/// <summary>
/// ChargeStateChildTopDownIqWorkflow
/// Generates theoretical isotopic profile, XIC, and creates ChromPeakIqTargets based on peaks found
/// </summary>
/// <param name="result"></param>
protected override void ExecuteWorkflow(IqResult result)
{
//Generate theoretical isotopic profile
result.Target.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(result.Target.EmpiricalFormula, result.Target.ChargeState);
if (!Parser.CheckSequenceIntegrity(result.Target.Code))
{
ShiftIsotopicProfile(result.Target.TheorIsotopicProfile, result.Target.MonoMassTheor, result.Target.ChargeState);
}
//Generate XIC and smooth
result.IqResultDetail.Chromatogram = ChromGen.GenerateChromatogram(Run, result.Target.TheorIsotopicProfile, result.Target.ElutionTimeTheor);
result.IqResultDetail.Chromatogram = ChromSmoother.Smooth(result.IqResultDetail.Chromatogram);
//Look for peaks in XIC
result.ChromPeakList = ChromPeakDetector.FindPeaks(result.IqResultDetail.Chromatogram);
ChromPeakDetector.CalculateElutionTimes(Run, result.ChromPeakList);
ChromPeakDetector.FilterPeaksOnNET(WorkflowParameters.ChromNETTolerance, result.Target.ElutionTimeTheor, result.ChromPeakList);
var tempMinScanWithinTol = (int)Run.NetAlignmentInfo.GetScanForNet(result.Target.ElutionTimeTheor - WorkflowParameters.ChromNETTolerance);
var tempMaxScanWithinTol = (int)Run.NetAlignmentInfo.GetScanForNet(result.Target.ElutionTimeTheor + WorkflowParameters.ChromNETTolerance);
var tempCenterTol = (int)Run.NetAlignmentInfo.GetScanForNet(result.Target.ElutionTimeTheor);
result.NumChromPeaksWithinTolerance = result.ChromPeakList.Count;
//General peak information output written to console.
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + WorkflowParameters.ChromNETTolerance + "; chromMinCenterMax= " +
tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + result.Target.ID + ";z= " + result.Target.ChargeState + "; mz= " + result.Target.MZTheor.ToString("0.000") +
"; ------------------------- PeaksWithinTol = " + result.ChromPeakList.Count);
//Creates a ChromPeakIqTarget for each peak found
foreach (ChromPeak peak in result.ChromPeakList)
{
var target = new ChromPeakIqTarget(new ChromPeakAnalyzerIqWorkflow(Run, WorkflowParameters));
TargetUtilities.CopyTargetProperties(result.Target, target, false);
target.ChromPeak = peak;
result.Target.AddTarget(target);
}
//Executes each grandchild ChromPeakAnalyzerIqWorkflow
var children = result.Target.ChildTargets();
foreach (var child in children)
{
child.DoWorkflow();
}
if (Utilities.SipperDataDump.OutputResults)
{
//Data Dump for use with Sipper
children = result.Target.ChildTargets();
foreach (var child in children)
{
Utilities.SipperDataDump.DataDump(child, Run);
}
}
}
protected override void ExecuteWorkflow(IqResult result)
{
if (ChromPeakAnalyzerIqWorkflow == null)
{
InitializeChromPeakAnalyzerWorkflow();
}
result.Target.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(result.Target.EmpiricalFormula, result.Target.ChargeState);
result.IqResultDetail.Chromatogram = ChromGen.GenerateChromatogram(Run, result.Target.TheorIsotopicProfile, result.Target.ElutionTimeTheor);
result.IqResultDetail.Chromatogram = ChromSmoother.Smooth(result.IqResultDetail.Chromatogram);
result.ChromPeakList = ChromPeakDetector.FindPeaks(result.IqResultDetail.Chromatogram);
ChromPeakDetector.CalculateElutionTimes(Run, result.ChromPeakList);
ChromPeakDetector.FilterPeaksOnNET(WorkflowParameters.ChromNETTolerance, result.Target.ElutionTimeTheor, result.ChromPeakList);
result.NumChromPeaksWithinTolerance = result.ChromPeakList.Count;
//Creates a ChromPeakIqTarget for each peak found
foreach (ChromPeak peak in result.ChromPeakList)
{
var target = new ChromPeakIqTarget(ChromPeakAnalyzerIqWorkflow);
TargetUtilities.CopyTargetProperties(result.Target, target, false);
target.ChromPeak = peak;
result.Target.AddTarget(target);
}
//Executes each grandchild ChromPeakAnalyzerIqWorkflow
var children = result.Target.ChildTargets();
var targetRemovalList = new List <IqTarget>();
foreach (var child in children)
{
child.DoWorkflow();
/*
* //Selects grandchildren with extremely poor metric scores for removal
* IqResult childResult = child.GetResult();
* if ((childResult.FitScore >= .8) || (childResult.CorrelationData.RSquaredValsMedian <= .15))
* {
* targetRemovalList.Add(child);
* }
*/
}
/*
* //Removes the poorly scoring grandchild ChromPeakIqTargets
* foreach (IqTarget iqTarget in targetRemovalList)
* {
* result.RemoveResult(iqTarget.GetResult());
* result.Target.RemoveTarget(iqTarget);
* }
*/
}
public static int Main(string[] args)
{
//Console.WriteLine(Process.GetCurrentProcess().Id);
//while (!Debugger.IsAttached)
//{
// Thread.Sleep(100);
//}
CommandLineApplication <ArgumentsModel> app = new CommandLineApplication <ArgumentsModel>();
IHostBuilder hostBuilder = new HostBuilder()
.ConfigureLogging(builder =>
{
builder.AddSerilog(dispose: true);
})
.ConfigureServices(services =>
{
services.AddSingleton(app.Model);
services.AddSingleton <Dumper>();
});
app.FullName = "RabbitMQ Dumper";
app.VersionOption("-v|--version", () => Assembly.GetEntryAssembly().GetName().Version.ToString());
app.Conventions
.UseAttributes()
.SetRemainingArgsPropertyOnModel()
.SetSubcommandPropertyOnModel()
.SetParentPropertyOnModel()
.UseOnValidateMethodFromModel()
.UseOnValidationErrorMethodFromModel()
.UseConstructorInjection()
.UseDefaultHelpOption();
CancellationTokenSource consoleCancelled = new CancellationTokenSource();
Console.CancelKeyPress += (sender, eventArgs) =>
{
eventArgs.Cancel = true;
consoleCancelled.Cancel();
};
app.OnExecute(() =>
{
LoggerConfiguration loggerConfiguration = new LoggerConfiguration()
.Enrich.FromLogContext()
.WriteTo.Console();
if (app.Model.Verbose)
{
loggerConfiguration.MinimumLevel.Debug();
}
Log.Logger = loggerConfiguration.CreateLogger();
consoleCancelled.Token.Register(() =>
{
Log.Logger.Warning("Ctrl+C pressed");
});
hostBuilder.ConfigureServices(services =>
{
Type inputType = TargetUtilities.GetSourceType(app.Model.InputType);
Type outputType = TargetUtilities.GetDestinationType(app.Model.OutputType);
services
.AddSingleton <ISource>(inputType)
.AddSingleton <IDestination>(outputType);
}).ConfigureServices(services =>
{
services.AddSingleton(new ConsoleLifetime(consoleCancelled.Token));
});
using (IHost host = hostBuilder.Build())
{
Dumper dumper = host.Services.GetRequiredService <Dumper>();
return((int)dumper.Run());
}
});
try
{
return(app.Execute(args));
}
catch (CommandParsingException e)
{
Console.Error.WriteLine($"There was an error processing the argumentsModel: {e.Message}");
return((int)DumperExitCode.ParsingFailure);
}
}
