public List <Task> getStandardTaskList(Run run)
{
Task peakChromGen = new PeakChromatogramGenerator(chromPPMTolerance);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task finder = new N14N15TFFTask(5);
Task quant = new N14N15QuantifierTask(1);
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
List <Task> taskList = new List <Task>();
taskList.Add(peakChromGen);
taskList.Add(smoother);
taskList.Add(peakDet);
taskList.Add(chromPeakSel);
taskList.Add(msgen);
taskList.Add(mspeakDet);
taskList.Add(theorFeatureGen);
taskList.Add(finder);
taskList.Add(quant);
taskList.Add(fitScoreCalc);
return(taskList);
}
public SmartChromPeakSelector(SmartChromPeakSelectorParameters parameters)
{
this.Parameters = parameters;
MSPeakDetector = new DeconToolsPeakDetectorV2(parameters.MSPeakDetectorPeakBR, parameters.MSPeakDetectorSigNoiseThresh, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var iterativeTFFParams = new IterativeTFFParameters();
iterativeTFFParams.ToleranceInPPM = parameters.MSToleranceInPPM;
iterativeTFFParams.MinimumRelIntensityForForPeakInclusion = parameters.IterativeTffMinRelIntensityForPeakInclusion;
if (parameters.MSFeatureFinderType == DeconTools.Backend.Globals.TargetedFeatureFinderType.BASIC)
{
throw new NotSupportedException("Currently the Basic TFF is not supported in the SmartChromPeakSelector");
//TargetedMSFeatureFinder = new TargetedFeatureFinders.BasicTFF(parameters.MSToleranceInPPM);
}
else
{
TargetedMSFeatureFinder = new IterativeTFF(iterativeTFFParams);
}
resultValidator = new ResultValidatorTask();
fitScoreCalc = new IsotopicProfileFitScoreCalculator();
InterferenceScorer = new InterferenceScorer();
}
protected virtual void DoMainInitialization()
{
ValidateParameters();
TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
ChromGen = new PeakChromatogramGenerator(WorkflowParameters.ChromGenTolerance, WorkflowParameters.ChromGeneratorMode,
DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED,
WorkflowParameters.ChromGenToleranceUnit)
{
TopNPeaksLowerCutOff = 0.333,
ChromWindowWidthForAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2,
ChromWindowWidthForNonAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2
};
//only
var allowNegativeValues = false;
ChromSmoother = new SavitzkyGolaySmoother(WorkflowParameters.ChromSmootherNumPointsInSmooth, 2, allowNegativeValues);
ChromPeakDetector = new ChromPeakDetector(WorkflowParameters.ChromPeakDetectorPeakBR, WorkflowParameters.ChromPeakDetectorSigNoise);
ChromPeakSelector = CreateChromPeakSelector(WorkflowParameters);
ChromPeakAnalyzer = new ChromPeakAnalyzer(WorkflowParameters);
IterativeTffParameters = new IterativeTFFParameters();
IterativeTffParameters.ToleranceInPPM = WorkflowParameters.MSToleranceInPPM;
MsfeatureFinder = new IterativeTFF(IterativeTffParameters);
FitScoreCalc = new IsotopicProfileFitScoreCalculator();
InterferenceScorer = new InterferenceScorer();
ResultValidator = new ResultValidatorTask();
ChromatogramCorrelator = new IqChromCorrelator(WorkflowParameters.ChromSmootherNumPointsInSmooth, 0.05, WorkflowParameters.ChromGenTolerance);
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
Console.WriteLine("Fit val = " + result.IsotopicProfile.Score);
/*
*
*
* ------------------- MassTag = 24769---------------------------
* monoMass = 2086.0595; monoMZ = 1044.0370; ChargeState = 2; NET = 0.452; Sequence = DFNEALVHQVVVAYAANAR
*
****** Match ******
******NET = 0.452
******ChromPeak ScanNum = 9016.48992535631
******ChromPeak NETVal = 0.453
******ScanSet = { 9010, 9017, 9024, }
******Observed MZ and intensity = 1044.03290771556 1.269842E+07
******------------------------------ end --------------------------
*
*
*
*
*
*/
}
public ChromPeakAnalyzer(TargetedWorkflowParameters parameters)
{
Parameters = parameters;
var iterativeTffParameters = new IterativeTFFParameters();
TargetedMSFeatureFinder = new IterativeTFF(iterativeTffParameters);
InterferenceScorer = new InterferenceScorer();
MSPeakDetector = new DeconToolsPeakDetectorV2();
FitScoreCalc = new IsotopicProfileFitScoreCalculator();
ResultValidator = new ResultValidatorTask();
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
Task exporter = new BasicMTResultSQLiteExporter(exporterOutputFile1);
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
exporter.Execute(run.ResultCollection);
exporter.Cleanup();
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
}
public void find_targetMassTag_131959Test1()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
var massTagColl = masstagImporter.Import();
Assert.AreEqual(2719, massTagColl.TargetList.Count);
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//int mtID = 635428;
var mtID = 131959;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1);
Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var basicChromPeakSelParam = new ChromPeakSelectorParameters();
basicChromPeakSelParam.NETTolerance = 0.1f;
basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID);
var mt = run.CurrentMassTag;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
Task targetedFeatureFinder = new BasicTFF();
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
theorFeatureGen.Execute(run.ResultCollection);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n");
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
msPeakDet.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
var massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
//Console.WriteLine("------------------------------ end --------------------------");
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(cysteineMassTagSourceFile1, '\t');
mtidImporter.Import(massTagColl);
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");
importer.Import(massTagColl);
Assert.AreEqual(737, massTagColl.MassTagIDList.Count);
Assert.AreEqual(826, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 0.75, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(6);
Task exporter = new BasicMTResultSQLiteExporter(cysteineAnalysisOutput1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
int successCounter = 0;
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
if (mt == massTagColl.MassTagList.Last())
{
exporter.Execute(run.ResultCollection);
}
}
exporter.Cleanup();
//List<IMassTagResult> successfulResults = run.ResultCollection.GetSuccessfulMassTagResults();
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
protected override void DoPostInitialization()
{
base.DoPostInitialization();
ValidateParameters();
theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
theorN15FeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
chromGenN14 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, _workflowParameters.ChromGeneratorMode);
chromGenN14.TopNPeaksLowerCutOff = 0.333;
chromGenN15 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, DeconTools.Backend.Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK, DeconTools.Backend.Globals.IsotopicProfileType.LABELLED);
chromGenN15.TopNPeaksLowerCutOff = 0.333;
var pointsToSmooth = (_workflowParameters.ChromSmootherNumPointsInSmooth + 1) / 2;
chromSmoother = new SavitzkyGolaySmoother(_workflowParameters.ChromSmootherNumPointsInSmooth, 2);
chromPeakDetector = new ChromPeakDetector(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise);
var smartchrompeakSelectorParams = new SmartChromPeakSelectorParameters();
smartchrompeakSelectorParams.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE;
smartchrompeakSelectorParams.MSPeakDetectorPeakBR = _workflowParameters.MSPeakDetectorPeakBR;
smartchrompeakSelectorParams.MSPeakDetectorSigNoiseThresh = _workflowParameters.MSPeakDetectorSigNoise;
smartchrompeakSelectorParams.MSToleranceInPPM = _workflowParameters.MSToleranceInPPM;
smartchrompeakSelectorParams.NETTolerance = (float)_workflowParameters.ChromNETTolerance;
smartchrompeakSelectorParams.NumScansToSum = _workflowParameters.NumMSScansToSum;
smartchrompeakSelectorParams.NumChromPeaksAllowed = 10;
smartchrompeakSelectorParams.IterativeTffMinRelIntensityForPeakInclusion = 0.5;
chromPeakSelectorN14 = new SmartChromPeakSelector(smartchrompeakSelectorParams);
var chromPeakSelectorParameters = new ChromPeakSelectorParameters();
chromPeakSelectorParameters.NumScansToSum = _workflowParameters.NumMSScansToSum;
chromPeakSelectorParameters.NETTolerance = (float)_workflowParameters.ChromNETTolerance;
chromPeakSelectorParameters.PeakSelectorMode = DeconTools.Backend.Globals.PeakSelectorMode.N15IntelligentMode;
chromPeakSelectorN15 = new BasicChromPeakSelector(chromPeakSelectorParameters);
chromPeakSelectorN15.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED;
msPeakDetector = new DeconToolsPeakDetectorV2(_workflowParameters.MSPeakDetectorPeakBR,
_workflowParameters.MSPeakDetectorSigNoise, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false);
var iterativeTFFParameters = new IterativeTFFParameters();
iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM;
iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33;
iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED;
unlabelledProfilefinder = new IterativeTFF(iterativeTFFParameters);
iterativeTFFParameters = new IterativeTFFParameters();
iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM;
iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33;
iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED;
labelledProfileFinder = new IterativeTFF(iterativeTFFParameters);
quantifier = new N14N15QuantifierTask(_n14N15Workflow2Parameters.NumPeaksUsedInQuant, _workflowParameters.MSToleranceInPPM);
fitScoreCalc = new IsotopicProfileFitScoreCalculator();
var minRelativeIntensityForScore = 0.2;
resultValidatorN14 = new ResultValidatorTask(minRelativeIntensityForScore, true);
resultValidatorN15 = new LabelledIsotopicProfileScorer(minRelativeIntensityForScore);
ChromatogramXYData = new XYData();
MassSpectrumXYData = new XYData();
ChromPeaksDetected = new List <ChromPeak>();
}
public void run_fullAnalysisTest1()
{
Run run = new BrukerRun(rsph_AOnly_28_run1File);
MassTagCollection massTagColl = new MassTagCollection();
run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT;
massTagColl.MassTagIDList = fourTestMTs;
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_R_sphaeroides241_P513", "Albert");
importer.chargeStateFilterThreshold = 0.05;
importer.Import(massTagColl);
Assert.AreEqual(7, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(rsph_Aonly_28_run1_scans500_1000_peaks);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
N14N15TFFTask finder = new N14N15TFFTask(0.01);
N14N15QuantifierTask quant = new N14N15QuantifierTask(1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
finder.Execute(run.ResultCollection);
quant.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
}
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
public void smartChromPeakSelectorTest_noSumming()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
run.Close();
run = new RunFactory().CreateRun(xcaliburTestfile);
var massTagColl = new TargetCollection();
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
massTagColl = masstagImporter.Import();
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var chromPeakDet = new ChromPeakDetector(0.5, 1);
var smartchromParam = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam);
var basicChromParam = new ChromPeakSelectorParameters();
var basicChromPeakSelector = new BasicChromPeakSelector(basicChromParam);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var iterativeTff = new IterativeTFF(new IterativeTFFParameters());
var fitscoreCalc = new IsotopicProfileFitScoreCalculator();
var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt";
var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile);
Assert.IsNotNull(xydata);
run.XYData = xydata;
// run.XYData.Display();
run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First();
Console.WriteLine("------MT = " + run.CurrentMassTag.ToString());
theorFeatureGen.Execute(run.ResultCollection);
chromPeakDet.Execute(run.ResultCollection);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
//first run the standard peak selector
basicChromPeakSelector.Execute(run.ResultCollection);
Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue));
//now run the smart chrom peak selector
run.XYData = xydata;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
fitscoreCalc.Execute(run.ResultCollection);
Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue));
//result.DisplayToConsole();
TestUtilities.DisplayIsotopicProfileData(result.Target.IsotopicProfile);
}
public void smartChromPeakSelectorTest_withDynamicSumming()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var massTagColl = new TargetCollection();
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
massTagColl = masstagImporter.Import();
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var chromPeakDet = new ChromPeakDetector(0.5, 1);
var smartchromParam = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam);
var basicChromPeakSelector = new BasicChromPeakSelector(new ChromPeakSelectorParameters());
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var iterativeTff = new IterativeTFF(new IterativeTFFParameters());
var fitscoreCalc = new IsotopicProfileFitScoreCalculator();
var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt";
var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile);
Assert.IsNotNull(xydata);
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
// run.XYData.Display();
run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First();
Console.WriteLine("------MT = " + run.CurrentMassTag.ToString());
theorFeatureGen.Execute(run.ResultCollection);
chromPeakDet.Execute(run.ResultCollection);
//first run the standard peak selector
basicChromPeakSelector.Execute(run.ResultCollection);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue));
//now run the smart chrom peak selector
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51;
smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC;
smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 1;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
fitscoreCalc.Execute(run.ResultCollection);
Console.WriteLine(result.ScanSet);
Assert.AreEqual(14, result.ScanSet.IndexValues.Count);
Assert.AreEqual(0.0104m, (decimal)Math.Round(result.Score, 4));
Assert.AreEqual("9575 {9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624}", result.ScanSet.ToString());
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51;
smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC;
smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 2;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
fitscoreCalc.Execute(run.ResultCollection);
result.DisplayToConsole();
Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue));
Assert.AreEqual(0.025m, (decimal)(Math.Round(result.Score, 4)));
//Console.WriteLine(result.ScanSet);
Assert.AreEqual(26, result.ScanSet.IndexValues.Count);
Assert.AreEqual("9575 {9493, 9500, 9506, 9513, 9520, 9527, 9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624, 9631, 9638, 9645, 9652, 9658, 9665}", result.ScanSet.ToString());
}
