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 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 void ExportMultipleScansTest1()
{
Run run = new IMFRun(imfFilepath);
ScanSetCollection scanSetCollection = new ScanSetCollection();
scanSetCollection.ScanSetList.Add(new ScanSet(232));
scanSetCollection.ScanSetList.Add(new ScanSet(233));
scanSetCollection.ScanSetList.Add(new ScanSet(234));
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msGen = new GenericMSGenerator();
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
Assert.AreEqual(3, results.ScanResultList.Count);
Assert.AreEqual(92, results.ScanResultList[0].NumPeaks);
Assert.AreEqual(82, results.ScanResultList[1].NumPeaks);
Assert.AreEqual(72, results.ScanResultList[2].NumPeaks);
Assert.AreEqual(11, results.ScanResultList[0].NumIsotopicProfiles);
Assert.AreEqual(9, results.ScanResultList[1].NumIsotopicProfiles);
Assert.AreEqual(9, results.ScanResultList[2].NumIsotopicProfiles);
Assert.AreEqual(830.045752112968, (Decimal)results.ScanResultList[0].BasePeak.XValue);
Assert.AreEqual(10438, results.ScanResultList[0].BasePeak.Height);
Assert.AreEqual(0.09454554, (Decimal)results.ScanResultList[0].BasePeak.Width);
Assert.AreEqual(434.9167, (Decimal)results.ScanResultList[0].BasePeak.SN);
Exporter <ResultCollection> exporter = new BasicScansExporter(scansExporterTest1output);
exporter.Export(results);
}
public void test1_summing()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1201);
project.RunCollection.Add(run);
int numFramesSummed = 3;
int numScansSummed = 3;
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 250, 270, numScansSummed, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, numFramesSummed, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(200, 2000);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
project.TaskCollection.TaskList.Add(originalIntensitiesExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
ResultCollection rc = project.RunCollection[0].ResultCollection;
Assert.AreEqual(180, rc.ResultList.Count);
StringBuilder sb = new StringBuilder();
IsosResultUtilities.DisplayResults(sb, rc.ResultList);
Console.Write(sb.ToString());
}
public void examineFPGAFileTest1()
{
UIMFRun run = new UIMFRun(uimfFPGAFilePath);
Task msGen = new UIMF_MSGenerator(200, 2000);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 300, 300, 1, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 5, 5, 1, 1);
fscc.Create();
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msGen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.XYData);
originalIntensitiesExtractor.Execute(run.ResultCollection);
TestUtilities.DisplayXYValues(run.XYData);
}
}
}
public void test1()
{
Run xcalRun = new XCaliburRun(xcaliburTestfile, 6000, 6020);
Run mzxmlRun = new MZXMLRun(mzxmlfile1, 1, 21);
List <Run> runCollection = new List <Run>();
runCollection.Add(xcalRun);
runCollection.Add(mzxmlRun);
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(xcalRun, xcalRun.MinScan, xcalRun.MaxScan, numScansSummed, 1, false);
scanSetCreator.Create();
scanSetCreator = new ScanSetCollectionCreator(mzxmlRun, mzxmlRun.MinScan, mzxmlRun.MaxScan, numScansSummed, 1);
scanSetCreator.Create();
Task msgen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detParams.PeakBackgroundRatio = 3;
detParams.SignalToNoiseThreshold = 3;
Task peakDet = new DeconToolsPeakDetector(detParams);
Task horn = new HornDeconvolutor();
TaskCollection taskColl = new TaskCollection();
taskColl.TaskList.Add(msgen);
taskColl.TaskList.Add(peakDet);
taskColl.TaskList.Add(horn);
TaskController taskController = new BasicTaskController(taskColl);
taskController.Execute(runCollection);
Assert.AreEqual(true, TestUtilities.AreIsosResultsTheSame(xcalRun.ResultCollection.ResultList, mzxmlRun.ResultCollection.ResultList));
}
public void ApplyFilter()
{
float[] xData = _msScan.RawMZs;
float[] yData = _msScan.RawIntensities;
DeconToolsV2.Peaks.clsPeakProcessor peakProcessor = new DeconToolsV2.Peaks.clsPeakProcessor();
DeconToolsV2.Peaks.clsPeakProcessorParameters parameters = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
parameters.PeakBackgroundRatio = PeakToBackgroundRatio;
parameters.SignalToNoiseThreshold = SignalToNoiseThreshold;
parameters.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
peakProcessor.SetOptions(parameters);
DeconToolsV2.Peaks.clsPeak[] peakList = new DeconToolsV2.Peaks.clsPeak[1];
peakProcessor.DiscoverPeaks(ref xData, ref yData, ref peakList, 0, float.MaxValue);
float[] mz = new float[peakList.Length];
float[] intensity = new float[peakList.Length];
for (int i = 0; i < peakList.Length; i++)
{
mz[i] = Convert.ToSingle(peakList[i].mdbl_mz);
intensity[i] = Convert.ToSingle(peakList[i].mdbl_intensity);
}
_msScan.MZs = mz;
_msScan.Intensities = intensity;
}
public void ApplyFilter()
{
float[] xData = _msScan.RawMZs;
float[] yData = _msScan.RawIntensities;
DeconToolsV2.Peaks.clsPeakProcessor peakProcessor = new DeconToolsV2.Peaks.clsPeakProcessor();
DeconToolsV2.Peaks.clsPeakProcessorParameters parameters = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
parameters.PeakBackgroundRatio = PeakToBackgroundRatio;
parameters.SignalToNoiseThreshold = SignalToNoiseThreshold;
parameters.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
peakProcessor.SetOptions(parameters);
DeconToolsV2.Peaks.clsPeak[] peakList = new DeconToolsV2.Peaks.clsPeak[1];
peakProcessor.DiscoverPeaks(ref xData, ref yData, ref peakList, 0, float.MaxValue);
float[] mz = new float[peakList.Length];
float[] intensity = new float[peakList.Length];
for (int i = 0; i < peakList.Length; i++)
{
mz[i] = Convert.ToSingle(peakList[i].mdbl_mz);
intensity[i] = Convert.ToSingle(peakList[i].mdbl_intensity);
}
_msScan.MZs = mz;
_msScan.Intensities = intensity;
}
public void smallExportTest1()
{
Project project = Project.getInstance();
//TODO: add project parameters (for summing)
project.RunCollection.Add(new UIMFRun(uimfFilepath, 1200, 1202, 250, 300));
Task msGen = new UIMF_MSGenerator(200, 2000);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new UIMFDriftTimeExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(driftTimeExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
UIMFIsosExporter isosExporter = new UIMFIsosExporter(uimfIsosExporterTest1output);
isosExporter.Export(project.RunCollection[0].ResultCollection);
}
