public void getPeakChromatogramTest2()
{
var mt = TestUtilities.GetMassTagStandard(1);
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new TomTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(10, Globals.ChromatogramGeneratorMode.TOP_N_PEAKS);
peakChromGen.TopNPeaksLowerCutOff = 0.4;
peakChromGen.Execute(run.ResultCollection);
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
//Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
run.XYData.Display();
}
public void getPeakChromatogramTest1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(toleranceInPPM);
peakChromGen.Execute(run.ResultCollection);
run.XYData.Display();
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
//make sure that the 0's are not trimmed off
Assert.AreEqual(0, run.XYData.Yvalues[1]);
}
public void GetPeakChromatogram_IQStyle_Test3()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1, FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var target = TestUtilities.GetIQTargetStandard(1);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 100;
var lowerScan = 6087;
var upperScan = 6418;
var massOfInterest = new List <double>();
massOfInterest.Add(target.TheorIsotopicProfile.Peaklist[0].XValue);
massOfInterest.Add(target.TheorIsotopicProfile.Peaklist[1].XValue);
var chromXYData = chromGen.GenerateChromatogram(run, massOfInterest, lowerScan, upperScan, chromGen.Tolerance, chromGen.ToleranceUnit);
Assert.IsNotNull(chromXYData);
Assert.AreEqual(96, chromXYData.Xvalues.Length);
TestUtilities.DisplayXYValues(chromXYData);
}
public void test2()
{
MassTag massTag = new MassTag();
massTag.ID = 56488;
massTag.MonoIsotopicMass = 2275.1694779;
massTag.ChargeState = 3;
massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649;
Run run = new XCaliburRun(xcaliburTestfile);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = massTag;
Task peakChromGen = new PeakChromatogramGenerator(10);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector();
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
TestUtilities.DisplayXYValues(run.ResultCollection);
}
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);
}
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 GetChromatogramsTest1()
{
string testDatasetPath =
@"D:\Data\From_Vlad\Bruker\2013_01_29_ALZ_CTRL_5_0p5_1_01_228.d";
Run run = RunUtilities.CreateAndLoadPeaks(testDatasetPath);
PeakChromatogramGenerator chromGen = new PeakChromatogramGenerator(10);
double targetMZ = 663.3404;
int chargeState = 2;
int peakNum = 4;
targetMZ = targetMZ + peakNum * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
double toleranceInPPM = 10;
int startScan = 230;
int stopScan = 300;
chromGen.GenerateChromatogram(run, startScan, stopScan, targetMZ, toleranceInPPM);
run.XYData = run.XYData.TrimData(startScan, stopScan);
TestUtilities.DisplayXYValues(run.XYData);
}
public void BadCorrelationTest1()
{
var dataset =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var run = new RunFactory().CreateRun(dataset);
var peaksDataFile = dataset.ToLower().Replace(".raw", "_peaks.txt");
var peakImporter = new PeakImporterFromText(peaksDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
double chromToleranceInPPM = 10;
var startScan = 2340;
var stopScan = 2440;
var smoother = new SavitzkyGolaySmoother(9, 2);
var testMZVal1 = 719.80349;
var peakChromGen = new PeakChromatogramGenerator(chromToleranceInPPM);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, testMZVal1, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var chromdata1 = run.XYData.TrimData(startScan, stopScan);
var testMZVal2 = 722.325;
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, testMZVal2, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var chromdata2 = run.XYData.TrimData(startScan, stopScan);
//chromdata1.Display();
//Console.WriteLine();
//chromdata2.Display();
ChromatogramCorrelatorBase correlator = new ChromatogramCorrelator(3);
double slope = 0;
double intercept = 0;
double rsquaredVal = 0;
correlator.GetElutionCorrelationData(chromdata1, chromdata2, out slope, out intercept, out rsquaredVal);
Console.WriteLine("slope = \t" + slope);
Console.WriteLine("intercept = \t" + intercept);
Console.WriteLine("rsquared = \t" + rsquaredVal);
for (var i = 0; i < chromdata1.Xvalues.Length; i++)
{
Console.WriteLine(chromdata1.Xvalues[i] + "\t" + chromdata1.Yvalues[i] + "\t" + chromdata2.Yvalues[i]);
}
}
/// <summary>
/// Finds the XIC based on the m/z and scan parameters.
/// </summary>
/// <param name="mz"></param>
/// <param name="scan"></param>
/// <returns></returns>
public List <XYData> FindXic(double mz, int scan, bool shouldSmooth)
{
LcmsFeatureTarget target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = mz;
target.ScanLCTarget = scan;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
m_run.CurrentMassTag = target;
var result = m_run.ResultCollection.GetTargetedResult(m_run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = MzPpmWindow;
Globals.ChromatogramGeneratorMode chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator(chromPeakGeneratorTolInPPM,
chromGeneratorMode);
chromGen.NETWindowWidthForNonAlignedData = Convert.ToSingle(NetWindow);
int pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
double chromPeakDetectorPeakBR = 1;
double chromPeakDetectorSigNoise = 1;
var chromPeakDetector = new ChromPeakDetector(chromPeakDetectorPeakBR,
chromPeakDetectorSigNoise);
ChromPeakSelectorParameters chromPeakSelectorParameters = new ChromPeakSelectorParameters();
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(m_run.ResultCollection);
//this smooths the data - very important step!
if (shouldSmooth)
{
chromSmoother.Execute(m_run.ResultCollection);
}
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(m_run.ResultCollection);
//this selects the peak
chromPeakSelector.Parameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
chromPeakSelector.Execute(m_run.ResultCollection);
//Here's the chromatogram data...
List <XYData> data = new List <XYData>();
for (int i = 0; i < m_run.XYData.Xvalues.Length; i++)
{
XYData datum = new XYData(m_run.XYData.Xvalues[i], m_run.XYData.Yvalues[i]);
data.Add(datum);
}
return(data);
}
public void test3()
{
MassTag massTag = new MassTag();
massTag.ID = 56488;
massTag.MonoIsotopicMass = 2275.1694779;
massTag.ChargeState = 3;
massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649;
massTag.NETVal = 0.3520239f;
Run run = new XCaliburRun(xcaliburTestfile);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = massTag;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector();
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.1);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
Console.WriteLine("Now generating MS....");
msgen.Execute(run.ResultCollection);
Console.WriteLine("----------- RESULTS ----------------------\n");
TestUtilities.DisplayPeaks(run.PeakList);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[massTag];
massTagResult.DisplayToConsole();
Assert.AreEqual(5512, massTagResult.ScanSet.PrimaryScanNumber);
}
protected ChromatogramCorrelatorBase(int numPointsInSmoother, double minRelativeIntensityForChromCorr,
double chromTolerance, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
SavitzkyGolaySmoothingOrder = 2;
NumPointsInSmoother = numPointsInSmoother;
ChromTolerance = chromTolerance;
MinimumRelativeIntensityForChromCorr = minRelativeIntensityForChromCorr;
ChromToleranceUnit = toleranceUnit;
PeakChromGen = new PeakChromatogramGenerator(ChromTolerance, Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK,
Globals.IsotopicProfileType.UNLABELLED, toleranceUnit);
Smoother = new SavitzkyGolaySmoother(NumPointsInSmoother, SavitzkyGolaySmoothingOrder, false);
}
public void GetPeakChromatogram_usePPMTolerance_Test1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var xydata = chromGen.GenerateChromatogram(run, startScan, stopScan, targetMZ, toleranceInPPM, Globals.ToleranceUnit.PPM);
Assert.IsNotNull(xydata);
TestUtilities.DisplayXYValues(xydata);
}
public void CorrelationTest2_UsingExecutorMethod()
{
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
double chromToleranceInPPM = 10;
var startScan = 5460;
var stopScan = 5755;
var smoother = new SavitzkyGolaySmoother(3, 2);
var peakChromGen = new PeakChromatogramGenerator(chromToleranceInPPM);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, mt.IsotopicProfile.Peaklist[0].XValue, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var result = run.ResultCollection.GetTargetedResult(mt);
ChromatogramCorrelatorBase correlator = new ChromatogramCorrelator(3);
var corrData = correlator.CorrelatePeaksWithinIsotopicProfile(run, mt.IsotopicProfile, startScan, stopScan);
Debug.Assert(corrData.CorrelationDataItems != null, "corrData.CorrelationDataItems != null");
Assert.AreEqual(0.98m, (decimal)Math.Round((double)corrData.CorrelationDataItems[1].CorrelationRSquaredVal, 2));
foreach (var item in corrData.CorrelationDataItems)
{
Console.WriteLine(item.CorrelationRSquaredVal);
}
}
public SimpleMsViewerViewModel(Run run)
{
this.Run = run;
PeakDetector = new DeconToolsPeakDetectorV2();
_peakChromatogramGenerator = new PeakChromatogramGenerator();
Peaks = new List<Peak>();
//the order matters here. See the properties.
MSGraphMaxX = 1500;
MSGraphMinX = 400;
ChromToleranceInPpm = 20;
ChromSourcePeakDetectorSigNoise = 2;
ChromSourcePeakDetectorPeakBr = 3;
NumMSScansToSum = 1;
ShowMsMsSpectra = false;
NavigateToNextMS1MassSpectrum();
}
public void GetPeakChromatogram_IQStyle_Test1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var target = TestUtilities.GetIQTargetStandard(1);
//TestUtilities.DisplayIsotopicProfileData(target.TheorIsotopicProfile);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 10;
var chromXYData = chromGen.GenerateChromatogram(run, target.TheorIsotopicProfile, target.ElutionTimeTheor);
Assert.IsNotNull(chromXYData);
TestUtilities.DisplayXYValues(chromXYData);
}
private double getCorrelation(double mzPeak1, double mzPeak2, double tolerancePPMpeak1, double tolerancePPMpeak2)
{
var chromgenPeak1 = new PeakChromatogramGenerator();
chromgenPeak1.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
chromgenPeak1.TopNPeaksLowerCutOff = 0.4;
//TODO: correlate narrow range. -100 +100
//TODO: for gord.
var scanWindow = 100;
var lowerScan = _run.CurrentScanSet.PrimaryScanNumber - scanWindow;
var upperScan = _run.CurrentScanSet.PrimaryScanNumber + scanWindow;
var chromxydataPeak1 = chromgenPeak1.GenerateChromatogram(_run, lowerScan, upperScan, mzPeak1, tolerancePPMpeak1, Globals.ToleranceUnit.PPM);
var chromxydataPeak2 = chromgenPeak1.GenerateChromatogram(_run, lowerScan, upperScan, mzPeak2, tolerancePPMpeak2, Globals.ToleranceUnit.PPM);
//var chromxydataPeak1 = chromgenPeak1.GenerateChromatogram(_run, 1, _run.GetNumMSScans(), mzPeak1, tolerancePPMpeak1, Globals.ToleranceUnit.PPM);
//var chromxydataPeak2 = chromgenPeak1.GenerateChromatogram(_run, 1, _run.GetNumMSScans(), mzPeak2, tolerancePPMpeak2, Globals.ToleranceUnit.PPM);
if (null == chromxydataPeak1 || null == chromxydataPeak2)
{
return(-3.0);
}
double[] arrayToCorrelatePeak1;
double[] arrayToCorrelatePeak2;
var overlap = AlignAndFillArraysToCorrelate(chromxydataPeak1, chromxydataPeak2, out arrayToCorrelatePeak1, out arrayToCorrelatePeak2);
if (overlap)
{
var corr = MathNet.Numerics.Statistics.Correlation.Pearson(arrayToCorrelatePeak1, arrayToCorrelatePeak2);
if (double.IsNaN(corr))
{
return(-2); //it's present, but they don't overlap any. same as other -2 value.
}
//TODO: implement iq standard of getting linear regression.
return(MathNet.Numerics.Statistics.Correlation.Pearson(arrayToCorrelatePeak1, arrayToCorrelatePeak2));
}
return(-2);
}
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 ChromPeakDetectorMedianBased(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise);
_chromPeakSelector = CreateChromPeakSelector(_workflowParameters);
_iterativeTFFParameters = new IterativeTFFParameters();
_iterativeTFFParameters.ToleranceInPPM = _workflowParameters.MSToleranceInPPM;
_msfeatureFinder = new IterativeTFF(_iterativeTFFParameters);
_fitScoreCalc = new IsotopicProfileFitScoreCalculator();
_resultValidator = new ResultValidatorTask();
_chromatogramCorrelator = new ChromatogramCorrelator(_workflowParameters.ChromSmootherNumPointsInSmooth, 0.01, _workflowParameters.ChromGenTolerance);
ChromatogramXYData = new XYData();
MassSpectrumXYData = new XYData();
ChromPeaksDetected = new List <ChromPeak>();
}
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 GetPeakChromatogram_IQStyle_Test1()
{
//Run run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
// FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var fileName =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
var run = RunUtilities.CreateAndLoadPeaks(fileName);
var target = TestUtilities.GetIQTargetStandard(1);
//TestUtilities.DisplayIsotopicProfileData(target.TheorIsotopicProfile);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
//chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 10;
//var chromXYData = chromGen.GenerateChromatogram(run, target.TheorIsotopicProfile, target.ElutionTimeTheor);
// var chromXYData = chromGen.GenerateChromatogram(run, new List<double> { 481.27410, 481.77542, 482.27683 }, 4000, 6500, 0.009, Globals.ToleranceUnit.MZ);
// var chromXYData = chromGen.GenerateChromatogram(run,500,7000,490.26483,0.005,Globals.ToleranceUnit.MZ);
// Assert.IsNotNull(chromXYData);
Console.WriteLine("481.27410");
var chromXYData1 = chromGen.GenerateChromatogram(run, 500, 7000, 481.27410, 0.005, Globals.ToleranceUnit.MZ); TestUtilities.DisplayXYValues(chromXYData1);
// TestUtilities.DisplayXYValues(chromXYData);
var minx1 = chromXYData1.Xvalues.Min();
var maxx1 = chromXYData1.Xvalues.Max();
Console.WriteLine("481.77542");
// chromXYData1.
var chromXYData2 = chromGen.GenerateChromatogram(run, 500, 7000, 481.77542, 0.005, Globals.ToleranceUnit.MZ); TestUtilities.DisplayXYValues(chromXYData2);
// TestUtilities.DisplayXYValues(chromXYData);
var minx2 = chromXYData2.Xvalues.Min();
var maxx2 = chromXYData2.Xvalues.Max();
Console.WriteLine("482.27683");
var chromXYData3 = chromGen.GenerateChromatogram(run, 500, 7000, 482.27683, 0.005, Globals.ToleranceUnit.MZ); TestUtilities.DisplayXYValues(chromXYData3);
TestUtilities.DisplayXYValues(chromXYData3);
var minx3 = chromXYData3.Xvalues.Min();
var maxx3 = chromXYData3.Xvalues.Max();
var minxhelper = Math.Max(minx1, minx2);
var minx = Math.Max(minxhelper, minx3);
var maxxhelper = Math.Min(maxx1, maxx2);
var maxX = Math.Min(maxxhelper, maxx3);
var c1start = chromXYData1.GetClosestXVal(minx);
var c2start = chromXYData2.GetClosestXVal(minx);
var c3start = chromXYData3.GetClosestXVal(minx);
var c1stop = chromXYData1.GetClosestXVal(maxX);
var c2stop = chromXYData2.GetClosestXVal(maxX);
var c3stop = chromXYData3.GetClosestXVal(maxX);
chromXYData1.NormalizeYData();
chromXYData2.NormalizeYData();
chromXYData3.NormalizeYData();
var c1 = new double[c1stop - c1start + 1];
var c2 = new double[c2stop - c2start + 1];
var c3 = new double[c3stop - c3start + 1];
for (int i = c1start, j = 0; i <= c1stop; i++, j++)
{
c1[j] = chromXYData1.Yvalues[i];
}
for (int i = c2start, j = 0; i <= c2stop; i++, j++)
{
c2[j] = chromXYData2.Yvalues[i];
}
for (int i = c3start, j = 0; i <= c3stop; i++, j++)
{
c3[j] = chromXYData3.Yvalues[i];
}
for (var i = 0; i < c1.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", c1[i], c2[i], c3[i]);
}
// double c1chromEven= chromXYData1.Xvalues
var corr1 = MathNet.Numerics.Statistics.Correlation.Pearson(c1, c2);
var corr2 = MathNet.Numerics.Statistics.Correlation.Pearson(c1, c3);
Console.WriteLine("HERE IS THE CORRELATION: " + corr1);
Console.WriteLine("HERE IS THE CORRELATION: " + corr2);
//bool alldone = false, done1 = false, done2 = false, done3 = false;
//int onestarting=0,twostarting=0,threestarting=0;
//while (!alldone)
//{
// if (!done1)
// {
// if (chromXYData1.Xvalues[onestarting]==minx)
// {
// done1 = true;
// }
// else
// {
// }
// }
// if (!done2)
// {
// }
// if (!done3)
// {
// }
// alldone = done1 && done2 && done3;
//}
}
public void ChromAnalysisForAllSelectedPrecursors()
{
var isDataSmoothed = true;
var numPointsInSmoothing = 9;
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(numPointsInSmoothing, 2);
var graphGenerator = new BasicGraphControl();
var thermoFile1 = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(thermoFile1);
var outputFolderForChromGraphs = @"\\protoapps\DataPkgs\Public\2012\684_DeconMSn_research1\ChromatogramImages";
if (!Directory.Exists(outputFolderForChromGraphs))
{
Directory.CreateDirectory(outputFolderForChromGraphs);
}
var scanSetCollection = new ScanSetCollection();
var scanStart = run.MinLCScan;
var scanStop = run.MaxLCScan;
scanSetCollection.Create(run, scanStart, scanStop, 1, 1, true);
var sb = new StringBuilder();
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (!File.Exists(expectedPeaksFile))
{
var peakCreatorParams = new PeakDetectAndExportWorkflowParameters();
peakCreatorParams.PeakBR = 1.75;
var peakCreator = new PeakDetectAndExportWorkflow(run, peakCreatorParams);
peakCreator.Execute();
}
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
double ppmTol = 50;
var peakChromatogramGenerator = new PeakChromatogramGenerator(ppmTol, Globals.ChromatogramGeneratorMode.MZ_BASED);
var scansetList = scanSetCollection.ScanSetList;
var scanCounter = 0;
var currentBin = 0;
foreach (var scanSet in scansetList)
{
run.CurrentScanSet = scanSet;
var currentScanLevel = run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentScanLevel > 1)
{
scanCounter++;
var precursorInfo = run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
var scanInfo = run.GetScanInfo(scanSet.PrimaryScanNumber);
var scanWindowSize = 400;
var startScan = scanSet.PrimaryScanNumber - scanWindowSize / 2;
var stopScan = scanSet.PrimaryScanNumber + scanWindowSize / 2;
run.XYData = peakChromatogramGenerator.GenerateChromatogram(run, startScan, stopScan, precursorInfo.PrecursorMZ, ppmTol);
if (run.XYData == null)
{
run.XYData = new XYData();
run.XYData.Xvalues = new double[] { 0, 1, 2 };
run.XYData.Yvalues = new double[] { 0, 1, 2 };
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan + "--------- NO XYData!!! -------------");
}
else
{
if (isDataSmoothed)
{
run.XYData = smoother.Smooth(run.XYData);
}
}
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan);
graphGenerator.GenerateGraph(run.XYData.Xvalues, run.XYData.Yvalues);
var line = graphGenerator.GraphPane.CurveList[0] as LineItem;
line.Line.IsVisible = true;
line.Symbol.Size = 2;
line.Symbol.Type = SymbolType.Circle;
graphGenerator.GraphPane.XAxis.Title.Text = "scan";
graphGenerator.GraphPane.YAxis.Title.Text = "intensity";
graphGenerator.GraphPane.XAxis.Scale.MinAuto = true;
graphGenerator.GraphPane.YAxis.Scale.MinAuto = false;
graphGenerator.GraphPane.YAxis.Scale.Min = 0;
graphGenerator.GraphPane.XAxis.Scale.FontSpec.Size = 12;
graphGenerator.AddVerticalLineToGraph(scanSet.PrimaryScanNumber, 3);
graphGenerator.AddAnnotationRelativeAxis(scanInfo, 0.3, 0.1);
if (scanCounter > 500)
{
currentBin++;
scanCounter = 0;
}
var currentOutputFolder = Path.Combine(outputFolderForChromGraphs, "bin" + currentBin);
if (!Directory.Exists(currentOutputFolder))
{
Directory.CreateDirectory(currentOutputFolder);
}
var baseFilename = Path.Combine(currentOutputFolder,
scanSet.PrimaryScanNumber.ToString().PadLeft(5, '0') + "_mz" + precursorInfo.PrecursorMZ);
string outputGraphFilename;
string outputXYData;
if (isDataSmoothed)
{
outputGraphFilename = baseFilename + "_smoothed_chrom.png";
outputXYData = baseFilename + "_smoothed_xydata.txt";
}
else
{
outputXYData = baseFilename + "_xydata.txt";
outputGraphFilename = baseFilename + "_chrom.png";
}
graphGenerator.SaveGraph(outputGraphFilename);
TestUtilities.WriteToFile(run.XYData, outputXYData);
}
}
Console.WriteLine(sb.ToString());
}
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();
}
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 CorrelationTest1()
{
//TODO: test something
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
double chromToleranceInPPM = 10;
var startScan = 5460;
var stopScan = 5755;
var smoother = new SavitzkyGolaySmoother(3, 2);
var peakChromGen = new PeakChromatogramGenerator(chromToleranceInPPM);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, mt.IsotopicProfile.Peaklist[0].XValue, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var chromdata1 = run.XYData.TrimData(startScan, stopScan);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, mt.IsotopicProfile.Peaklist[3].XValue, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var chromdata2 = run.XYData.TrimData(startScan, stopScan);
//chromdata1.Display();
//Console.WriteLine();
//chromdata2.Display();
ChromatogramCorrelatorBase correlator = new ChromatogramCorrelator(3);
double slope = 0;
double intercept = 0;
double rsquaredVal = 0;
correlator.GetElutionCorrelationData(chromdata1, chromdata2, out slope, out intercept, out rsquaredVal);
Console.WriteLine(mt);
Console.WriteLine("slope = \t" + slope);
Console.WriteLine("intercept = \t" + intercept);
Console.WriteLine("rsquared = \t" + rsquaredVal);
for (var i = 0; i < chromdata1.Xvalues.Length; i++)
{
Console.WriteLine(chromdata1.Xvalues[i].ToString("0") + "\t" + chromdata1.Yvalues[i].ToString("0") + "\t" + chromdata2.Yvalues[i]);
}
}
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();
}
public void Test1()
{
var testFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27.RAW";
var peaksTestFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = 715.39214;
target.ScanLCTarget = 7343;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
run.CurrentMassTag = target;
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = 20;
var chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator(chromPeakGeneratorTolInPPM, chromGeneratorMode);
// If we want to use the Execute Command
//BLL .1 and .5 NET windows work. .02 NET window does not BR and SN was set to 1 however)
chromGen.ChromWindowWidthForNonAlignedData = .02F;
var pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
//BLL We also tried to set the BR and SIG NOISE to 0. This did not work
var chromPeakDetectorPeakBR = 0.5;
var chromPeakDetectorSigNoise = 0.5;
var chromPeakDetector = new ChromPeakDetector(chromPeakDetectorPeakBR, chromPeakDetectorSigNoise);
var chromPeakSelectorParameters = new ChromPeakSelectorParameters();
chromPeakSelectorParameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
var smartChromPeakParameters = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartChromPeakParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(run.ResultCollection);
//this smooths the data - very important step!
//BLL. This didnt work for me when we first started, instead of using the NET window above.
//chromGen.GenerateChromatogram(run,
// target.ScanLCTarget - 300,
// target.ScanLCTarget + 300,
// target.MZ,
// chromPeakGeneratorTolInPPM);
chromSmoother.Execute(run.ResultCollection);
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(run.ResultCollection);
//this selects the peak
chromPeakSelector.Execute(run.ResultCollection);
//smartChromPeakSelector.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.XYData);
TestUtilities.DisplayPeaks(run.PeakList);
Console.WriteLine("Number of peaks detected = " + run.PeakList.Count);
Console.WriteLine("Selected peak= " + result.ChromPeakSelected);
}
public IqChargeCorrelator(int numPointsInSmoother, double minRelativeIntensityForChromCorr = 0.01, double chromToleranceInPPM = 20, DeconTools.Backend.Globals.ToleranceUnit toleranceUnit = DeconTools.Backend.Globals.ToleranceUnit.PPM)
: base(numPointsInSmoother, minRelativeIntensityForChromCorr, chromToleranceInPPM, toleranceUnit)
{
_chromGen = new PeakChromatogramGenerator();
}
/// <summary>
/// Finds the XIC based on the m/z and scan parameters.
/// </summary>
/// <param name="mz"></param>
/// <param name="scan"></param>
/// <returns></returns>
public List<PNNLOmics.Data.XYData> FindXic(double mz, int scan, bool shouldSmooth)
{
LcmsFeatureTarget target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = mz;
target.ScanLCTarget = scan;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
m_run.CurrentMassTag = target;
var result = m_run.ResultCollection.GetTargetedResult(m_run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = MzPpmWindow;
Globals.ChromatogramGeneratorMode chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator( chromPeakGeneratorTolInPPM,
chromGeneratorMode);
chromGen.NETWindowWidthForNonAlignedData = Convert.ToSingle(NetWindow);
int pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
double chromPeakDetectorPeakBR = 1;
double chromPeakDetectorSigNoise = 1;
var chromPeakDetector = new ChromPeakDetector( chromPeakDetectorPeakBR,
chromPeakDetectorSigNoise);
ChromPeakSelectorParameters chromPeakSelectorParameters = new ChromPeakSelectorParameters();
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(m_run.ResultCollection);
//this smooths the data - very important step!
if (shouldSmooth)
{
chromSmoother.Execute(m_run.ResultCollection);
}
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(m_run.ResultCollection);
//this selects the peak
chromPeakSelector.Parameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
chromPeakSelector.Execute(m_run.ResultCollection);
//Here's the chromatogram data...
List<PNNLOmics.Data.XYData> data = new List<PNNLOmics.Data.XYData>();
for (int i = 0; i < m_run.XYData.Xvalues.Length; i++)
{
PNNLOmics.Data.XYData datum = new PNNLOmics.Data.XYData(m_run.XYData.Xvalues[i], m_run.XYData.Yvalues[i]);
data.Add(datum);
}
return data;
}
