/// <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.");
}
/// <summary>
/// Initializes a new instance of the <see cref="LibraryMatchResult"/> class.
/// </summary>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="conlusion">
/// The conlusion.
/// </param>
/// <param name="distance">
/// The distance.
/// </param>
public LibraryMatchResult(StandardImsPeak peak, AnalysisStatus conlusion, DriftTimeFeatureDistance distance)
{
this.AnalysisStatus = conlusion;
this.ImsFeature = peak;
this.distance = distance;
}
