//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);
}
