input.Equals("3"))
{
Console.WriteLine("Displaying only info headers");
DataProcessor.SetOutputLevel(3);
}
else if (input.Equals("q"))
{
Console.WriteLine("Quitting listening");
ExclusionExplorer.EndMealTimeMS();
}
}
private void Orbitrap_AcquisitionStreamClosing(object sender, EventArgs e)
{
log.Info(String.Format("\n{0:HH:mm:ss,fff} {1}", DateTime.Now, "Acquisition stream closed (end of method)"));
log.Info("press y to continue finish processing");
while (!Console.ReadKey().KeyChar.ToString().Equals("y"))
{
}
ExclusionExplorer.EndMealTimeMS();
}
internal void DoJob(ExclusionProfile exclusionProfile)
{
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
if (instrument == null)
{
Console.WriteLine("Failed to create Instrument, program will now exit");
return;
}
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
//if (GlobalVar.SeeExclusionFormat)
//{
// m_methods = instrument.Control.Methods;
// m_replacementTable = CreateReplacementTable();
//}
Console.WriteLine("Waiting 60 seconds for scans on detector " + orbitrap.DetectorClass + "...");
DataProcessor.reset();
Thread DataProcessingThread = new Thread(() => DataProcessor.StartProcessing(exclusionProfile));
//Thread InputHandling = new Thread(() => InputHandler.ReadConsoleInput());
DataProcessingThread.Start();
//InputHandling.Start();
while (!DataProcessor.SetupFinished())
{
Thread.Sleep(500);
}
orbitrap.AcquisitionStreamOpening += Orbitrap_AcquisitionStreamOpening;
orbitrap.AcquisitionStreamClosing += Orbitrap_AcquisitionStreamClosing;
Console.WriteLine("Waiting on acquisition stream to open");
while (!acquisitionStreamOpened && !Console.ReadKey().KeyChar.ToString().Equals("y"))
{
Console.WriteLine("Waiting on acquisition stream to open");
Thread.CurrentThread.Join(1000);
}
Console.WriteLine("MSScan Arrive event listener added");
orbitrap.MsScanArrived += Orbitrap_MsScanArrived;
int durationCounter = 0;
while (durationCounter < GlobalVar.listeningDuration && (ExclusionExplorer.IsListening()))
{
Thread.CurrentThread.Join(1000); //does the same thing as Thread.Sleep() but Join
//allows standard sendmessage pumping and COM to continue
durationCounter++;
}
orbitrap.MsScanArrived -= Orbitrap_MsScanArrived;
orbitrap.AcquisitionStreamClosing -= Orbitrap_AcquisitionStreamClosing;
orbitrap.AcquisitionStreamOpening -= Orbitrap_AcquisitionStreamOpening;
DataProcessor.EndProcessing();
DataProcessingThread.Join(); //wait until dataProcessor finishes processing/outputing the scan
//queue then returns to Main thread;
}
}
public static void DoJob()
{
String resultFile = "C:\\Coding\\2019LavalleeLab\\GitProjectRealTimeMS\\TestData\\MLGESequentialRun_Full.txt_Summary.txt";
String outputFile = "C:\\Coding\\2019LavalleeLab\\GitProjectRealTimeMS\\Output\\ParamsParsed.txt";
List <ExperimentResult> experiments = ExclusionExplorer.ParseExperimentResult(resultFile);
StreamWriter sw = new StreamWriter(outputFile);
String[] paramName = { "ppmTol", "rtWin", "xCorr", "numDB", "prThr" };
sw.Write("expName\t");
foreach (String param in paramName)
{
sw.Write(param + "\t");
}
sw.WriteLine();
foreach (ExperimentResult exp in experiments)
{
String expName = exp.experimentName;
sw.Write(expName + "\t");
foreach (String param in paramName)
{
if (!expName.Contains(param))
{
sw.Write("-1\t");
continue;
}
int startPos = expName.IndexOf(param) + param.Length + 1;
int endPos = expName.IndexOf("_", startPos + 1);
endPos = (endPos < 0) ? expName.Length : endPos;
String sub = expName.Substring(startPos, endPos - startPos);
double value = double.Parse(sub);
String sss = param + "sdsd";
sw.Write(value + "\t");
}
sw.WriteLine();
}
sw.Close();
}
//static string mzmlFileBaseName="MS_QC_240min";
public static void ExtractFeatures(String ms2File, out String extractedFeatureSavedFile_posAndNeg, out String extractedFeatureSavedFile_posAndNonPos)
{
Console.WriteLine("Extracting features from {0}", ms2File);
InputFileOrganizer.MS2SimulationTestFile = ms2File;
//InputFileOrganizer.MZMLSimulationTestFile = mzmlFile;
String ms2FileBaseName = Path.GetFileNameWithoutExtension(ms2File);
OutputFile_PositiveAndNegative = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, ms2FileBaseName + "_extractedFeatures_PositiveAndNegative.tsv");
OutputFile_PositiveAndNonPositive = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, ms2FileBaseName + "_extractedFeatures_positiveAndNonPositive.tsv");
OutputFile_PositiveAndNonPositive_NoDecoy = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, ms2FileBaseName + "_extractedFeatures_positiveAndNonPositive_NoDecoy.tsv");
//the current feature extraction will include decoy proteins in the database and testing set
SimulationWithDecoyParamsSetUp();
//placeholder values, dont matter
GlobalVar.ppmTolerance = 1;
GlobalVar.retentionTimeWindowSize = 1;
GlobalVar.AccordThreshold = 1;
GlobalVar.XCorr_Threshold = 1;
GlobalVar.NumDBThreshold = 1;
//
log.Info("Running No Exclusion Simulation");
ExclusionProfile exclusionProfile = ExclusionExplorer.SingleSimulationRun(ExclusionProfileEnum.NO_EXCLUSION_PROFILE);
log.Info("Extracting identification feature from exclusion profile");
List <IdentificationFeatures> idf = exclusionProfile.getFeatures();
log.Info("Recalibrating stDev");
idf = IdentificationFeatureExtractionUtil.recalibrateStDev(idf);
writeFeatures(idf);
extractedFeatureSavedFile_posAndNeg = OutputFile_PositiveAndNegative;
extractedFeatureSavedFile_posAndNonPos = OutputFile_PositiveAndNonPositive;
Console.WriteLine("Extracted Feature written to {0} and {1}", OutputFile_PositiveAndNegative, OutputFile_PositiveAndNonPositive);
}
