public void agilentDeconTest1()
{
RunFactory runFact = new RunFactory();
Run run = runFact.CreateRun(agilentFile);
MSGeneratorFactory msfactory = new MSGeneratorFactory();
Task msgen = msfactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 7;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
ScanSet scan1821 = new ScanSet(1821);
run.CurrentScanSet = scan1821;
msgen.Execute(run.ResultCollection);
run.XYData = run.XYData.TrimData(450, 520, TODO);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void weirdZeroValuesForMZsAtEarlyFramesTest1()
{
UIMFRun run = new UIMFRun(uimfTestfile1);
FrameSetCollectionCreator framecreator = new FrameSetCollectionCreator(run, 1, 10, 5, 1);
framecreator.Create();
ScanSetCollectionCreator scanCreator = new ScanSetCollectionCreator(run, 1, 1);
scanCreator.Create();
Task msgen = new UIMF_MSGenerator(0, 5000);
Task peakDet = new DeconToolsPeakDetector();
int scanstop = 599;
int scanstart = 0;
for (int i = scanstart; i < scanstop; i++)
{
run.CurrentFrameSet = run.FrameSetCollection.GetFrameSet(1);
run.CurrentScanSet = run.ScanSetCollection.GetScanSet(i);
msgen.Execute(run.ResultCollection);
if (run.XYData != null && run.XYData.Xvalues != null && run.XYData.Xvalues[0] == 0)
{
reportXYValues(run);
}
}
}
public void test1()
{
Run run = new XCaliburRun(lowmwRawfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(1);
Task msgen = new GenericMSGenerator(0, 1000);
msgen.Execute(results);
DeconToolsPeakDetector peakdetector = new DeconToolsPeakDetector();
peakdetector.PeakBackgroundRatio = 0.5;
peakdetector.PeakFitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
peakdetector.SigNoiseThreshold = 3;
peakdetector.IsDataThresholded = true;
peakdetector.Execute(results);
//Task rapidDecon = new RapidDeconvolutor();
//rapidDecon.Execute(results);
Task simpleDecon = new SimpleDecon(0.0005);
simpleDecon.Execute(results);
Console.WriteLine(results.Run.PeakList.Count);
Console.WriteLine(results.ResultList.Count);
string reportedResults = reportResults(results.ResultList);
Console.WriteLine(reportedResults);
}
public void test1()
{
Run run = new ICR2LSRun(icr2LSRawDatafile1);
run.CurrentScanSet = new ScanSet(2210);
Task msGen = new GenericMSGenerator(732, 746);
msGen.Execute(run.ResultCollection);
Task peakdetector = new DeconToolsPeakDetector();
((DeconToolsPeakDetector)peakdetector).PeakBackgroundRatio = 5;
((DeconToolsPeakDetector)peakdetector).SigNoiseThreshold = 2;
peakdetector.Execute(run.ResultCollection);
Console.WriteLine("Peaks detected = " + run.PeakList.Count);
TomN14N15Analyzer analyzer = new TomN14N15Analyzer();
analyzer.ExtractN14N15Values(run.ResultCollection);
Console.WriteLine("Peaks detected = " + run.PeakList.Count);
Assert.AreEqual(14, run.PeakList.Count);
}
public void test1()
{
Run run = new XCaliburRun(bsaO16O18file1);
MSGeneratorFactory msgenFact = new MSGeneratorFactory();
Task msgen = msgenFact.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
O16O18FeatureFinder finder = new O16O18FeatureFinder();
List <MassTag> massTagList = TestUtilities.CreateO16O18TestMassTagList1();
run.CurrentMassTag = massTagList[0];
TomTheorFeatureGenerator theorFeatureGen = new TomTheorFeatureGenerator();
theorFeatureGen.GenerateTheorFeature(run.CurrentMassTag);
run.CurrentScanSet = new ScanSet(3294);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
IsotopicProfile o16O18profile = finder.FindFeature(run.PeakList, run.CurrentMassTag.IsotopicProfile, 10, true);
TestUtilities.DisplayIsotopicProfileData(o16O18profile);
}
public void outputToSqlite_uimf_test1()
{
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 809, 3, 1);
fsc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 220, 9, 1);
sscc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new RapidDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task scanResultUpdater = new ScanResultUpdater();
Task sqliteExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.UIMFScanResult_SqliteExporter(uimf_Sqlite_ScanResultOutputFile1);
Stopwatch sw;
foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
scanResultUpdater.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
sqliteExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("SqliteExporter execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
}
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 exporterTest1()
{
Run run = new IMFRun(imfFilepath);
run.CurrentScanSet = new ScanSet(233);
ResultCollection results = new ResultCollection(run);
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);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
Task decon = new HornDeconvolutor(hornParams);
decon.Execute(results);
Exporter <ResultCollection> exporter = new BasicIsosExporter(exporterTest1OutputName);
exporter.Export(results);
}
public void deconvoluteXCalibur_MS_DataTest1() //good ms data... expect to find isotopic profiles...
{
Run run = new XCaliburRun(xcaliburTestfile);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(6067);
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator();
msGen.Execute(rc);
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);
peakdetector.Execute(rc);
Task rapid = new RapidDeconvolutor();
rapid.Execute(rc);
Assert.AreEqual(95, rc.ResultList.Count);
}
public void criticalErrorInPeakDetectorTest1()
{
UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 425, 432, 3, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 500, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 4;
peakDet.SigNoiseThreshold = 3;
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
}
}
}
public void exportAllPeaksInXCaliburFile()
{
if (File.Exists(xcaliburAllPeaksFileName))
{
File.Delete(xcaliburAllPeaksFileName);
}
Run run = new XCaliburRun(xcaliburTestfile);
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false);
scansetCreator.Create();
Task msgen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task peakDetector = new DeconToolsPeakDetector(peakParams);
((DeconToolsPeakDetector)peakDetector).StorePeakData = true;
Task exporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListTextExporter(run.MSFileType, 1000000, xcaliburAllPeaksFileName); //trigger of 1E5 = 310 sec (memory = 150 MB); trigger of 1E6 = 231 Sec (memory = 250 MB);
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
exporter.Execute(run.ResultCollection);
}
exporter.Cleanup();
Assert.AreEqual(true, File.Exists(xcaliburAllPeaksFileName));
}
public void uimfTest1()
{
UIMFRun run = new UIMFRun(uimfFile1);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task suspPeakFlagger = new LeftOfMonoPeakLooker();
run.CurrentFrameSet = new FrameSet(501, 500, 502);
run.CurrentScanSet = new ScanSet(250, 246, 254);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
foreach (var result in run.ResultCollection.ResultList)
{
((LeftOfMonoPeakLooker)suspPeakFlagger).CurrentResult = result;
suspPeakFlagger.Execute(run.ResultCollection);
}
Assert.AreEqual(38, run.ResultCollection.ResultList.Count);
List <IsosResult> flaggedResults = run.ResultCollection.ResultList.Where(p => p.Flags.Count > 0).ToList();
Assert.AreEqual(13, flaggedResults.Count);
TestUtilities.DisplayIsotopicProfileData(flaggedResults[0].IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(flaggedResults[1].IsotopicProfile);
}
public void peakDetectionOnXCaliburTest2_effectOfThresholdingOnPeakDetector()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(4003);
Task msgen = new GenericMSGenerator(0, 2000);
msgen.Execute(results);
run.IsDataThresholded = true; //fyi... by default, xcalibur runs are set to be true
Task peakDetector = new DeconToolsPeakDetector();
((DeconToolsPeakDetector)(peakDetector)).PeakBackgroundRatio = 1.3;
((DeconToolsPeakDetector)(peakDetector)).PeakFitType = Globals.PeakFitType.QUADRATIC;
((DeconToolsPeakDetector)(peakDetector)).SigNoiseThreshold = 2;
peakDetector.Execute(results);
Assert.AreEqual(646, results.Run.PeakList.Count);
run.IsDataThresholded = false;
peakDetector = new DeconToolsPeakDetector();
((DeconToolsPeakDetector)(peakDetector)).PeakBackgroundRatio = 1.3;
((DeconToolsPeakDetector)(peakDetector)).PeakFitType = Globals.PeakFitType.QUADRATIC;
((DeconToolsPeakDetector)(peakDetector)).SigNoiseThreshold = 2;
peakDetector.Execute(results);
Assert.AreEqual(636, results.Run.PeakList.Count);
}
public void peakDetectionOnXCaliburTest1()
{
Run run = new XCaliburRun(xcaliburTestfile, 6000, 7000);
ScanSetCollection scansetCollection = new ScanSetCollection();
for (int i = 6000; i < 6015; i++)
{
scansetCollection.ScanSetList.Add(new ScanSet(i));
}
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scansetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
Assert.AreEqual(2, results.ScanResultList.Count);
}
public MercuryDistributionCreator()
{
avergineFormulaCreator = new DeconToolsV2.HornTransform.clsAveragine();
hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
decon2LSMercuryDistribution = new DeconToolsV2.clsMercuryIsotopeDistribution();
peakDetector = new DeconToolsPeakDetector();
}
public void serializeUIMFDataTest1()
{
Run run = new UIMFRun(uimfFilepath2);
List <Run> runCollection = new List <Run>();
runCollection.Add(run);
int startFrame = 1200;
int stopFrame = 1205;
int numFramesSummed = 3;
int numScansSummed = 3;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, numScansSummed, 1);
scanSetCreator.Create();
Task msgen = new UIMF_MSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = true;
Task peakdetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new RapidDeconvolutor();
TaskCollection taskcollection = new TaskCollection();
taskcollection.TaskList.Add(msgen);
taskcollection.TaskList.Add(peakdetector);
taskcollection.TaskList.Add(decon);
TaskController taskcontroller = new UIMF_TaskController(taskcollection);
taskcontroller.IsosResultThresholdNum = 50;
taskcontroller.Execute(runCollection);
ResultCollection results;
IsosResultDeSerializer deserializer = new IsosResultDeSerializer(run.Filename + "_tmp.bin");
int counter = 0;
do
{
counter++;
results = deserializer.GetNextSetOfResults();
} while (results != null);
Assert.AreEqual(8, counter);
}
public void fitterOnHornDataTest1()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
Task msGen = new GenericMSGenerator(1154, 1158);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParameters.PeptideMinBackgroundRatio = 2;
Task decon = new HornDeconvolutor(hornParameters);
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
StringBuilder sb = new StringBuilder();
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
Console.WriteLine(sb.ToString());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0209385414928986, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void turnRAPIDScoreIntoHornScoreAndCompareTest1()
{
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050);
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, numScansSummed, 1, false);
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 rapid = new RapidDeconvolutor();
Task horn = new HornDeconvolutor();
Task fitcalc = new DeconToolsFitScoreCalculator();
run.CurrentScanSet = run.ScanSetCollection.GetScanSet(6005);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
horn.Execute(run.ResultCollection);
//string isosData = reportIsotopicProfiles(run);
//Console.Write(isosData);
//First evaluate HornTransform score
Assert.AreEqual(481.274105402604, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.GetMZ());
Assert.AreEqual(0.0101245114907111, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.Score);
run.ResultCollection.ClearAllResults();
horn.Execute(run.ResultCollection);
fitcalc.Execute(run.ResultCollection);
Assert.AreEqual(0.00583991502104572, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.Score);
run.ResultCollection.ClearAllResults();
//Run RAPID and evaluate the score Rapid gives it
rapid.Execute(run.ResultCollection);
Assert.AreEqual(481.274105402604, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.GetMZ());
Assert.AreEqual(1.52062147024669, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score);
//Run the DeconToolsFitScoreCalculator
fitcalc.Execute(run.ResultCollection);
//Evaluate the score given by the fitscore calculator
Assert.AreNotEqual(1.52062147024669, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score);
Assert.AreEqual(0.00583991502104572m, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score);
}
public void simpleAddTest1()
{
//first deconvolute with THRASH
//then deconvolute with RAPID, using comboMode = 'simplyAddIt'
//so there will be duplicate results
Project.Reset();
Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050);
Project.getInstance().RunCollection.Add(run);
ResultCollection results = new ResultCollection(run);
TaskCollection taskCollection = new TaskCollection();
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false);
scansetCreator.Create();
Task msgen = new GenericMSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters peakDetParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
peakDetParams.SignalToNoiseThreshold = 3;
peakDetParams.PeakBackgroundRatio = 0.5;
Task peakDetector = new DeconToolsPeakDetector(peakDetParams);
Task thrashDecon = new HornDeconvolutor();
Task rapidDecon = new RapidDeconvolutor();
taskCollection.TaskList.Add(msgen);
taskCollection.TaskList.Add(peakDetector);
taskCollection.TaskList.Add(thrashDecon);
TaskController taskcontroller = new BasicTaskController(taskCollection);
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
taskCollection.TaskList.Remove(thrashDecon);
taskCollection.TaskList.Add(rapidDecon);
Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear();
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(2472, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear();
taskCollection.TaskList.Remove(rapidDecon);
taskCollection.TaskList.Add(thrashDecon);
taskCollection.TaskList.Add(rapidDecon);
taskcontroller.Execute(Project.getInstance().RunCollection);
Assert.AreEqual(2472 + 644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
}
public void uimf_data_preLoaded() // in this case, data is preloaded, preventing re-accessing the same drifttimes over and over
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
((UIMFRun)run).GetFrameDataAllFrameSets(); // this is the key line... loads data necessary for drift time calc and correction
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public void fitterOnHornDataTest2()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
Task msGen = new GenericMSGenerator(579, 582);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
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 HornDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[1];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
StringBuilder sb = new StringBuilder();
XYData theorXYData = distcreator.Data;
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
distcreator.OffsetDistribution(result1.IsotopicProfile);
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
Console.WriteLine(sb.ToString());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0704215577242672, (decimal)fitval);
}
public void checkIntegrityOfUIMF_RawDataTest1()
{
UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 696, 696, 3, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 350, 500, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
StringBuilder sb = new StringBuilder();
sb.Append("frame\tscan\tmaxIntens\tnumZeros\n");
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
List <int> indices = getIndicesOf0MZValues(run.XYData.Xvalues);
double maxY = run.XYData.GetMaxY();
if (indices.Count > -1)
{
sb.Append(frame.PrimaryFrame);
sb.Append("\t");
sb.Append(scan.PrimaryScanNumber);
sb.Append("\t");
sb.Append(maxY);
sb.Append("\t");
sb.Append(indices.Count);
sb.Append("\n");
}
}
}
Console.WriteLine(sb.ToString());
}
public void xcaliburSpeed_RAPID_Test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
int startScan = 6005;
int stopScan = 7000;
int numScansSummed = 1;
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, startScan, stopScan, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection results = new ResultCollection(run);
List <timingResult> timingResults = new List <timingResult>();
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
if (results.Run.GetMSLevel(scanset.PrimaryScanNumber) != 1)
{
continue;
}
sw.Reset();
timingResult timeresult = new timingResult();
timeresult.frameNum = -1;
timeresult.scanNum = scanset.PrimaryScanNumber;
sw.Start();
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
timeresult.msGenTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(results);
timeresult.peakDetectorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task rapid = new RapidDeconvolutor();
rapid.Execute(results);
timeresult.deconTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
timeresult.resultUpdaterTime = sw.ElapsedMilliseconds;
timingResults.Add(timeresult);
}
reportTimingEachScan(timingResults);
}
public void uimf_data_not_preLoaded() // in this case the drift time is calculated every time by looking up sqlite data from uimf file
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
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 examineIMFFile_Scan233MZ630()
{
Run run = new IMFRun(imfFilepath);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(233, 229, 237);
run.MSParameters.MinMZ = 100;
run.MSParameters.MaxMZ = 631.5;
int numPeaks = 0;
for (double n = 629; n < 630; n = n + 0.01)
{
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator(n, run.MSParameters.MaxMZ);
msGen.Execute(rc);
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 zeroFiller = new DeconToolsZeroFiller(3);
//zeroFiller.Execute(rc);
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(rc);
Task decon = new RapidDeconvolutor();
decon.Execute(rc);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < rc.ResultList.Count; i++)
{
IsosResult result = rc.ResultList[i];
if (result.IsotopicProfile.Peaklist[0].XValue > 629 && result.IsotopicProfile.Peaklist[0].XValue < 631)
{
sb.Append(n.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Score.ToString("0.00"));
sb.Append("\t");
sb.Append(result.Run.PeakList.Count);
sb.Append("\t");
sb.Append(result.Run.XYData.Xvalues.Length);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
}
public void test1()
{
Run run = new MSScanFromTextFileRun(imfMSScanTextfile);
ResultCollection resultcollection = new ResultCollection(run);
Task msgen = new GenericMSGenerator();
msgen.Execute(resultcollection);
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(resultcollection);
Task rapidDecon = new RapidDeconvolutor();
rapidDecon.Execute(resultcollection);
int counter = 0;
foreach (StandardIsosResult result in resultcollection.ResultList)
{
IsotopicProfile profile = result.IsotopicProfile;
Console.Write("------------ profile" + counter + "; Charge state = " + profile.ChargeState
+ "; Score= " + profile.Score.ToString("0.00") + " ----------------\n");
int peakcounter = 0;
Console.Write("idx" + "\t" + "mz" + "\t" + "intensity" + "\t" + "SN" + "\t" + "FWHM" + "\n");
foreach (MSPeak peak in profile.Peaklist)
{
Console.Write(peakcounter + "\t" + peak.XValue + "\t" + peak.Height + "\t" + peak.SN + "\t" + peak.Width + "\n");
peakcounter++;
}
counter++;
}
Assert.AreEqual(9, resultcollection.ResultList.Count);
Assert.AreEqual(582.820684517665, Convert.ToDecimal(resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].XValue));
Assert.AreEqual(2984.0, resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].Height);
Assert.AreEqual(0.05905123, (decimal)resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].Width);
Assert.AreEqual(157.0526, (decimal)resultcollection.ResultList[0].IsotopicProfile.Peaklist[0].SN);
Assert.AreEqual(4593, resultcollection.ResultList[0].IsotopicProfile.GetAbundance());
Assert.AreEqual(1, resultcollection.ResultList[8].IsotopicProfile.GetNumOfIsotopesInProfile());
Assert.AreEqual(2488.07303881522, Convert.ToDecimal(resultcollection.ResultList[8].IsotopicProfile.AverageMass));
Assert.AreEqual(3, resultcollection.ResultList[8].IsotopicProfile.ChargeState);
Assert.AreEqual(18802, Convert.ToDecimal(resultcollection.ResultList[8].IsotopicProfile.IntensityAggregate));
Assert.AreEqual(2486.09777364184, Convert.ToDecimal(resultcollection.ResultList[8].IsotopicProfile.MonoIsotopicMass));
}
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 examineRAWFile_Scan6757()
{
Run run = new XCaliburRun(xcaliburTestfile);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(6757);
run.MSParameters.MinMZ = 0;
run.MSParameters.MaxMZ = 10000;
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator(run.MSParameters.MinMZ, run.MSParameters.MaxMZ);
msGen.Execute(rc);
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 zeroFiller = new DeconToolsZeroFiller(3);
//zeroFiller.Execute(rc);
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(rc);
Task decon = new RapidDeconvolutor();
decon.Execute(rc);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < rc.ResultList.Count; i++)
{
IsosResult result = rc.ResultList[i];
if (result.IsotopicProfile.Peaklist[0].XValue > 0 && result.IsotopicProfile.Peaklist[0].XValue < 10000)
{
sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Score.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Peaklist[0].SN.ToString("0.0"));
sb.Append("\t");
sb.Append(result.Run.PeakList.Count);
sb.Append("\t");
sb.Append(result.Run.XYData.Xvalues.Length);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
