////MLGE parameters:
//static readonly List<double> PPM_TOLERANCE_LIST = new List<double>(new double[] { 10.0 / 1000000.0 });
//static readonly List<double> RETENTION_TIME_WINDOW_LIST = new List<double>(new double[] { 0.75, 1.0, 2.0 });
//static readonly List<double> LR_PROBABILITY_THRESHOLD_LIST = new List<double>(new double[] { 0.3, 0.5, 0.7, 0.9 });
////Nora parameters:
//static readonly List<double> XCORR_THRESHOLD_LIST = new List<double>(new double[] { 1.5, 2, 2.5 });
////static readonly List<double> XCORR_THRESHOLD_LIST = new List<double>(new double[] {1.5, 2.0 });
//static readonly List<int> NUM_DB_THRESHOLD_LIST = new List<int>(new int[] { 2 });
public static void RunExclusionExplorer(ExclusionProfileEnum exclusionType)
{
PreExperimentSetUp();
WriterClass.writeln(new PerformanceEvaluator().getHeader());
int experimentNumber = 0;
if (exclusionType == ExclusionProfileEnum.MACHINE_LEARNING_GUIDED_EXCLUSION_PROFILE)
{
foreach (double ppmTol in GlobalVar.PPM_TOLERANCE_LIST)
{
foreach (double rtWin in GlobalVar.RETENTION_TIME_WINDOW_LIST)
{
foreach (double prThr in GlobalVar.LR_PROBABILITY_THRESHOLD_LIST)
{
experimentNumber++;
double startTime = getCurrentTime();
GlobalVar.ppmTolerance = ppmTol;
GlobalVar.retentionTimeWindowSize = rtWin;
GlobalVar.AccordThreshold = prThr;
ExclusionProfile exclusionProfile = new MachineLearningGuidedExclusion(InputFileOrganizer.AccordNet_LogisticRegressionClassifier_WeightAndInterceptSavedFile, database, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize);
String experimentName = "EXP_" + experimentNumber + GlobalVar.experimentName + String.Format("_MachineLearningGuidedExclusion:ppmTol_{0}_rtWin_{1}_prThr_{2}", ppmTol, rtWin, prThr);
Experiment experiment = new Experiment(exclusionProfile, experimentName, experimentNumber, exclusionType, startTime);
RunSimulationAndPostProcess(experiment);
}
}
}
}
else if (exclusionType == ExclusionProfileEnum.NORA_EXCLUSION_PROFILE)
{
foreach (double xCorr in GlobalVar.XCORR_THRESHOLD_LIST)
{
foreach (int numDB in GlobalVar.NUM_DB_THRESHOLD_LIST)
{
foreach (double ppmTol in GlobalVar.PPM_TOLERANCE_LIST)
{
foreach (double rtWin in GlobalVar.RETENTION_TIME_WINDOW_LIST)
{
experimentNumber++;
double startTime = getCurrentTime();
GlobalVar.ppmTolerance = ppmTol;
GlobalVar.retentionTimeWindowSize = rtWin;
GlobalVar.XCorr_Threshold = xCorr;
GlobalVar.NumDBThreshold = numDB;
ExclusionProfile exclusionProfile = new NoraExclusion(database, GlobalVar.XCorr_Threshold, GlobalVar.ppmTolerance, GlobalVar.NumDBThreshold, GlobalVar.retentionTimeWindowSize);
String experimentName = "EXP_" + experimentNumber + GlobalVar.experimentName + String.Format("_HeuristicExclusion:xCorr_{0}_numDB_{1}_ppmTol_{2}_rtWin_{3}", xCorr, numDB, ppmTol, rtWin) + "_expNum" + experimentNumber;
Experiment experiment = new Experiment(exclusionProfile, experimentName, experimentNumber, exclusionType, startTime);
RunSimulationAndPostProcess(experiment);
}
}
}
}
}
else if (exclusionType == ExclusionProfileEnum.COMBINED_EXCLUSION)
{
foreach (double rtWin in GlobalVar.RETENTION_TIME_WINDOW_LIST)
{
foreach (double prThr in GlobalVar.LR_PROBABILITY_THRESHOLD_LIST)
{
foreach (int numDB in GlobalVar.NUM_DB_THRESHOLD_LIST)
{
foreach (double xCorr in GlobalVar.XCORR_THRESHOLD_LIST)
{
foreach (double ppmTol in GlobalVar.PPM_TOLERANCE_LIST)
{
experimentNumber++;
double startTime = getCurrentTime();
GlobalVar.ppmTolerance = ppmTol;
GlobalVar.retentionTimeWindowSize = rtWin;
GlobalVar.AccordThreshold = prThr;
GlobalVar.XCorr_Threshold = xCorr;
GlobalVar.NumDBThreshold = numDB;
ExclusionProfile exclusionProfile = new CombinedExclusion(InputFileOrganizer.AccordNet_LogisticRegressionClassifier_WeightAndInterceptSavedFile, database, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize, xCorr, numDB);
String experimentName = "EXP_" + experimentNumber + GlobalVar.experimentName + String.Format("_CombinedExclusion:xCorr_{0}_numDB_{1}_ppmTol_{2}_rtWin_{3}_prThr_{4}",
xCorr, numDB, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize, GlobalVar.AccordThreshold);
Experiment experiment = new Experiment(exclusionProfile, experimentName, experimentNumber, exclusionType, startTime);
RunSimulationAndPostProcess(experiment);
}
}
}
}
}
}
else if (exclusionType == ExclusionProfileEnum.SVMEXCLUSION)
{
foreach (double ppmTol in GlobalVar.PPM_TOLERANCE_LIST)
{
foreach (double rtWin in GlobalVar.RETENTION_TIME_WINDOW_LIST)
{
experimentNumber++;
double startTime = getCurrentTime();
GlobalVar.ppmTolerance = ppmTol;
GlobalVar.retentionTimeWindowSize = rtWin;
ExclusionProfile exclusionProfile = new SVMExclusion(InputFileOrganizer.SVMSavedFile, database, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize);
String experimentName = "EXP_" + experimentNumber + GlobalVar.experimentName + String.Format("_SVM:ppmTol_{0}_rtWin_{1}", ppmTol, rtWin);
Experiment experiment = new Experiment(exclusionProfile, experimentName, experimentNumber, exclusionType, startTime);
RunSimulationAndPostProcess(experiment);
}
}
}
else if (exclusionType == ExclusionProfileEnum.NO_EXCLUSION_PROFILE)
{
foreach (double rtWin in GlobalVar.RETENTION_TIME_WINDOW_LIST)
{
experimentNumber++;
double startTime = getCurrentTime();
GlobalVar.ppmTolerance = 0;
GlobalVar.retentionTimeWindowSize = rtWin;
ExclusionProfile exclusionProfile = new NoExclusion(database, GlobalVar.retentionTimeWindowSize);
String experimentName = "EXP_" + experimentNumber + GlobalVar.experimentName + String.Format("_NoExclusion:ppmTol_rtWin_{0}", rtWin);
Experiment experiment = new Experiment(exclusionProfile, experimentName, experimentNumber, exclusionType, startTime);
RunSimulationAndPostProcess(experiment);
if (exclusionType == ExclusionProfileEnum.NO_EXCLUSION_PROFILE)
{
List <ObservedPeptideRtTrackerObject> peptideIDRT = ((NoExclusion)exclusionProfile).peptideIDRT;
//actual arrival time, xcorr, rtCalc predicted RT, corrected RT, offset
//WriterClass.writeln("pepSeq\tarrivalTime\txcorr\trtPeak\tcorrectedRT\toffset\trtCalcPredicted\tisPredicted1", writerClassOutputFile.peptideRTTime);
//foreach (ObservedPeptideRtTrackerObject observedPeptracker in peptideIDRT)
//{
// WriterClass.writeln(observedPeptracker.ToString(), writerClassOutputFile.peptideRTTime);
//}
WriterClass.writeln("peptideSequence\tObservedRetentionTime", writerClassOutputFile.peptideRTTime);
foreach (ObservedPeptideRtTrackerObject observedPeptracker in peptideIDRT)
{
WriterClass.writeln(String.Format("{0}\t{1}", observedPeptracker.peptideSequence, observedPeptracker.arrivalTime), writerClassOutputFile.peptideRTTime);
}
}
break;
}
}
else if (exclusionType == ExclusionProfileEnum.RANDOM_EXCLUSION_PROFILE)
{
List <ExperimentResult> resultList = ParseExperimentResult(InputFileOrganizer.SummaryFileForRandomExclusion);
foreach (ExperimentResult expResult in resultList)
{
//Do 5 random experiments per normal experiment
for (int i = 0; i < GlobalVar.randomRepeatsPerExperiment; i++)
{
experimentNumber++;
double startTime = getCurrentTime();
String originalExperimentName = expResult.experimentName;
int numExcluded = expResult.numSpectraExcluded;
int numAnalyzed = expResult.numSpectraAnalyzed;
ExclusionProfile exclusionProfile = new RandomExclusion_Fast(database, ms2SpectraList, numExcluded, numAnalyzed, 12);
String experimentName = "EXP_" + experimentNumber + String.Format("Random:originalExperiment_{0}", originalExperimentName);
Experiment experiment = new Experiment(exclusionProfile, experimentName, experimentNumber, exclusionType, startTime);
RunSimulationAndPostProcess(experiment);
}
}
}
}
public static ExclusionProfile SingleSimulationRun(ExclusionProfileEnum expType)
{
PreExperimentSetUp();
int experimentNumber = 1;
double startTime = getCurrentTime();
//parameters:
//GlobalVar.ppmTolerance = 5.0 / 1000000.0;
//GlobalVar.retentionTimeWindowSize = 1.0;
//GlobalVar.AccordThreshold = 0.5;
//GlobalVar.XCorr_Threshold = 1.5;
//GlobalVar.NumDBThreshold = 2;
if (GlobalVar.isSimulationForFeatureExtraction == false)
{
GlobalVar.ppmTolerance = GlobalVar.PPM_TOLERANCE_LIST[0];
GlobalVar.retentionTimeWindowSize = GlobalVar.RETENTION_TIME_WINDOW_LIST[0];
GlobalVar.AccordThreshold = GlobalVar.LR_PROBABILITY_THRESHOLD_LIST[0];
GlobalVar.XCorr_Threshold = GlobalVar.XCORR_THRESHOLD_LIST[0];
GlobalVar.NumDBThreshold = GlobalVar.NUM_DB_THRESHOLD_LIST[0];
}
//random
int numExcluded = 14826;
int numAnalyzed = 22681;
//end parameters
ExclusionProfile exclusionProfile = null;
switch (expType)
{
case ExclusionProfileEnum.NORA_EXCLUSION_PROFILE:
exclusionProfile = new NoraExclusion(database, GlobalVar.XCorr_Threshold, GlobalVar.ppmTolerance, GlobalVar.NumDBThreshold, GlobalVar.retentionTimeWindowSize);
break;
case ExclusionProfileEnum.MACHINE_LEARNING_GUIDED_EXCLUSION_PROFILE:
exclusionProfile = new MachineLearningGuidedExclusion(InputFileOrganizer.AccordNet_LogisticRegressionClassifier_WeightAndInterceptSavedFile, database, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize);
break;
case ExclusionProfileEnum.RANDOM_EXCLUSION_PROFILE:
exclusionProfile = new RandomExclusion_Fast(database, ms2SpectraList, numExcluded, numAnalyzed, 12);
break;
case ExclusionProfileEnum.NO_EXCLUSION_PROFILE:
exclusionProfile = new NoExclusion(database, GlobalVar.retentionTimeWindowSize);
break;
case ExclusionProfileEnum.MLGE_SEQUENCE_EXCLUSION_PROFILE:
exclusionProfile = new MLGESequenceExclusion(InputFileOrganizer.AccordNet_LogisticRegressionClassifier_WeightAndInterceptSavedFile, database, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize);
break;
case ExclusionProfileEnum.NORA_SEQUENCE_EXCLUSION_PROFILE:
exclusionProfile = new NoraSequenceExclusion(database, GlobalVar.XCorr_Threshold, GlobalVar.ppmTolerance, GlobalVar.NumDBThreshold, GlobalVar.retentionTimeWindowSize);
break;
case ExclusionProfileEnum.SVMEXCLUSION:
exclusionProfile = new SVMExclusion(InputFileOrganizer.SVMSavedFile, database, GlobalVar.ppmTolerance, GlobalVar.retentionTimeWindowSize);
break;
}
WriterClass.writeln(exclusionProfile.GetPerformanceEvaluator().getHeader());
String experimentName = "EXP_" + experimentNumber + GlobalVar.experimentName;
Experiment experiment = new Experiment(exclusionProfile, experimentName, 1, expType, startTime);
new DataReceiverSimulation().DoJob(exclusionProfile, ms2SpectraList);
double analysisTime = getCurrentTime() - startTime;
//WriteScanArrivalProcessedTime(DataProcessor.scanArrivalAndProcessedTimeList);
//WriteExcludedProteinList(exclusionProfile.getDatabase().getExcludedProteins());
#if IGNORE
WriteScanArrivalProcessedTime(DataProcessor.spectraNotAdded);
foreach (double[] ignoredSpectra in DataProcessor.spectraNotAdded)
{
int scanNum = ms2SpectraList[(int)ignoredSpectra[0] - 1].getScanNum();
exclusionProfile.getSpectraUsed().Add(scanNum);
}
#endif
//if (expType == ExclusionProfileEnum.NO_EXCLUSION_PROFILE)
//{
// List<ObservedPeptideRtTrackerObject> peptideIDRT = ((NoExclusion)exclusionProfile).peptideIDRT;
// //actual arrival time, xcorr, rtCalc predicted RT, corrected RT, offset
// WriterClass.writeln("pepSeq\tarrivalTime\txcorr\trtPeak\tcorrectedRT\toffset\trtCalcPredicted\tisPredicted1", writerClassOutputFile.peptideRTTime);
// foreach (ObservedPeptideRtTrackerObject observedPeptracker in peptideIDRT)
// {
// WriterClass.writeln(observedPeptracker.ToString(), writerClassOutputFile.peptideRTTime);
// }
//}
//if (expType == ExclusionProfileEnum.MACHINE_LEARNING_GUIDED_EXCLUSION_PROFILE)
//{
// List<double[]> peptideIDRT = ((MachineLearningGuidedExclusion)exclusionProfile).peptideIDRT;
// //actual arrival time, xcorr, rtCalc predicted RT, corrected RT, offset
// WriterClass.writeln("arrivalTime\txcorr\trtPeak\tcorrectedRT\toffset\trtCalcPredicted\tisPredicted1", writerClassOutputFile.peptideRTTime);
// foreach(double[] id in peptideIDRT)
// {
// String str = "";
// foreach(double d in id)
// {
// str = str + "\t" + d;
// }
// str= str.Trim();
// WriterClass.writeln(str, writerClassOutputFile.peptideRTTime);
// }
//}
#if TRACKEXCLUDEDPROTEINFEATURE
if (expType == ExclusionProfileEnum.MACHINE_LEARNING_GUIDED_EXCLUSION_PROFILE)
{
List <object[]> excludedProteinFeatures = ((MachineLearningGuidedExclusion)exclusionProfile).excludedProteinFeatureList;
WriterClass.writeln("Accession\tCardinality\tHighestXCorr\tMeanXCorr\tMedianXCorr\tStDev", writerClassOutputFile.ExcludedSpectraScanNum);
foreach (object[] feature in excludedProteinFeatures)
{
String featureStr = "";
foreach (object o in feature)
{
featureStr = featureStr + o.ToString() + "\t";
}
featureStr = featureStr.Trim();
WriterClass.writeln(featureStr, writerClassOutputFile.ExcludedSpectraScanNum);
}
}
#endif
//WriteUnusedSpectra(exclusionProfile);
//WriteUsedSpectra(exclusionProfile);
PostExperimentProcessing(experiment);
//WriteUnusedSpectra(exclusionProfile);
return(exclusionProfile);
}
