public abstract void Execute(BackgroundWorker worker, ExperimentBase experimentBase);
public override void Execute(BackgroundWorker worker, ExperimentBase experimentBase)
{
currentProgress = 1;
System.Diagnostics.Stopwatch stopWatch = new System.Diagnostics.Stopwatch();
stopWatch.Start();
Experiment experiment = experimentBase as Experiment;
_eventAggregator.GetEvent<ClearOutputEvent>().Publish(null);
_eventAggregator.GetEvent<OutputEvent>().Publish("------ Processing Started (" + DateTime.Now.ToString() + ") ------ " + DateTime.Now);
OutputEvent output = _eventAggregator.GetEvent<OutputEvent>();
progressFinish = experiment.Runs.Count * experiment.Peptides.PeptideCollection.Count * ProcessingSteps.Count;
Result result = new Result("Result (" + DateTime.Now.ToString() + ")", (Experiment)experimentBase);
try
{
for (int j = 0; j < experiment.ProteinStates.Count; ++j)
{
ProteinState proteinState = experiment.ProteinStates[j];
OutputText("-PROTEIN STATE '" + proteinState.Name + "'");
IList<Run> runs = experiment.GetRunsByProteinState(proteinState);
for (int i = 0; i < runs.Count; i++)
{
Run run = runs[i];
OutputText("-RUN '" + run.FileName + "'");
// TODO: crashed here when I closed the progress bar; seems to be a threading issue
foreach (Peptide peptide in experiment.Peptides.PeptideCollection)
{
OutputText("-PEPTIDE '" + peptide.Sequence + "'");
ReportProgress(worker, "Processing " + Path.GetFileName(run.FileName) + " (" + proteinState.Name + ")");
ReportStepProgress(worker, " 1: MSMS Spectrum Selection", "MSMS Spectrum Selection");
IXYData msmsSpectrum = msmsSpectrumSelection.Execute(run, peptide.RT, peptide.MonoIsotopicMass);
ReportStepProgress(worker, " 2: MSMS Smoothing", "MSMS Smoothing");
msmsSpectrum = _smoothing.Execute(msmsSpectrum);
ReportStepProgress(worker, " 3: MSMS Fragment Analyzer", "MSMS Fragment Analyzer");
foreach (FragmentIon fragmentIon in peptide.FragmentIonList)
{
RunResult runResult = new RunResult(fragmentIon, run);
runResult.CachedSpectrum = msmsSpectrum;
try
{
msmsFragmentAnalyzer.Execute(runResult, msmsSpectrum);
}
catch (Exception ex)
{
OutputText(" ERROR: '" + ex.Message + "'");
PeptideUtility pu = new PeptideUtility();
pu.GetIsotopicProfileForFragmentIon(runResult, 20);
runResult.TheoreticalAverageMass = MSUtility.GetAverageMassFromPeakList(runResult.TheoreticalIsotopicPeakList, runResult.ActualPeaksInCalculation);
}
result.RunResults.Add(runResult);
}
currentProgress++;
}
run.SetDataProvider(_serviceLocator.GetAllInstances<IDataProvider>().Where(item => item.GetType().Name.Contains("Proteo")).First());
}
}
ReportProgress(worker, "Generating Deuteration Results");
deuterationResultGenerator.Execute(experiment, result);
experiment.IsProcessed = true;
experiment.Results.Add(result);
stopWatch.Stop();
OutputText("------ Processing Completed (" + DateTime.Now.ToString() + ") - Duration=" + stopWatch.Elapsed.ToString() + " ------");
}
catch (Exception ex)
{
stopWatch.Stop();
OutputText("------- ERROR: Processing Failed (" + DateTime.Now.ToString() + ") - Duration=" + stopWatch.Elapsed.ToString() + " ------");
OutputText(ex.Message);
OutputText(ex.StackTrace);
if (ex.InnerException != null)
{
OutputText(ex.InnerException.Message);
OutputText(ex.StackTrace);
}
_eventAggregator.GetEvent<StatusUpdateEvent>().Publish("Processing Failed");
return;
}
result.AlgorithmUsed = new MassSpecStudio.Core.Domain.Algorithm(this);
RecentAlgorithms.Write(result.AlgorithmUsed);
// Publish event with new result so we can create a ResultViewModel for it and display the results.
_eventAggregator.GetEvent<ResultAddedEvent>().Publish(result);
_eventAggregator.GetEvent<ViewResultsEvent>().Publish(result);
_eventAggregator.GetEvent<StatusUpdateEvent>().Publish("Processing Succeeded");
}
public override void Execute(BackgroundWorker worker, ExperimentBase experimentBase)
{
currentProgress = 1;
System.Diagnostics.Stopwatch stopWatch = new System.Diagnostics.Stopwatch();
stopWatch.Start();
Experiment experiment = experimentBase as Experiment;
_eventAggregator.GetEvent<ClearOutputEvent>().Publish(null);
_eventAggregator.GetEvent<OutputEvent>().Publish("------ Processing Started (" + DateTime.Now.ToString() + ") ------ " + DateTime.Now);
progressFinish = experiment.Runs.Count * experiment.Peptides.PeptideCollection.Count * ProcessingSteps.Count;
Result result = new Result("Result (" + DateTime.Now.ToString() + ")", (Experiment)experimentBase);
try
{
for (int j = 0; j < experiment.ProteinStates.Count; ++j)
{
ProteinState proteinState = experiment.ProteinStates[j];
OutputText("-PROTEIN STATE '" + proteinState.Name + "'");
IList<Run> runs = experiment.GetRunsByProteinState(proteinState);
for (int i = 0; i < runs.Count; i++)
{
Run run = runs[i];
OutputText("-RUN '" + run.FileName + "'");
// TODO: crashed here when I closed the progress bar; seems to be a threading issue
foreach (Peptide peptide in experiment.Peptides.PeptideCollection)
{
RunResult runResult = new RunResult(peptide, run);
try
{
OutputText("-PEPTIDE '" + peptide.Sequence + "'");
ReportProgress(worker, "Processing " + Path.GetFileName(run.FileName) + " (" + proteinState.Name + ")");
ReportStepProgress(worker, " 1: XIC Selection", "XIC Selection");
IXYData xicData = _xicSelection.Execute(run, peptide.XicMass1);
ReportStepProgress(worker, " 2: XIC Smoothing", "XIC Smoothing");
xicData = _xicSmoothing.Execute(xicData);
ReportStepProgress(worker, " 3: Chromatographic Peak Detection", "Chromatographic Peak Detection");
IList<ChromatographicPeak> xicPeakList = _chromatographicPeakDetection.Execute(xicData);
ReportStepProgress(worker, " 4: XIC Peak Picking", "XIC Peak Picking");
ChromatographicPeak xicPeak = _xicPeakPicker.Execute(xicPeakList, peptide);
runResult.CachedXicPeak = xicPeak;
runResult.CachedXicPeakList = xicPeakList;
runResult.CachedXic = xicData;
if (xicPeak != null)
{
double rt1 = xicPeak.Rt + peptide.XicAdjustment - (peptide.XicSelectionWidth / 2);
double rt2 = xicPeak.Rt + peptide.XicAdjustment + (peptide.XicSelectionWidth / 2);
OutputText(" Calculated retention time window for spectrum selection is " + rt1 + "-" + rt2 + "(Peptide=" + peptide.Sequence + ", XicAdjustment=" + peptide.XicAdjustment + ", XicSelectionWidth=" + peptide.XicSelectionWidth + ")");
ReportStepProgress(worker, " 5: Spectrum Selection", "Spectrum Selection");
IXYData spectralData = _spectrumSelection.Execute(run, rt1, rt2, peptide.MonoIsotopicMass);
ReportStepProgress(worker, " 6: MS Smoothing", "MS Smoothing");
spectralData = _spectrumSmoothing.Execute(spectralData);
ReportStepProgress(worker, " 7: Spectral Peak Detection", "Spectral Peak Detection");
IList<MSPeak> msPeakList = _spectralPeakDetection.Execute(spectralData);
runResult.CachedSpectrum = spectralData;
runResult.CachedMSPeakList = msPeakList;
ReportStepProgress(worker, " 8: Isotopic Profile Finder", "Isotopic Profile Finder");
_isotopicProfileFinder.Execute(runResult, msPeakList);
ReportStepProgress(worker, " 9: Label Amount Calculation", "Label Amount Calculation");
_labelAmountCalculator.Execute(runResult);
}
}
catch (Exception ex)
{
runResult.Note = ex.Message;
OutputText("ERROR:");
OutputText(ex.Message);
OutputText(ex.StackTrace);
}
result.RunResults.Add(runResult);
currentProgress++;
}
run.SetDataProvider(_serviceLocator.GetAllInstances<IDataProvider>().Where(item => item.TypeId == experiment.DataProviderType).First());
}
}
ReportProgress(worker, "Generating Deuteration Results");
_deuterationResultGenerator.Execute(experiment, result);
experiment.IsProcessed = true;
experiment.Results.Add(result);
stopWatch.Stop();
OutputText("------ Processing Completed (" + DateTime.Now.ToString() + ") - Duration=" + stopWatch.Elapsed.ToString() + " ------");
}
catch (Exception ex)
{
ReportError(ex, stopWatch);
return;
}
result.AlgorithmUsed = new MassSpecStudio.Core.Domain.Algorithm(this);
RecentAlgorithms.Write(result.AlgorithmUsed);
// Publish event with new result so we can create a ResultViewModel for it and display the results.
_eventAggregator.GetEvent<ResultAddedEvent>().Publish(result);
_eventAggregator.GetEvent<ViewResultsEvent>().Publish(result);
_eventAggregator.GetEvent<StatusUpdateEvent>().Publish("Processing Succeeded");
}
