/// <summary>
/// The find optimum hypothesis.
/// </summary>
/// <param name="observations">
/// The observations.
/// </param>
/// <param name="driftTubeLength">
/// The drift Tube Length.
/// </param>
/// <param name="massTarget">
/// The mass Target.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
/// <returns>
/// The <see cref="AssociationHypothesis"/>.
/// </returns>
/// <exception cref="NotImplementedException">
/// </exception>
public AssociationHypothesis FindOptimumHypothesis(IEnumerable<ObservedPeak> observations, double driftTubeLength, IImsTarget massTarget, CrossSectionSearchParameters parameters, int numberOfVoltageGroups)
{
observations = observations.ToList();
ObservationTransitionGraph<IonTransition> transitionGraph = new ObservationTransitionGraph<IonTransition>(observations, (a, b) => new IonTransition(a, b));
// Visualize the graph.
// transitionGraph.PlotGraph();
// Find all the possible combinotorial tracks
// IList<IsomerTrack> candidateTracks = this.FindAllReasonableTracks(transitionGraph, driftTubeLength, massTarget, parameters).ToList();
// Find the top N tracks using K shorestest path algorithm
IEnumerable<IEnumerable<IonTransition>> kShorestPaths = transitionGraph.PeakGraph.RankedShortestPathHoffmanPavley(t => 0 - Math.Log(t.TransitionProbability), transitionGraph.SourceVertex, transitionGraph.SinkVertex, this.maxTracks);
IEnumerable<IsomerTrack> candidateTracks = MinCostFlowIonTracker.ToTracks(kShorestPaths, parameters, numberOfVoltageGroups, parameters.RegressionSelection);
// filter paths
TrackFilter filter = new TrackFilter();
Predicate<IsomerTrack> trackPredicate = track => filter.IsTrackPossible(track, massTarget, parameters);
List<IsomerTrack> filteredTracks = candidateTracks.ToList().FindAll(trackPredicate);
// Select the top N tracks to proceed to next step.
var hypotheses = this.FindAllHypothesis(filteredTracks, observations).ToArray();
// Find the combination of tracks that produces the highest posterior probablity.
IOrderedEnumerable<AssociationHypothesis> sortedAssociationHypotheses = hypotheses.OrderByDescending(h => h.ProbabilityOfHypothesisGivenData);
return sortedAssociationHypotheses.FirstOrDefault();
}
public AssociationHypothesis FindOptimumHypothesis(
IEnumerable<ObservedPeak> observations,
double driftTubeLength,
IImsTarget target,
CrossSectionSearchParameters parameters)
{
throw new NotImplementedException();
}
public void PlotAssociationHypothesis(AssociationHypothesis hypothesis, string plotLocation, string datasetName, IImsTarget target, IDictionary<string, IList<ObservedPeak>> preFilteredPeaks)
{
//int width = 450;
//int height = 256;
int width = 675;
int height = 384;
PlotModel associationHypothsisPlot = this.AssociationHypothesisPlot(hypothesis, datasetName, target);
associationHypothsisPlot = this.AnnotateRemovedPeaks(associationHypothsisPlot, preFilteredPeaks);
this.PlotDiagram(plotLocation, associationHypothsisPlot, width, height);
}
/// <summary>
/// The add result to scores table.
/// </summary>
/// <param name="dataset">
/// The dataset.
/// </param>
/// <param name="chemicalResult">
/// The chemical result.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="table">
/// The table.
/// </param>
/// <param name="colDef">
/// The col def.
/// </param>
/// <returns>
/// The <see cref="int"/>.
/// </returns>
public static int AddResultToScoresTable(string dataset, CrossSectionWorkflowResult chemicalResult, IImsTarget target, NumericTable table, IList<string> colDef)
{
TableRow dict = new TableRow(dataset + target);
dict.Name += "(" + chemicalResult.AnalysisStatus + ")";
dict.Add(colDef[1], chemicalResult.AverageObservedPeakStatistics.IntensityScore);
dict.Add(colDef[2], chemicalResult.AverageObservedPeakStatistics.IsotopicScore);
dict.Add(colDef[3], chemicalResult.AverageObservedPeakStatistics.PeakShapeScore);
dict.Add(colDef[0], chemicalResult.AverageVoltageGroupStability);
dict.Add(colDef[4], chemicalResult.AssociationHypothesisInfo.ProbabilityOfHypothesisGivenData);
table.Add(dict);
return 1;
}
/// <summary>
/// The score feature using isotopic profile.
/// </summary>
/// <param name="imsPeak">
/// The ims Peak.
/// </param>
/// <param name="reader">
/// The reader.
/// </param>
/// <param name="target">
/// The Target.
/// </param>
/// <param name="isotopicPeakList">
/// The isotopic peak list.
/// </param>
/// <param name="voltageGroup">
/// The voltage Group.
/// </param>
/// <param name="selectedMethod">
/// The selected Method.
/// </param>
/// <param name="globalMaxIntensities">
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
/// <exception cref="InvalidOperationException">
/// </exception>
public static double IsotopicProfileScore(StandardImsPeak imsPeak, DataReader reader, IImsTarget target, List<Peak> isotopicPeakList, VoltageGroup voltageGroup, IsotopicScoreMethod selectedMethod, double globalMaxIntensities, double totalScans)
{
// No need to move on if the isotopic profile is not found
// if (observedIsotopicProfile == null || observedIsotopicProfile.MonoIsotopicMass < 1)
// {
// result.AnalysisStatus = AnalysisStatus.IsotopicProfileNotFound;
// continue;
// }
// Find Isotopic Profile
// List<Peak> massSpectrumPeaks;
// IsotopicProfile observedIsotopicProfile = _msFeatureFinder.IterativelyFindMSFeature(massSpectrum, theoreticalIsotopicProfile, out massSpectrumPeaks);
if (target.CompositionWithoutAdduct == null)
{
throw new InvalidOperationException("Cannot score feature using isotopic profile for Ims Target without CompositionWithoutAdduct provided.");
}
// Bad Feature, so get out
if (imsPeak == null)
{
return 0;
}
// Get the scanWindow size
int scanNumberMax = imsPeak.PeakApex.DriftTimeFullWidthHalfMaxHigherBondInScanNumber;
int scanNumberMin = imsPeak.PeakApex.DriftTimeFullWidthHalfMaxLowerBondInScanNumber;
if ((scanNumberMin < 0) || (scanNumberMax > totalScans - 1))
{
return 0;
}
// Get the mass error from the observed feature peak from the Target theoretical peak
double mzOffset = imsPeak.PeakApex.MzCenterInDalton - target.MassWithAdduct;
List<double> observedIsotopicPeakList = new List<double>();
int totalIsotopicIndex = isotopicPeakList.Count;
int[] isotopicIndexMask = new int[totalIsotopicIndex];
// Find an unsaturated peak in the isotopic profile
for (int i = 0; i < totalIsotopicIndex; i++)
{
// Isotopic centerMz
double Mz = isotopicPeakList[i].XValue;
var peakList = reader.GetXic(Mz + mzOffset,
imsPeak.PeakApex.MzWindowToleranceInPpm,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
scanNumberMin,
scanNumberMax,
DataReader.FrameType.MS1,
DataReader.ToleranceType.PPM);
// Sum the intensities
double sumIntensities = 0;
foreach (var point in peakList)
{
sumIntensities += point.Intensity;
if (point.IsSaturated)
{
isotopicIndexMask[i] = 1;
}
}
sumIntensities /= voltageGroup.FrameAccumulationCount;
observedIsotopicPeakList.Add(sumIntensities);
}
// Return 0 if the intensity sum is really small
if (observedIsotopicPeakList.Sum() < globalMaxIntensities * 0.0003)
{
return 0;
}
// If the unsaturated isotopes are below a certain threshold
if (totalIsotopicIndex - isotopicIndexMask.Sum() <= 1)
{
return 0;
}
if (selectedMethod == IsotopicScoreMethod.Angle)
{
return IsotopicProfileScoreAngle(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.EuclideanDistance)
{
return IsotopicProfileScoreEuclidean(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.PearsonCorrelation)
{
return PearsonCorrelation(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.Bhattacharyya)
{
return BhattacharyyaDistance(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.EuclideanDistanceAlternative)
{
return EuclideanAlternative(observedIsotopicPeakList, isotopicPeakList);
}
else
{
throw new NotImplementedException();
}
}
/// <summary>
/// The score feature.
/// </summary>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="globalMaxIntensity">
/// The global max intensity.
/// </param>
/// <param name="uimfReader">
/// The uimf reader.
/// </param>
/// <param name="massToleranceInPpm">
/// The mass tolerance in ppm.
/// </param>
/// <param name="driftTimeToleranceInMs">
/// The drift time tolerance in ms.
/// </param>
/// <param name="voltageGroup">
/// The voltage group.
/// </param>
/// <param name="voltageGroupScans">
/// The voltage group scans.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="isotopicScoreMethod">
/// The isotopic score method.
/// </param>
/// <param name="theoreticalIsotopicProfile">
/// The theoretical isotopic profile.
/// </param>
/// <returns>
/// The <see cref="PeakScores"/>.
/// </returns>
public static PeakScores ScoreFeature(this StandardImsPeak peak, double globalMaxIntensity, DataReader uimfReader, double massToleranceInPpm, double driftTimeToleranceInMs, VoltageGroup voltageGroup, int voltageGroupScans, IImsTarget target, IsotopicScoreMethod isotopicScoreMethod, List<Peak> theoreticalIsotopicProfile)
{
double intensityScore = IntensityScore(peak, globalMaxIntensity);
double peakShapeScore = PeakShapeScore(
peak,
uimfReader,
massToleranceInPpm,
driftTimeToleranceInMs,
voltageGroup,
globalMaxIntensity,
voltageGroupScans);
double isotopicScore = 0;
if (target.HasCompositionInfo)
{
isotopicScore = IsotopicProfileScore(
peak,
uimfReader,
target,
theoreticalIsotopicProfile,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
voltageGroupScans);
}
return new PeakScores(intensityScore, isotopicScore, peakShapeScore);
}
/// <summary>
/// The report feature evaluation.
/// </summary>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="scores">
/// The scores.
/// </param>
/// <param name="verbose">
/// The verbose.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="badScanRange">
/// The bad scan range.
/// </param>
/// <param name="lowAbsoluteIntensity">
/// The low intensity.
/// </param>
/// <param name="lowRelativeIntensity"></param>
/// <param name="badPeakShape">
/// The bad peak shape.
/// </param>
/// <param name="lowIsotopicAffinity">
/// The low isotopic affinity.
/// </param>
/// <returns>
/// If the feature pass all the filters <see cref="bool"/>.
/// </returns>
private static string ReportFeatureEvaluation(StandardImsPeak peak, PeakScores scores, bool verbose, IImsTarget target, bool badScanRange, bool lowAbsoluteIntensity, bool lowRelativeIntensity, bool badPeakShape, bool lowIsotopicAffinity)
{
Trace.WriteLine(string.Format(" Candidate feature found at [centerMz = {0:F4}, drift time = {1:F2} ms(#{2})] ", peak.PeakApex.MzCenterInDalton, peak.PeakApex.DriftTimeCenterInMs, peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(string.Format(" IntensityScore: {0:F4}", scores.IntensityScore));
if (!lowAbsoluteIntensity)
{
Trace.WriteLine(string.Format(" peakShapeScore: {0:F4}", scores.PeakShapeScore));
if (target.HasCompositionInfo)
{
Trace.WriteLine(string.Format(" isotopicScore: {0:F4}", scores.IsotopicScore));
}
}
string rejectionReason = badScanRange ? "[Bad scan range] " :
lowAbsoluteIntensity ? "[Low Absolute Intensity] " :
badPeakShape ? "[Bad Peak Shape] " :
lowIsotopicAffinity ? "[Different Isotopic Profile] " :
lowRelativeIntensity ? "[Low Relative Intensity] " : string.Empty;
bool rejected = badScanRange || lowAbsoluteIntensity || lowIsotopicAffinity || badPeakShape || lowRelativeIntensity;
if (verbose)
{
if (rejected)
{
Trace.WriteLine(" " + rejectionReason);
}
else
{
Trace.WriteLine(" [PASS]");
}
Trace.WriteLine(string.Empty);
}
return rejectionReason;
}
/// <summary>
/// The run molecule informed work flow.
/// </summary>
/// <param name="target">
/// The Target.
/// </param>
/// <param name="detailedVerbose">
/// </param>
/// <returns>
/// The <see cref="CrossSectionWorkflowResult"/>.
/// </returns>
public CrossSectionWorkflowResult RunCrossSectionWorkFlow(IImsTarget target, bool detailedVerbose = true)
{
// Reassign trace listener to print to console as well as the target directory.
using (this.ResetTraceListenerToTarget(target, this.DatasetName))
{
try
{
// Get the monoisotopic mass for viper, which is different from anything else.
double viperFriendlyMass = target.MassWithAdduct;
if (target.ChargeState < 0)
{
viperFriendlyMass = viperFriendlyMass + new Composition(0, target.ChargeState, 0, 0, 0).Mass;
}
else
{
viperFriendlyMass = viperFriendlyMass - new Composition(0, Math.Abs(target.ChargeState), 0, 0, 0).Mass;
}
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.HasCompositionInfo)
{
int chargeStateAbs = Math.Abs(target.ChargeState);
// Again this isotopic profile generator auto adds hydrogen for you depending on charge states. So here take it out.
Composition compensatedComposition = target.CompositionWithAdduct - new Composition(0, chargeStateAbs, 0, 0, 0);
string empiricalFormula = compensatedComposition.ToPlainString();
IsotopicProfile theoreticalIsotopicProfile = this.theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, chargeStateAbs);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
Trace.WriteLine(string.Format("Dataset: {0}", this.uimfReader.UimfFilePath));
ReportTargetInfo(target, detailedVerbose);
double targetMz = Math.Abs(target.MassWithAdduct / target.ChargeState);
// Voltage grouping. Note that we only accumulate frames as needed. Accumulate frames globally is too costly.
// Here we accumulate the XICs around target MZ.
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(this.uimfReader, targetMz, this.Parameters.MzWindowHalfWidthInPpm, this.Parameters.DriftTubeLengthInCm);
// Remove voltage groups that don't have sufficient frame accumulations
IEnumerable<VoltageGroup> remainingVGs = accumulatedXiCs.Keys;
IEnumerable<VoltageGroup> toBeRemoved = VoltageGroupFilters.RemoveVoltageGroupsWithInsufficentFrames(remainingVGs, this.Parameters.InsufficientFramesFraction);
foreach (VoltageGroup voltageGroup in toBeRemoved)
{
accumulatedXiCs.Remove(voltageGroup);
}
// Perform feature detection and scoring and the given MzInDalton range on the accumulated XICs to get the base peaks.
if (detailedVerbose)
{
Trace.WriteLine("Feature detection and scoring: ");
}
IList<VoltageGroup> rejectedVoltageGroups = new List<VoltageGroup>();
IList<ObservedPeak> filteredObservations = new List<ObservedPeak>();
IList<ObservedPeak> allObservations = new List<ObservedPeak>();
IDictionary<string, IList<ObservedPeak>> rejectedObservations = new Dictionary<string, IList<ObservedPeak>>();
var numberOfParticipatingVGs = accumulatedXiCs.Keys.Count;
// Iterate through the features and perform filtering on isotopic affinity, intensity, drift time and peak shape.
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, this.uimfReader);
List<StandardImsPeak> standardPeaks = this.FindPeaksBasedOnXIC(voltageGroup, accumulatedXiCs[voltageGroup], target);
// Score features
IDictionary<StandardImsPeak, PeakScores> scoresTable = new Dictionary<StandardImsPeak, PeakScores>();
if (detailedVerbose)
{
Trace.WriteLine(
string.Format(
" Voltage group: {0:F2} V, Frame {1}-{2}, {3:F2}K, {4:F2}Torr",
voltageGroup.MeanVoltageInVolts,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
voltageGroup.MeanTemperatureInKelvin,
voltageGroup.MeanPressureInTorr));
}
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = FeatureScoreUtilities.ScoreFeature(
peak,
globalMaxIntensity,
this.uimfReader,
this.Parameters.MzWindowHalfWidthInPpm,
this.Parameters.DriftTimeToleranceInMs,
voltageGroup,
this.NumberOfScans,
target,
IsotopicScoreMethod.Angle,
theoreticalIsotopicProfilePeakList);
scoresTable.Add(peak, currentStatistics);
}
double maxIntensity = standardPeaks.Max(x => x.SummedIntensities);
Predicate<StandardImsPeak> relativeIntensityThreshold = imsPeak => FeatureFilters.FilterOnRelativeIntesity(imsPeak, maxIntensity, this.Parameters.RelativeIntensityPercentageThreshold);
// filter out non Target peaks and noise.
Predicate<StandardImsPeak> absoluteIntensityThreshold = imsPeak => FeatureFilters.FilterOnAbsoluteIntensity(imsPeak, scoresTable[imsPeak].IntensityScore, this.Parameters.AbsoluteIntensityThreshold);
// filter out features with Ims scans at 1% left or right.
Predicate<StandardImsPeak> scanPredicate = imsPeak => FeatureFilters.FilterExtremeDriftTime(imsPeak, this.NumberOfScans);
// filter out features with bad peak shapes.
Predicate<StandardImsPeak> shapeThreshold = imsPeak => FeatureFilters.FilterBadPeakShape(imsPeak, scoresTable[imsPeak].PeakShapeScore, this.Parameters.PeakShapeThreshold);
// filter out features with distant isotopic profile.
Predicate<StandardImsPeak> isotopeThreshold = imsPeak => FeatureFilters.FilterBadIsotopicProfile(imsPeak, scoresTable[imsPeak].IsotopicScore, this.Parameters.IsotopicThreshold);
// Print out candidate features and how they were rejected.
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = scoresTable[peak];
string rejectionReason = ReportFeatureEvaluation(
peak,
currentStatistics,
detailedVerbose,
target,
scanPredicate(peak),
absoluteIntensityThreshold(peak),
relativeIntensityThreshold(peak),
shapeThreshold(peak),
isotopeThreshold(peak));
bool pass = string.IsNullOrEmpty(rejectionReason);
ObservedPeak analyzedPeak = new ObservedPeak(voltageGroup, peak, currentStatistics);
if (pass)
{
filteredObservations.Add(analyzedPeak);
}
else
{
if (rejectedObservations.ContainsKey(rejectionReason))
{
rejectedObservations[rejectionReason].Add(analyzedPeak);
}
else
{
rejectedObservations.Add(rejectionReason, new List<ObservedPeak>(){analyzedPeak});
}
}
allObservations.Add(analyzedPeak);
}
standardPeaks.RemoveAll(scanPredicate);
standardPeaks.RemoveAll(absoluteIntensityThreshold);
standardPeaks.RemoveAll(relativeIntensityThreshold);
standardPeaks.RemoveAll(shapeThreshold);
if (target.HasCompositionInfo)
{
standardPeaks.RemoveAll(isotopeThreshold);
}
if (standardPeaks.Count == 0)
{
if (detailedVerbose)
{
Trace.WriteLine(string.Format(" (All features were rejected in voltage group {0:F4} V)", voltageGroup.MeanVoltageInVolts));
Trace.WriteLine(string.Empty);
Trace.WriteLine(string.Empty);
}
rejectedVoltageGroups.Add(voltageGroup);
}
// Rate the feature's VoltageGroupScoring score. VoltageGroupScoring score measures how likely the voltage group contains and detected the Target ion.
voltageGroup.VoltageGroupScore = VoltageGroupScoring.ComputeVoltageGroupStabilityScore(voltageGroup);
}
// Remove voltage groups that were rejected
foreach (VoltageGroup voltageGroup in rejectedVoltageGroups)
{
accumulatedXiCs.Remove(voltageGroup);
}
IEnumerable<ObservedPeak> rejectedPeaks = rejectedObservations.Values.SelectMany(x => x);
// Report analysis as negative
if (accumulatedXiCs.Keys.Count == 0)
{
CrossSectionWorkflowResult informedResult = CrossSectionWorkflowResult.CreateNegativeResult(rejectedPeaks, rejectedVoltageGroups, target, this.DatasetPath, this.OutputPath, this.SampleCollectionDate);
ReportAnslysisResultAndMetrics(informedResult, detailedVerbose);
return informedResult;
}
else
{
// Perform the data association algorithm.
IIonTracker tracker = new CombinatorialIonTracker(3000);
// Because for somereason we are not keeping track of drift tube length in UIMF...so we kind of have to go ask the instrument operator..
double driftTubeLength = this.Parameters.DriftTubeLengthInCm;
AssociationHypothesis optimalAssociationHypothesis = tracker.FindOptimumHypothesis(filteredObservations, driftTubeLength, target, this.Parameters, numberOfParticipatingVGs);
if (optimalAssociationHypothesis == null)
{
CrossSectionWorkflowResult negResult = CrossSectionWorkflowResult.CreateNegativeResult(rejectedPeaks, rejectedVoltageGroups, target, this.DatasetPath, this.OutputPath, this.SampleCollectionDate);
ReportAnslysisResultAndMetrics(negResult, detailedVerbose);
return negResult;
}
if (detailedVerbose)
{
Console.WriteLine("Writes QC plot of fitline to " + this.OutputPath);
Trace.WriteLine(string.Empty);
}
string extension = (this.Parameters.GraphicsExtension.StartsWith(".")) ?
this.Parameters.GraphicsExtension : "." + this.Parameters.GraphicsExtension;
string outputPath = string.Format("{0}target_{1}_in_{2}_QA{3}", this.OutputPath, target.TargetDescriptor, this.DatasetName, extension);
ImsInformedPlotter plotter = new ImsInformedPlotter();
plotter.PlotAssociationHypothesis(optimalAssociationHypothesis, outputPath, this.DatasetName, target, rejectedObservations);
// Printout results
if (detailedVerbose)
{
Trace.WriteLine("Target Data Association");
int count = 0;
foreach (IsomerTrack track in optimalAssociationHypothesis.Tracks)
{
Trace.WriteLine(string.Format(" T{0}: ", count));
foreach (ObservedPeak peak in track.ObservedPeaks)
{
Trace.WriteLine(string.Format(" [td: {0:F4}ms, V: {1:F4}V, T: {2:F4}K, P: {3:F4}Torr]",
peak.Peak.PeakApex.DriftTimeCenterInMs,
peak.VoltageGroup.MeanVoltageInVolts,
peak.VoltageGroup.MeanTemperatureInKelvin,
peak.VoltageGroup.MeanPressureInTorr));
}
count++;
Trace.WriteLine("");
}
Trace.WriteLine("");
}
// Remove outliers with high influence.
// FitLine.RemoveOutliersAboveThreshold(3, minFitPoints);
// Remove outliers until min fit point is reached or good R2 is achieved.
// while (TrackFilter.IsLowR2(FitLine.RSquared) && FitLine.FitPointCollection.Count > minFitPoints)
// {
// FitLine.RemoveOutlierWithHighestCookDistance(minFitPoints);
// }
// Remove the voltage considered outliers
// foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys.Where(p => FitLine.OutlierCollection.Contains(p.FitPoint)).ToList())
// {
// accumulatedXiCs.Remove(voltageGroup);
// }
CrossSectionWorkflowResult informedResult = CrossSectionWorkflowResult.CreateResultFromAssociationHypothesis(
this.Parameters,
optimalAssociationHypothesis,
target,
accumulatedXiCs.Keys,
allObservations,
this.DatasetPath,
this.OutputPath,
this.SampleCollectionDate,
viperFriendlyMass
);
ReportAnslysisResultAndMetrics(informedResult, detailedVerbose);
Trace.Listeners.Clear();
return informedResult;
}
}
catch (Exception e)
{
// Print result
Trace.WriteLine(e.Message);
Trace.WriteLine(e.StackTrace);
Trace.Listeners.Clear();
Trace.Close();
Trace.Listeners.Clear();
// create the error result
return CrossSectionWorkflowResult.CreateErrorResult(target, this.DatasetName, this.DatasetPath, this.OutputPath, this.SampleCollectionDate);
}
}
}
/// <summary>
/// The create error result.
/// </summary>
/// <param name="target">
/// The target.
/// </param>
/// <param name="datasetName">
/// The dataset name.
/// </param>
/// <param name="datasetPath"></param>
/// <returns>
/// The <see cref="CrossSectionWorkflowResult"/>.
/// </returns>
public static CrossSectionWorkflowResult CreateErrorResult(IImsTarget target, string datasetName, string datasetPath, string analysisPath, string SampleCollectionTime)
{
// No hypothesis can be made.
return new CrossSectionWorkflowResult(
datasetPath,
target,
AnalysisStatus.UknownError,
null,
null,
null,
0,
analysisPath,
SampleCollectionTime
);
}
internal static CrossSectionWorkflowResult CreateResultFromAssociationHypothesis(CrossSectionSearchParameters parameters, AssociationHypothesis optimalHypothesis, IImsTarget target, IEnumerable<VoltageGroup> allVoltageGroups, IEnumerable<ObservedPeak> allPeaks, string datasetPath, string analysisPath, string sampleCollectionDate, double viperCompatibleMass = 0)
{
// Initialize the result struct.
AssociationHypothesisInfo associationHypothesisInfo = new AssociationHypothesisInfo(optimalHypothesis.ProbabilityOfDataGivenHypothesis, optimalHypothesis.ProbabilityOfHypothesisGivenData);
double averageVoltageGroupScore = VoltageGroupScoring.ComputeAverageVoltageGroupStabilityScore(allVoltageGroups);
IEnumerable<PeakScores> allFeatureStatistics = allPeaks.Select(x => x.Statistics);
PeakScores averageObservedPeakStatistics = FeatureScoreUtilities.AverageFeatureStatistics(allFeatureStatistics);
IEnumerable<IsomerTrack> tracks = optimalHypothesis.Tracks.ToList();
// Find the conformer with the closest m/z
IsomerTrack trackWithBestMz = tracks.OrderBy(x => Math.Abs(Metrics.DaltonToPpm(x.AverageMzInDalton - target.MassWithAdduct, target.MassWithAdduct))).First();
double bestMzInPpm = Metrics.DaltonToPpm(trackWithBestMz.AverageMzInDalton - target.MassWithAdduct, target.MassWithAdduct);
IList<IdentifiedIsomerInfo> isomersInfo = tracks.Select(x => x.ExportIdentifiedIsomerInfo(viperCompatibleMass, allVoltageGroups.Count() - parameters.MaxOutliers, parameters.MinR2, target, bestMzInPpm)).ToList();
AnalysisStatus finalStatus = TrackToHypothesisConclusionLogic(isomersInfo.Select(info => info.AnalysisStatus));
CrossSectionWorkflowResult informedResult = new CrossSectionWorkflowResult(
datasetPath,
target,
finalStatus,
associationHypothesisInfo,
isomersInfo,
averageObservedPeakStatistics,
averageVoltageGroupScore,
analysisPath,
sampleCollectionDate
);
return informedResult;
}
/// <summary>
/// The compute mobility info.
/// </summary>
/// <param name="target">
/// The inferred target.
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
private MobilityInfo ComputeMobilityInfo(IImsTarget target)
{
// Convert the track into a Continuous XY data points.
this.mobilityInfo.Mobility = this.driftTubeLengthInMeters * this.driftTubeLengthInMeters * 1000 / (this.FitLine.Slope);
this.mobilityInfo.RSquared = this.FitLine.RSquared;
this.mobilityInfo.T0 = this.FitLine.Intercept;
Composition bufferGas = new Composition(0, 0, 2, 0, 0);
double reducedMass = MoleculeUtil.ComputeReducedMass(target.MassWithAdduct, bufferGas);
double meanTemperatureInKelvin = this.GetGlobalMeanTemperature();
this.mobilityInfo.CollisionCrossSectionArea = MoleculeUtil.ComputeCrossSectionalArea(
meanTemperatureInKelvin,
this.mobilityInfo.Mobility,
target.ChargeState,
reducedMass);
return this.mobilityInfo;
}
/// <summary>
/// The equals.
/// </summary>
/// <param name="other">
/// The other.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
public override bool Equals(IImsTarget other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
if (other.TargetType != TargetType.MoleculeWithKnownDriftTime) return false;
return this.Equals(other as DriftTimeTarget);
}
/// <summary>
/// The export identified isomer info.
/// </summary>
/// <param name="viperCompatibleMass">
/// The viper compatible mass.
/// </param>
/// <param name="minFitPoints">
/// The min fit points.
/// </param>
/// <param name="minR2">
/// The min r 2.
/// </param>
/// <param name="target"></param>
/// <returns>
/// The <see cref="IdentifiedIsomerInfo"/>.
/// </returns>
public IdentifiedIsomerInfo ExportIdentifiedIsomerInfo(double viperCompatibleMass, int minFitPoints, double minR2, IImsTarget target, double bestMzInPpm)
{
double averageVoltageGroupStabilityScore = VoltageGroupScoring.ComputeAverageVoltageGroupStabilityScore(this.definedVoltageGroups);
IList<ArrivalTimeSnapShot> snapshots = new List<ArrivalTimeSnapShot>();
foreach (var observation in this.observedPeaks)
{
snapshots.Add(this.ExtractArrivalTimeSnapShot(observation));
}
IdentifiedIsomerInfo info = new IdentifiedIsomerInfo(
this.observedPeaks.Count,
this.AverageMzInDalton,
this.mobilityInfo.RSquared,
this.mobilityInfo.Mobility,
this.mobilityInfo.CollisionCrossSectionArea,
averageVoltageGroupStabilityScore,
snapshots,
viperCompatibleMass,
this.ConcludeStatus(minFitPoints, minR2),
this.TrackStatistics,
target,
this.mobilityInfo.T0,
bestMzInPpm
);
return info;
}
/// <summary>
/// The report target info.
/// </summary>
/// <param name="target">
/// The target.
/// </param>
/// <param name="verbose">
/// The verbose.
/// </param>
private static void ReportTargetInfo(IImsTarget target, bool verbose)
{
Trace.WriteLine(string.Empty);
if (verbose)
{
Trace.WriteLine("Target chemical: " + target.CorrespondingChemical);
Trace.WriteLine("Target description: " + target.TargetDescriptor);
if (target.HasCompositionInfo)
{
Trace.WriteLine("Target Empirical Formula: " + target.EmpiricalFormula);
}
Trace.WriteLine("Targeting centerMz: " + target.MassWithAdduct);
Trace.WriteLine(string.Empty);
}
else
{
Trace.WriteLine("Target: " + target.TargetDescriptor);
}
}
/// <summary>
/// The association hypothesis plot.
/// </summary>
/// <param name="hypothesis">
/// The hypothesis.
/// </param>
/// <param name="datasetName">
/// The dataset name.
/// </param>
/// <param name="targetDescriptor">
/// The target descriptor.
/// </param>
/// <returns>
/// The <see cref="PlotModel"/>.
/// </returns>
private PlotModel AssociationHypothesisPlot(AssociationHypothesis hypothesis, string datasetName, IImsTarget target, bool plotXAxisFromZero = false)
{
PlotModel model = new PlotModel();
model.LegendBorderThickness = 0;
model.LegendOrientation = LegendOrientation.Vertical;
model.LegendPlacement = LegendPlacement.Inside;
model.LegendPosition = LegendPosition.LeftTop;
model.TitlePadding = 0;
model.Title = "Optimal Association Hypothesis Plot";
model.Subtitle = string.Format("Target: {0}, dataset: {1}", target.TargetDescriptor, datasetName) ;
model.Axes.Add(
new LinearAxis
{
Title = "IMS arrival time (milliseconds)",
MajorGridlineStyle = LineStyle.Solid,
Position = AxisPosition.Left,
});
model.Axes.Add(
new LinearAxis
{
Title = "P/(T*V) with P and T nondimensionalized (1/V)",
Position = AxisPosition.Bottom,
MajorGridlineStyle = LineStyle.Solid,
});
// Add all the points
IEnumerable<ObservedPeak> onTrackPeaks = hypothesis.OnTrackObservations;
IEnumerable<ObservedPeak> offTrackPeaks = hypothesis.AllObservations.Where(x => !hypothesis.IsOnTrack(x));
Func<ObservedPeak, ScatterPoint> fitPointMap = obj =>
{
ObservedPeak observation = obj;
ContinuousXYPoint xyPoint = observation.ToContinuousXyPoint(false, 0);
double size = MapToPointSize(observation);
ScatterPoint sp = new ScatterPoint(xyPoint.X, xyPoint.Y, size);
return sp;
};
var ontrackSeries= new ScatterSeries
{
Title = "[Peaks On Tracks]",
MarkerFill = OxyColors.BlueViolet,
MarkerType = MarkerType.Circle
};
var offtrackSeries= new ScatterSeries
{
Title = "[Peaks Off Tracks]",
MarkerFill = OxyColors.Red,
MarkerType = MarkerType.Circle
};
ontrackSeries.Points.AddRange(onTrackPeaks.Select(x => fitPointMap(x)));
offtrackSeries.Points.AddRange(offTrackPeaks.Select(x => fitPointMap(x)));
model.Series.Add(ontrackSeries);
model.Series.Add(offtrackSeries);
var allTracks = hypothesis.Tracks;
// Add the tracks as linear axes
int count = 1;
foreach (var track in allTracks)
{
FitLine fitline = track.FitLine;
LineAnnotation annotation = new LineAnnotation();
annotation.Slope = fitline.Slope;
annotation.Intercept = fitline.Intercept;
annotation.TextPadding = 3;
annotation.TextMargin = 2;
annotation.Text = string.Format("Conformer {0} - mz: {1:F2}; ccs: {2:F2}, Isotopic Score: {3:F3}; Track Probability: {4:F2}; R2: {5:F5};",
count, track.AverageMzInDalton, track.GetMobilityInfoForTarget(target).CollisionCrossSectionArea, track.TrackStatistics.IsotopicScore, track.TrackProbability, track.FitLine.RSquared);
count++;
model.Annotations.Add(annotation);
//Func<object, DataPoint> lineMap = obj =>
//{
// ObservedPeak observation = (ObservedPeak)obj;
// ContinuousXYPoint xyPoint = observation.ToContinuousXyPoint();
// double x = xyPoint.X;
// double y = fitline.ModelPredictX2Y(x);
// DataPoint sp = new DataPoint(x, y);
// return sp;
//};
//model.Series.Add(new LineSeries()
//{
// Mapping = lineMap,
// ItemsSource = track.ObservedPeaks,
// Color = OxyColors.Purple
//});
}
return model;
}
/// <summary>
/// The reset trace listener to target.
/// </summary>
/// <param name="target">
/// The target.
/// </param>
/// <returns>
/// The <see cref="FileStream"/>.
/// </returns>
private FileStream ResetTraceListenerToTarget(IImsTarget target, string datasetName)
{
Trace.Listeners.Clear();
string targetResultFileName = Path.Combine(this.OutputPath, "target_" + target.TargetDescriptor + "_in_" + datasetName + ".txt");
FileStream resultFile = new FileStream(targetResultFileName, FileMode.Create, FileAccess.Write, FileShare.None);
ConsoleTraceListener consoleTraceListener = new ConsoleTraceListener(false);
consoleTraceListener.TraceOutputOptions = TraceOptions.DateTime;
TextWriterTraceListener targetResultTraceListener = new TextWriterTraceListener(resultFile)
{
TraceOutputOptions = TraceOptions.ThreadId | TraceOptions.DateTime
};
Trace.Listeners.Add(consoleTraceListener);
Trace.Listeners.Add(targetResultTraceListener);
Trace.AutoFlush = true;
return resultFile;
}
/// <summary>
/// The find peaks based on xic.
/// </summary>
/// <param name="group">
/// The group.
/// </param>
/// <param name="chromatogram">
/// The chromatogram.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <returns>
/// The <see cref="IList"/>.
/// </returns>
/// <exception cref="NotImplementedException">
/// </exception>
private List<StandardImsPeak> FindPeaksBasedOnXIC(VoltageGroup voltageGroup, ExtractedIonChromatogram chromatogram, IImsTarget target)
{
if (this.Parameters.PeakDetectorSelection == PeakDetectorEnum.WaterShed)
{
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = chromatogram.IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, this.smoother, this.Parameters.FeatureFilterLevel);
// Recapture the 2D peak using the 1D feature blob from multidimensional peak finder.
return featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, this.uimfReader, voltageGroup, target.MassWithAdduct, this.Parameters.MzWindowHalfWidthInPpm)).ToList();
}
else if (this.Parameters.PeakDetectorSelection == PeakDetectorEnum.MASICPeakFinder)
{
// Find peaks using MASIC peak finder
List<IntensityPoint> intensityPoints = chromatogram.IntensityPoints;
IList<clsPeak> masicPeaks = PeakFinding.FindPeakUsingMasic(intensityPoints, this.NumberOfScans);
// Recapture the 2D peak using the 1D feature blob from multidimensional peak finder.
return masicPeaks.Select(peak => new StandardImsPeak(peak)).ToList();
}
else
{
throw new NotImplementedException(string.Format("{0} not supported", this.Parameters.PeakDetectorSelection));
}
}
/// <summary>
/// Gets the mobility info for inferedTarget
/// </summary>
/// <param name="inferedTarget">
/// The inferedTarget.
/// </param>
public MobilityInfo GetMobilityInfoForTarget(IImsTarget inferedTarget)
{
return this.ComputeMobilityInfo(inferedTarget);
}
public bool Equals(IImsTarget other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
if (other.TargetType != TargetType.Peptide) return false;
return this.Equals(other as PeptideTarget);
}
/// <summary>
/// The equals.
/// </summary>
/// <param name="other">
/// The other.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
public virtual bool Equals(IImsTarget other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
if (other.TargetType != TargetType.Molecule) return false;
return this.Equals(other as MolecularTarget);
}
/// <summary>
/// The initiate from workflow result.
/// </summary>
/// <param name="result">
/// The result.
/// </param>
private void InitiateFromWorkflowResult(CrossSectionWorkflowResult result)
{
this.Target = result.Target;
this.AnalysisStatus = result.AnalysisStatus;
this.FusionNumber = 1;
this.DetectedIsomers = result.IdentifiedIsomers;
}
/// <summary>
/// Initializes a new instance of the <see cref="CrossSectionWorkflowResult"/> class.
/// Multiple isomer result constructor
/// </summary>
/// <param name="datasetName">
/// The dataset name.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="analysisStatus">
/// The analysis status.
/// </param>
/// <param name="associationHypothesisInfo">
/// The analysis scores holder.
/// </param>
/// <param name="isomerResults">
/// The isomer results.
/// </param>
/// <param name="averageObservedPeakStatistics"></param>
/// <param name="averageVoltageGroupStability"></param>
/// <param name="datasetPath"></param>
/// <param name="analysisDirectory"></param>
/// <param name="dateTime"></param>
public CrossSectionWorkflowResult(
string datasetPath,
IImsTarget target,
AnalysisStatus analysisStatus,
AssociationHypothesisInfo associationHypothesisInfo,
IList<IdentifiedIsomerInfo> isomerResults,
PeakScores averageObservedPeakStatistics,
double averageVoltageGroupStability,
string analysisDirectory,
string dateTime)
{
this.Target = target;
this.AnalysisStatus = analysisStatus;
this.AssociationHypothesisInfo = associationHypothesisInfo;
this.isomerResults = isomerResults;
this.AverageObservedPeakStatistics = averageObservedPeakStatistics;
this.AverageVoltageGroupStability = averageVoltageGroupStability;
this.AnalysisDirectory = analysisDirectory;
this.DateTime = dateTime;
this.DatasetPath = datasetPath;
this.DatasetName = Path.GetFileNameWithoutExtension(datasetPath);
this.DateTime = dateTime;
}
/// <summary>
/// The more likely than targeted.
/// </summary>
/// <param name="a">
/// The a.
/// </param>
/// <param name="b">
/// The b.
/// </param>
/// <param name="likelihoodFunc">
/// The likelihood func.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
/// <exception cref="NotImplementedException">
/// </exception>
public static bool MoreLikelyThanTargeted(ObservedPeak a, ObservedPeak b, LikelihoodFunc likelihoodFunc, IImsTarget target)
{
throw new NotImplementedException();
}
/// <summary>
/// The create negative result.
/// </summary>
/// <param name="rejectedPeaks">
/// The rejected peaks.
/// </param>
/// <param name="rejectedVoltageGroups">
/// The rejected voltage groups.
/// </param>
/// <param name="datasetName">
/// The dataset name.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <returns>
/// The <see cref="CrossSectionWorkflowResult"/>.
/// </returns>
internal static CrossSectionWorkflowResult CreateNegativeResult(IEnumerable<ObservedPeak> rejectedPeaks, IEnumerable<VoltageGroup> rejectedVoltageGroups, IImsTarget target, string datasetPath, string analysisPath, string sampleCollectionTime)
{
// No valid feature peaks were identified. No hypothesis.
double voltageGroupScore = VoltageGroupScoring.ComputeAverageVoltageGroupStabilityScore(rejectedVoltageGroups);
// quantize the VG score from VGs in the removal list.
IEnumerable<PeakScores> featureStats = rejectedPeaks.Select(x => x.Statistics);
PeakScores averagePeakScores = FeatureScoreUtilities.AverageFeatureStatistics(featureStats);
CrossSectionWorkflowResult informedResult = new CrossSectionWorkflowResult(
datasetPath,
target,
AnalysisStatus.Negative,
null,
averagePeakScores,
voltageGroupScore,
analysisPath,
sampleCollectionTime);
return informedResult;
}
private async Task<string> InsertChemical(SQLiteCommand cmd, IImsTarget target)
{
// Query if chemical is already added.
string chemicalName = target.CorrespondingChemical;
cmd.CommandText = string.Format("SELECT count(*) FROM chemicals WHERE name='{0}'", chemicalName);
int count = Convert.ToInt32(cmd.ExecuteScalar());
if(count == 0)
{
// Insert chemical info to chemicals table
cmd.CommandText = "INSERT INTO chemicals (name, empirical_formula, chemical_class) VALUES (@name, @empirical_formula, @chemical_class)";
cmd.Parameters.AddWithValue("@name", chemicalName);
cmd.Parameters.AddWithValue("@empirical_formula", target.EmpiricalFormula);
cmd.Parameters.AddWithValue("@chemical_class", "");
await Task.Run(() => cmd.ExecuteNonQuery());
return chemicalName;
}
return "";
}
/// Initializes a new instance of the <see cref="CrossSectionWorkflowResult"/> class.
/// Constructor for no isomer result.
public CrossSectionWorkflowResult(
string datasetPath,
IImsTarget target,
AnalysisStatus analysisStatus,
AssociationHypothesisInfo associationHypothesisInfo,
PeakScores averageObservedPeakStatistics,
double averageVoltageGroupStability,
string analysisDirectory, string dateTime)
: this(datasetPath,
target,
analysisStatus,
associationHypothesisInfo,
new List<IdentifiedIsomerInfo>(),
averageObservedPeakStatistics,
averageVoltageGroupStability,
analysisDirectory,
dateTime)
{
}
private async Task<long> InsertTarget(SQLiteCommand cmd, IImsTarget target)
{
cmd.CommandText = string.Format("SELECT count(*) FROM targets WHERE target_description ='{0}' AND target_chemical = '{1}'", target.TargetDescriptor, target.CorrespondingChemical);
int count = Convert.ToInt32(cmd.ExecuteScalar());
if(count == 0)
{
// Insert target info to chemicals table
cmd.CommandText = "INSERT INTO targets (target_chemical, target_type, adduct, target_description, monoisotopic_mass, composition_with_adduct, mass_with_adduct, charge_state) VALUES (@target_chemical, @target_type, @adduct, @target_description, @monoisotopic_mass, @composition_with_adduct, @mass_with_adduct, @charge_state)";
cmd.Parameters.AddWithValue("@target_chemical", target.CorrespondingChemical);
cmd.Parameters.AddWithValue("@target_type", target.TargetType);
cmd.Parameters.AddWithValue("@adduct", target.Adduct);
cmd.Parameters.AddWithValue("@target_description", target.TargetDescriptor);
cmd.Parameters.AddWithValue("@monoisotopic_mass", target.MonoisotopicMass);
cmd.Parameters.AddWithValue("@composition_with_adduct", target.CompositionWithAdduct);
cmd.Parameters.AddWithValue("@mass_with_adduct", target.MassWithAdduct);
cmd.Parameters.AddWithValue("@charge_state", target.ChargeState);
await Task.Run(() => cmd.ExecuteNonQuery());
return await this.LastID(cmd);
}
else
{
cmd.CommandText = string.Format("SELECT rowid FROM targets WHERE target_description ='{0}'", target.TargetDescriptor);
int id = Convert.ToInt32(cmd.ExecuteScalar());
return id;
}
}
/// <summary>
/// The is track possible.
/// </summary>
/// <param name="track">
/// The track.
/// </param>
/// <param name="target"></param>
/// <param name="crossSectionSearchParameters"></param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
public bool IsTrackPossible(IsomerTrack track, IImsTarget target, CrossSectionSearchParameters crossSectionSearchParameters)
{
int minFitPoints = track.TotalNumberOfVoltageGroups - crossSectionSearchParameters.MaxOutliers;
if (this.FilterLowFitPointNumber(track.RealPeakCount, minFitPoints))
{
return false;
}
MobilityInfo trackMobilityInfo = track.GetMobilityInfoForTarget(target);
if (!this.IsConsistentWithIonDynamics(trackMobilityInfo))
{
return false;
}
if (this.IsLowR2(trackMobilityInfo.RSquared, crossSectionSearchParameters.MinR2))
{
return false;
}
return true;
}
/// <summary>
/// Initializes a new instance of the <see cref="IdentifiedIsomerInfo"/> class.
/// </summary>
/// <param name="numberOfFeaturePointsUsed">
/// The number of feature points used.
/// </param>
/// <param name="mzInDalton"></param>
/// <param name="rSquared">
/// The r squred.
/// </param>
/// <param name="mobility">
/// The mobility.
/// </param>
/// <param name="crossSectionalArea">
/// The cross sectional area.
/// </param>
/// <param name="averageVoltageGroupStabilityScore">
/// The average voltage group stability score.
/// </param>
/// <param name="arrivalTimeSnapShots">
/// The arrival time snap shots.
/// </param>
/// <param name="viperCompatibleMass">
/// The viper Compatible Mass.
/// </param>
/// <param name="analysisStatus"></param>
/// <param name="peakScores"></param>
/// <param name="target"></param>
public IdentifiedIsomerInfo(
int numberOfFeaturePointsUsed,
double mzInDalton,
double rSquared,
double mobility,
double crossSectionalArea,
double averageVoltageGroupStabilityScore,
IEnumerable<ArrivalTimeSnapShot> arrivalTimeSnapShots,
double viperCompatibleMass,
AnalysisStatus analysisStatus,
PeakScores peakScores,
IImsTarget target,
double t0,
double bestMzInPpm)
{
this.NumberOfFeaturePointsUsed = numberOfFeaturePointsUsed;
this.RSquared = rSquared;
this.Mobility = mobility;
this.CrossSectionalArea = crossSectionalArea;
this.AverageVoltageGroupStabilityScore = averageVoltageGroupStabilityScore;
this.ArrivalTimeSnapShots = arrivalTimeSnapShots;
this.ViperCompatibleMass = viperCompatibleMass;
this.AnalysisStatus = analysisStatus;
this.PeakScores = peakScores;
this.T0 = t0;
this.MzInDalton = mzInDalton;
this.MzInPpm = Metrics.DaltonToPpm(mzInDalton - target.MassWithAdduct, target.MassWithAdduct);
this.RelativeMzInPpm = Math.Abs(MzInPpm - bestMzInPpm);
}