protected XYData GetCorrelatedChromPeakXYData(Run run, int startScan, int stopScan, XYData basePeakChromXYData, double correlatedMZValue)
{
var xydata = PeakChromGen.GenerateChromatogram(run, startScan, stopScan, correlatedMZValue, ChromTolerance, ChromToleranceUnit);
XYData chromPeakXYData;
if (xydata == null || xydata.Xvalues.Length == 0)
{
chromPeakXYData = new XYData();
chromPeakXYData.Xvalues = basePeakChromXYData.Xvalues;
chromPeakXYData.Yvalues = new double[basePeakChromXYData.Xvalues.Length];
}
else
{
chromPeakXYData = Smoother.Smooth(xydata);
}
var chromDataIsOK = chromPeakXYData != null && chromPeakXYData.Xvalues != null &&
chromPeakXYData.Xvalues.Length > 3;
if (chromDataIsOK)
{
chromPeakXYData = chromPeakXYData.TrimData(startScan, stopScan);
}
return(chromPeakXYData);
}
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]);
}
}
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 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);
}
/// <summary>
/// Pulls all XICs needed to perform charge correlation
/// </summary>
/// <param name="peaksToCorrelate"></param>
/// <param name="MZList"></param>
/// <param name="run"></param>
/// <param name="startScan"></param>
/// <param name="stopScan"></param>
/// <returns></returns>
private XYData[] GetCorrelationXICs(int peaksToCorrelate, IEnumerable <double> MZList, Run run, int startScan, int stopScan)
{
var XICArray = new XYData[peaksToCorrelate];
var index = 0;
foreach (var mz in MZList)
{
XICArray[index] = Smoother.Smooth(_chromGen.GenerateChromatogram(run, startScan, stopScan, mz, 20));
index++;
}
return(XICArray);
}
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);
}
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 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);
}
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 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 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());
}
protected virtual void ExecuteWorkflow(IqResult result)
{
result.Target.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(result.Target.EmpiricalFormula, result.Target.ChargeState);
result.IqResultDetail.Chromatogram = ChromGen.GenerateChromatogram(Run, result.Target.TheorIsotopicProfile, result.Target.ElutionTimeTheor);
result.IqResultDetail.Chromatogram = ChromSmoother.Smooth(result.IqResultDetail.Chromatogram);
result.ChromPeakList = ChromPeakDetector.FindPeaks(result.IqResultDetail.Chromatogram);
ChromPeakDetector.CalculateElutionTimes(Run, result.ChromPeakList);
ChromPeakDetector.FilterPeaksOnNET(WorkflowParameters.ChromNETTolerance, result.Target.ElutionTimeTheor, result.ChromPeakList);
result.IqResultDetail.ChromPeakQualityData = ChromPeakAnalyzer.GetChromPeakQualityData(Run, result.Target, result.ChromPeakList);
var filterOutFlagged = result.Target.TheorIsotopicProfile.GetIndexOfMostIntensePeak() == 0;
result.ChromPeakSelected = ChromPeakSelector.SelectBestPeak(result.IqResultDetail.ChromPeakQualityData, filterOutFlagged);
result.LCScanSetSelected = ChromPeakUtilities.GetLCScanSetForChromPeak(result.ChromPeakSelected, Run,
WorkflowParameters.NumMSScansToSum);
result.LcScanObs = result.LCScanSetSelected == null ? -1 : result.LCScanSetSelected.PrimaryScanNumber;
result.IqResultDetail.MassSpectrum = MSGenerator.GenerateMS(Run, result.LCScanSetSelected);
TrimData(result.IqResultDetail.MassSpectrum, result.Target.MZTheor, MsLeftTrimAmount, MsRightTrimAmount);
List <Peak> mspeakList;
result.ObservedIsotopicProfile = MsfeatureFinder.IterativelyFindMSFeature(result.IqResultDetail.MassSpectrum, result.Target.TheorIsotopicProfile, out mspeakList);
result.FitScore = FitScoreCalc.CalculateFitScore(result.Target.TheorIsotopicProfile, result.ObservedIsotopicProfile,
result.IqResultDetail.MassSpectrum);
result.InterferenceScore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//if (_workflowParameters.ChromatogramCorrelationIsPerformed)
//{
// ExecuteTask(_chromatogramCorrelator);
//}
result.MonoMassObs = result.ObservedIsotopicProfile == null ? 0 : result.ObservedIsotopicProfile.MonoIsotopicMass;
result.MZObs = result.ObservedIsotopicProfile == null ? 0 : result.ObservedIsotopicProfile.MonoPeakMZ;
result.MZObsCalibrated = result.ObservedIsotopicProfile == null ? 0 : Run.GetAlignedMZ(result.ObservedIsotopicProfile.MonoPeakMZ, result.LcScanObs);
result.MonoMassObsCalibrated = result.ObservedIsotopicProfile == null
? 0
: (result.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * result.Target.ChargeState;
var elutionTime = result.ChromPeakSelected == null ? 0d : ((ChromPeak)result.ChromPeakSelected).NETValue;
result.ElutionTimeObs = elutionTime;
result.Abundance = GetAbundance(result);
}