public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
string testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
string peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
Run run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
ChromPeakIqTarget testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
ChromPeak testPeak = new ChromPeak(5184, 840963, 50, 0);
testTarget.SetWorkflow(new ChromPeakAnalyzerIqWorkflow(run, parameters));
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
testTarget.DoWorkflow();
IqResult result = testTarget.GetResult();
Console.WriteLine("Fit Score: " + result.FitScore + " Flagged: " + result.IsIsotopicProfileFlagged);
}
public void ChromCorrelatorTest1()
{
var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
var run = new RunFactory().CreateRun(rawFilename);
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new IqExecutor(executorBaseParameters, run);
executor.LoadChromData(run);
var workflowAssigner = new IqWorkflowAssigner();
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters);
IqTarget iqTarget = new IqChargeStateTarget();
iqTarget.EmpiricalFormula = "C58H100N18O20";
iqTarget.Code = "GAAQNIIPASTGAAK";
iqTarget.ID = 1093;
iqTarget.ChargeState = 0;
var iqTargetList = new List <IqTarget>();
iqTargetList.Add(iqTarget);
var utilities = new IqTargetUtilities();
utilities.CreateChildTargets(iqTargetList);
workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList);
workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
foreach (var target in iqTarget.ChildTargets())
{
utilities.UpdateTargetMissingInfo(target);
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
}
foreach (var childTarget in iqTarget.ChildTargets())
{
var result = childTarget.CreateResult();
var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM);
var corrData = correlator.CorrelateData(run, result, 5700, 6500);
var corrDataItem1 = corrData.CorrelationDataItems.First();
Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1);
}
}
public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var testPeak = new ChromPeak(5184, 840963, 50, 0);
var executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
var workflow = new ChromPeakAnalyzerIqWorkflow(run, parameters);
testTarget.SetWorkflow(workflow);
testTarget.ID = 1;
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
var testTargetList = new List <IqTarget>();
IqTarget testParent = new IqChargeStateTarget();
testParent.AddTarget(testTarget);
testTargetList.Add(testTarget);
executor.Execute(testTargetList);
var result = testTarget.GetResult();
Assert.NotNull(result.LCScanSetSelected);
Assert.AreNotEqual(1, result.FitScore);
Assert.AreEqual(true, result.IsotopicProfileFound);
}
public static IqTarget GetIQTargetStandard(int standardNum)
{
//MassTagID MonoisotopicMass NET NETStDev Obs minMSGF mod_count mod_description pmt_quality_score peptide peptideex Multiple_Proteins
//86963986 1516.791851 0.227147 0.007416702 3 1 0 2.00000 AAKEGISCEIIDLR M.AAKEGISCEIIDLR.T 0
IqTarget target = new IqChargeStateTarget(null);
target.ID = 86963986;
target.MonoMassTheor = 1516.791851;
target.EmpiricalFormula = "C64H112N18O22S";
target.Code = "AAKEGISCEIIDLR";
target.ChargeState = 2;
target.ElutionTimeTheor = 0.227147;
target.MZTheor = target.MonoMassTheor / target.ChargeState + Globals.PROTON_MASS;
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
return(target);
}
/// <summary>
/// The run libray match workflow.
/// </summary>
/// <param name="target">
/// The Target.
/// </param>
/// <returns>
/// The <see cref="LibraryMatchResult"/>.
/// </returns>
private LibraryMatchResult RunLibrayMatchWorkflow(DriftTimeTarget target)
{
Trace.WriteLine(" Target: " + target.CorrespondingChemical);
Trace.WriteLine(" Target Info: " + target.TargetDescriptor);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
ITheorFeatureGenerator featureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = featureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
// Voltage grouping
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(this.uimfReader, target.MassWithAdduct, this.Parameters.InitialSearchMassToleranceInPpm, target.NormalizedDriftTimeInMs, this.Parameters.DriftTimeToleranceInMs, this.Parameters.DriftTubeLengthInCm);
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
// TODO Verify the temperature, pressure and drift tube voltage of the voltage group
// Because we don't record TVP info in the AMT library. we can't verify it yet, so stick with last voltage group.
if (IMSUtil.IsLastVoltageGroup(voltageGroup, this.NumberOfFrames))
{
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, this.uimfReader);
Trace.WriteLine(string.Format(" Temperature/Pressure/Voltage Adjusted Drift time: {0:F4} ms", IMSUtil.DeNormalizeDriftTime(target.NormalizedDriftTimeInMs, voltageGroup)));
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, this.smoother, this.Parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, this.uimfReader, voltageGroup, target.MassWithAdduct, this.Parameters.InitialSearchMassToleranceInPpm)).ToList();
// Score features
IDictionary<StandardImsPeak, PeakScores> scoresTable = new Dictionary<StandardImsPeak, PeakScores>();
Trace.WriteLine(string.Format(" Voltage Group: {0:F4} V, [{1}-{2}]", voltageGroup.MeanVoltageInVolts, voltageGroup.FirstFrameNumber, voltageGroup.LastFrameNumber));
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = FeatureScoreUtilities.ScoreFeature(
peak,
globalMaxIntensity,
this.uimfReader,
this.Parameters.InitialSearchMassToleranceInPpm,
this.Parameters.DriftTimeToleranceInMs,
voltageGroup,
this.NumberOfScans,
target,
IsotopicScoreMethod.Angle,
theoreticalIsotopicProfilePeakList);
scoresTable.Add(peak, currentStatistics);
}
// filter out features with Ims scans at 1% left or right.
Predicate<StandardImsPeak> scanPredicate = blob => FeatureFilters.FilterExtremeDriftTime(blob, (int)this.NumberOfScans);
Predicate<StandardImsPeak> shapeThreshold = blob => FeatureFilters.FilterBadPeakShape(blob, scoresTable[blob].PeakShapeScore, this.Parameters.PeakShapeThreshold);
Predicate<StandardImsPeak> isotopeThreshold = blob => FeatureFilters.FilterBadIsotopicProfile(blob, scoresTable[blob].IsotopicScore, this.Parameters.IsotopicThreshold);
Predicate<StandardImsPeak> massDistanceThreshold = blob => FeatureFilters.FilterHighMzDistance(blob, target, this.Parameters.MatchingMassToleranceInPpm);
// Print out candidate features that pass the intensity threshold.
foreach (StandardImsPeak peak in standardPeaks)
{
DriftTimeFeatureDistance distance = new DriftTimeFeatureDistance(target, peak, voltageGroup);
bool badScanRange = scanPredicate(peak);
bool badPeakShape = shapeThreshold(peak);
bool lowIsotopicAffinity = isotopeThreshold(peak);
bool lowMzAffinity = massDistanceThreshold(peak);
PeakScores currentStatistics = scoresTable[peak];
Trace.WriteLine(string.Empty);
Trace.WriteLine(string.Format(" Candidate feature found at drift time {0:F2} ms (scan number {1})",
peak.PeakApex.DriftTimeCenterInMs,
peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(
string.Format(
" M/Z: {0:F2} Dalton", peak.PeakApex.MzCenterInDalton));
Trace.WriteLine(
string.Format(
" Drift time: {0:F2} ms (scan number {1})",
peak.PeakApex.DriftTimeCenterInMs,
peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(
string.Format(" MzInDalton difference: {0:F2} ppm", distance.MassDifferenceInPpm));
Trace.WriteLine(
string.Format(" Drift time difference: {0:F4} ms", distance.DriftTimeDifferenceInMs));
Trace.WriteLine(string.Format(" Intensity Score: {0:F4}", currentStatistics.IntensityScore));
Trace.WriteLine(string.Format(" Peak Shape Score: {0:F4}", currentStatistics.PeakShapeScore));
Trace.WriteLine(string.Format(" Isotopic Score: {0:F4}", currentStatistics.IsotopicScore));
Trace.WriteLine(string.Format(" AveragedPeakIntensities: {0:F4}", peak.SummedIntensities));
string rejectionReason = badScanRange ? " [Bad scan range] " : " ";
rejectionReason += badPeakShape ? "[Bad Peak Shape] " : string.Empty;
rejectionReason += lowMzAffinity ? "[Inaccurate Mass] " : string.Empty;
rejectionReason += lowIsotopicAffinity ? "[Different Isotopic Profile] " : string.Empty;
if (badScanRange || lowIsotopicAffinity || badPeakShape)
{
Trace.WriteLine(rejectionReason);
}
else
{
Trace.WriteLine(" [Pass]");
}
}
standardPeaks.RemoveAll(scanPredicate);
standardPeaks.RemoveAll(massDistanceThreshold);
standardPeaks.RemoveAll(shapeThreshold);
standardPeaks.RemoveAll(isotopeThreshold);
if (standardPeaks.Count == 0)
{
Trace.WriteLine(string.Format(" [No Match]"));
Trace.WriteLine(string.Empty);
return new LibraryMatchResult(null, AnalysisStatus.Negative, null);
}
StandardImsPeak closestPeak = standardPeaks.First();
DriftTimeFeatureDistance shortestDistance = new DriftTimeFeatureDistance(target, standardPeaks.First(), voltageGroup);
foreach (var peak in standardPeaks)
{
DriftTimeFeatureDistance distance = new DriftTimeFeatureDistance(target, peak, voltageGroup);
if (distance.CompareTo(shortestDistance) < 0)
{
closestPeak = peak;
}
}
Trace.WriteLine(string.Format(" [Match]"));
Trace.WriteLine(string.Empty);
return new LibraryMatchResult(closestPeak, AnalysisStatus.Positive, shortestDistance);
}
}
throw new Exception("No voltage groups in the Dataset match temerature, pressure, or drift tube voltage setting from the library. Matching failed.");
}
public void TestScoring()
{
string formula = "C9H13ClN6";
string fileLocation = Cae;
MolecularTarget target = new MolecularTarget(formula, IonizationMethod.Protonated, "CAE");
Console.WriteLine("CompositionWithoutAdduct: " + target.CompositionWithoutAdduct);
Console.WriteLine("Monoisotopic ViperCompatibleMass: " + target.MonoisotopicMass);
CrossSectionSearchParameters parameters = new CrossSectionSearchParameters(driftTubeLength);
var smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
CrossSectionWorkfow workflow = new CrossSectionWorkfow(fileLocation, "output", parameters);
Console.WriteLine("Ionization method: " + target.Adduct);
Console.WriteLine("Targeting centerMz: " + target.MassWithAdduct);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.CompositionWithAdduct != null)
{
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
var theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
// Generate VoltageSeparatedAccumulatedXICs
var uimfReader = new DataReader(fileLocation);
Console.WriteLine("Input file: {0}", fileLocation);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(uimfReader, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm, driftTubeLength);
Console.WriteLine();
// For each voltage, find 2D XIC features
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
Console.WriteLine("Voltage group: {0} V, Frame {1}-{2}, {3:F2}K, {4:F2}Torr",
voltageGroup.MeanVoltageInVolts,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
voltageGroup.MeanTemperatureInKelvin,
voltageGroup.MeanPressureInTorr);
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, smoother, parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, uimfReader, voltageGroup, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm)).ToList();
// feature scorings and Target selection.
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, uimfReader);
// Check each XIC Peak found
foreach (var featurePeak in standardPeaks)
{
// Evaluate feature scores.
double intensityScore = FeatureScoreUtilities.IntensityScore(featurePeak, globalMaxIntensity);
double isotopicScoreAngle = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistance = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistance,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScorePerson = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.PearsonCorrelation,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreBhattacharyya = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Bhattacharyya,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistanceAlternative = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistanceAlternative,
globalMaxIntensity,
workflow.NumberOfScans);
double peakShapeScore = FeatureScoreUtilities.PeakShapeScore(featurePeak, workflow.uimfReader, workflow.Parameters.MzWindowHalfWidthInPpm, workflow.Parameters.DriftTimeToleranceInMs, voltageGroup, globalMaxIntensity, workflow.NumberOfScans);
// Report all features.
Console.WriteLine(" feature found at scan number {0}", featurePeak.PeakApex.DriftTimeCenterInScanNumber);
Console.WriteLine(" IntensityScore: {0}", intensityScore);
Console.WriteLine(" peakShapeScore: {0}", peakShapeScore);
Console.WriteLine(" isotopicScore - Angle: {0}", isotopicScoreAngle);
Console.WriteLine(" isotopicScore - Distance: {0}", isotopicScoreDistance);
Console.WriteLine(" isotopicScore - Distance2:{0}", isotopicScoreDistanceAlternative);
Console.WriteLine(" isotopicScore - Pearson: {0}", isotopicScorePerson);
Console.WriteLine(" isotopicScore - Bhattacharyya: {0}", isotopicScoreBhattacharyya);
Console.WriteLine();
}
Console.WriteLine();
}
workflow.Dispose();
}
public void TestFormulaPerturbance()
{
List<Tuple<string, string>> formulas = new List<Tuple<string, string>>();
// truth
formulas.Add(new Tuple<string, string>("True formula", "C12H10O4S"));
formulas.Add(new Tuple<string, string>("1 extra H", "C12H11O4S"));
formulas.Add(new Tuple<string, string>("2 extra H", "C12H12O4S"));
formulas.Add(new Tuple<string, string>("3 extra H", "C12H13O4S"));
formulas.Add(new Tuple<string, string>("3 extra H", "C12H14O4S"));
formulas.Add(new Tuple<string, string>("4 extra H", "C12H15O4S"));
formulas.Add(new Tuple<string, string>("5 extra H", "C12H16O4S"));
formulas.Add(new Tuple<string, string>("1 less H", "C12H9O4S"));
formulas.Add(new Tuple<string, string>("2 less H", "C12H8O4S"));
formulas.Add(new Tuple<string, string>("3 less H", "C12H7O4S"));
formulas.Add(new Tuple<string, string>("4 less H", "C12H6O4S"));
Console.WriteLine("[Intensity], [Distance1], [Distance2], [Angle], [Pearson], [Bucha]");
string fileLocation = BPSNegative;
CrossSectionSearchParameters parameters = new CrossSectionSearchParameters(driftTubeLength);
CrossSectionWorkfow workflow = new CrossSectionWorkfow(fileLocation, "output", parameters);
foreach (var form in formulas)
{
bool found = false;
MolecularTarget target = new MolecularTarget(form.Item2, new IonizationAdduct(IonizationMethod.Deprotonated), form.Item1);
Console.Write(form.Item1 + ": ");
var smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.CompositionWithAdduct != null)
{
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
var theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
// Generate VoltageSeparatedAccumulatedXICs
var uimfReader = new DataReader(fileLocation);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(uimfReader, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm, parameters.DriftTubeLengthInCm);
var voltageGroup = accumulatedXiCs.Keys.First();
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, smoother, parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, uimfReader, voltageGroup, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm)).ToList();
// feature scorings and Target selection.
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, uimfReader);
// Check each XIC Peak found
foreach (var peak in standardPeaks)
{
// Evaluate feature scores.
double intensityScore = FeatureScoreUtilities.IntensityScore(peak, globalMaxIntensity);
double isotopicScoreAngle = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistance = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistance,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScorePerson = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.PearsonCorrelation,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreBhattacharyya = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Bhattacharyya,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistanceAlternative = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistanceAlternative,
globalMaxIntensity,
workflow.NumberOfScans);
double peakShapeScore = FeatureScoreUtilities.PeakShapeScore(peak, workflow.uimfReader, workflow.Parameters.MzWindowHalfWidthInPpm, workflow.Parameters.DriftTimeToleranceInMs, voltageGroup, globalMaxIntensity, workflow.NumberOfScans);
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", intensityScore);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreDistance);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreDistanceAlternative);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreAngle);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScorePerson);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreBhattacharyya);
found = true;
}
}
if (!found)
{
Console.Write("No features");
}
Console.WriteLine();
}
// Manually dispose so it doesn't interfere with other tests.
workflow.Dispose();
}