/// <summary>
/// Generates alignment functions for alignment between features in each separation dimension.
/// Warps the elution value for each feature based on the alignment function.
/// </summary>
/// <param name="aligneeFeatures">The features to warp.</param>
/// <param name="baselineFeatures">The features to warp to.</param>
/// <param name="includeMassInMatchScore">
/// Should mass be considered when scoring a match between an alignee feature and baseline feature?
/// </param>
/// <returns>The list of alignment results for each separation dimension.</returns>
public NewAlignmentData WarpNet(List <UMCLight> aligneeFeatures, List <UMCLight> baselineFeatures, bool includeMassInMatchScore)
{
// Generate candidate matches: Match alignee features -> baseline features by mass only
var featureMatcher = new LcmsWarpFeatureMatcher(this.options);
featureMatcher.GenerateCandidateMatches(aligneeFeatures, baselineFeatures);
var warpedFeatures = new List <UMCLight>(aligneeFeatures);
var results = new Dictionary <FeatureLight.SeparationTypes, LcmsWarpResults>();
// Perform warp on each separation dimension.
foreach (var separationType in this.options.SeparationTypes)
{
// Get matches for given separation dimension
var matches = featureMatcher.GetMatchesAs(separationType);
// Calculate two dimensional statistics for mass and the current separation dimension.
var statistics = LcmsWarpStatistics.CalculateAndGetStatistics(matches);
// Calculate alignee sections
var aligneeSections = new LcmsWarpSectionInfo(this.options.NumTimeSections);
aligneeSections.InitSections(aligneeFeatures);
// Calculate baseline sections
var baselineSections = new LcmsWarpSectionInfo(this.options.NumTimeSections * this.options.ContractionFactor);
baselineSections.InitSections(baselineFeatures);
// Generate alignment function, only score sections based on NET.
var alignmentScorer = new LcmsWarpAlignmentScorer(this.options, includeMassInMatchScore, statistics);
var alignmentFunction = alignmentScorer.GetAlignment(aligneeSections, baselineSections, matches);
alignmentFunction.SeparationType = separationType;
// Create alignment score heatmap
var alignmentScoreHeatMap = LcmsWarpPlotDataCreator.GetAlignmentHeatMap(
alignmentScorer.AlignmentScoreMatrix,
true,
this.options.NumTimeSections,
this.options.NumBaselineSections,
this.options.MaxExpansionWidth);
// Warp the values in the features for this separation type
warpedFeatures = alignmentFunction.GetWarpedFeatures(warpedFeatures).ToList();
var dimensionResults = new LcmsWarpResults
{
AlignmentFunction = alignmentFunction,
Statistics = statistics,
AlignmentScoreHeatMap = alignmentScoreHeatMap
};
results.Add(separationType, dimensionResults);
}
return(new NewAlignmentData
{
SeparationAlignments = results,
AlignedFeatures = warpedFeatures,
});
}
/// <summary>
/// Generates alignment functions for alignment between features in each separation dimension.
/// Warps the elution value for each feature based on the alignment function.
/// </summary>
/// <param name="aligneeFeatures">The features to warp.</param>
/// <param name="baselineFeatures">The features to warp to.</param>
/// <returns>The features with all NET values warped.</returns>
public NewAlignmentData WarpNetMass(List <UMCLight> aligneeFeatures, List <UMCLight> baselineFeatures)
{
// First pass NET warp: Perform warp by only scoring matches in NET
var netWarpedFirstPass = this.WarpNet(aligneeFeatures, baselineFeatures, false);
// Generate matches from features by matching in both mass and NET
var featureMatcher = new LcmsWarpFeatureMatcher(this.options);
featureMatcher.GenerateCandidateMatches(
netWarpedFirstPass.AlignedFeatures,
baselineFeatures,
this.options.SeparationTypes);
var matches = featureMatcher.Matches;
// Calculate mass alignment
var massCalibrator = MassCalibrationFactory.GetCalibrator(this.options);
var massCalibrations = massCalibrator.CalculateCalibration(matches);
// Warp features.
var warpedFeatures = massCalibrations.GetWarpedFeatures(aligneeFeatures).ToList();
// Calculate histograms/plots for mass alignment
var massErrorHistogram = LcmsWarpPlotDataCreator.GetMassErrorHistogram(matches, 10);
// Create results object
var massAlignmentResult = new LcmsWarpResults
{
AlignmentFunction = massCalibrations,
ErrorHistogram = massErrorHistogram,
};
// Second pass NET warp: Perform warp that scores matches in mass AND NET
var netMassWarpedSecondPass = this.WarpNet(warpedFeatures, baselineFeatures, true);
// Add mass alignment results to existing alignment results from the NET alignment.
netMassWarpedSecondPass.MassAlignment = massAlignmentResult;
return(netMassWarpedSecondPass);
}
