/// <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 find_targetMassTag_131959Test1()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
var massTagColl = masstagImporter.Import();
Assert.AreEqual(2719, massTagColl.TargetList.Count);
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//int mtID = 635428;
var mtID = 131959;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1);
Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var basicChromPeakSelParam = new ChromPeakSelectorParameters();
basicChromPeakSelParam.NETTolerance = 0.1f;
basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID);
var mt = run.CurrentMassTag;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
Task targetedFeatureFinder = new BasicTFF();
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
theorFeatureGen.Execute(run.ResultCollection);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n");
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
msPeakDet.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
var massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
//Console.WriteLine("------------------------------ end --------------------------");
}
public void Test1()
{
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);
}
/// <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;
}
public void smartChromPeakSelectorTest_noSumming()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
run.Close();
run = new RunFactory().CreateRun(xcaliburTestfile);
var massTagColl = new TargetCollection();
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
massTagColl = masstagImporter.Import();
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var chromPeakDet = new ChromPeakDetector(0.5, 1);
var smartchromParam = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam);
var basicChromParam = new ChromPeakSelectorParameters();
var basicChromPeakSelector = new BasicChromPeakSelector(basicChromParam);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var iterativeTff = new IterativeTFF(new IterativeTFFParameters());
var fitscoreCalc = new IsotopicProfileFitScoreCalculator();
var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt";
var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile);
Assert.IsNotNull(xydata);
run.XYData = xydata;
// run.XYData.Display();
run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First();
Console.WriteLine("------MT = " + run.CurrentMassTag.ToString());
theorFeatureGen.Execute(run.ResultCollection);
chromPeakDet.Execute(run.ResultCollection);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
//first run the standard peak selector
basicChromPeakSelector.Execute(run.ResultCollection);
Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue));
//now run the smart chrom peak selector
run.XYData = xydata;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
fitscoreCalc.Execute(run.ResultCollection);
Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue));
//result.DisplayToConsole();
TestUtilities.DisplayIsotopicProfileData(result.Target.IsotopicProfile);
}
public void smartChromPeakSelectorTest_withDynamicSumming()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var massTagColl = new TargetCollection();
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
massTagColl = masstagImporter.Import();
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var chromPeakDet = new ChromPeakDetector(0.5, 1);
var smartchromParam = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam);
var basicChromPeakSelector = new BasicChromPeakSelector(new ChromPeakSelectorParameters());
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var iterativeTff = new IterativeTFF(new IterativeTFFParameters());
var fitscoreCalc = new IsotopicProfileFitScoreCalculator();
var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt";
var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile);
Assert.IsNotNull(xydata);
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
// run.XYData.Display();
run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First();
Console.WriteLine("------MT = " + run.CurrentMassTag.ToString());
theorFeatureGen.Execute(run.ResultCollection);
chromPeakDet.Execute(run.ResultCollection);
//first run the standard peak selector
basicChromPeakSelector.Execute(run.ResultCollection);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue));
//now run the smart chrom peak selector
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51;
smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC;
smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 1;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
fitscoreCalc.Execute(run.ResultCollection);
Console.WriteLine(result.ScanSet);
Assert.AreEqual(14, result.ScanSet.IndexValues.Count);
Assert.AreEqual(0.0104m, (decimal)Math.Round(result.Score, 4));
Assert.AreEqual("9575 {9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624}", result.ScanSet.ToString());
run.XYData = new XYData();
run.XYData.Xvalues = xydata.Xvalues;
run.XYData.Yvalues = xydata.Yvalues;
chromPeakDet.Execute(run.ResultCollection);
smartChromPeakSelector.Parameters.NETTolerance = 0.025f;
smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51;
smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC;
smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 2;
smartChromPeakSelector.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
iterativeTff.Execute(run.ResultCollection);
fitscoreCalc.Execute(run.ResultCollection);
result.DisplayToConsole();
Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue));
Assert.AreEqual(0.025m, (decimal)(Math.Round(result.Score, 4)));
//Console.WriteLine(result.ScanSet);
Assert.AreEqual(26, result.ScanSet.IndexValues.Count);
Assert.AreEqual("9575 {9493, 9500, 9506, 9513, 9520, 9527, 9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624, 9631, 9638, 9645, 9652, 9658, 9665}", result.ScanSet.ToString());
}