/// <summary>
/// Aligns the dataset to the data stored in the alignment processor.
/// </summary>
/// <param name="alignmentProcessor">Aligner</param>
/// <param name="features">LC-MS Features to align to the baseline</param>
/// <param name="alignmentOptions">Options</param>
/// <param name="progress"></param>
/// <returns></returns>
private AlignmentData AlignFeatures(LcmsWarpAlignmentProcessor alignmentProcessor,
IEnumerable <UMCLight> features,
LcmsWarpAlignmentOptions alignmentOptions,
IProgress <ProgressData> progress = null)
{
var progData = new ProgressData(progress);
var localProgress = new Progress <ProgressData>(p => progData.Report(p.Percent, p.Status));
var alignmentData = new AlignmentData();
OnStatus("Starting alignment of features.");
// Set minMtdbnet and maxMtdbnet to 0
alignmentData.MinMTDBNET = 0;
alignmentData.MaxMTDBNET = 0;
var umcLights = features as List <UMCLight> ?? features.ToList();
progData.StepRange(5, "Starting alignment of features.");
var filteredFeatures = FilterFeaturesByAbundance(umcLights, alignmentOptions);
// Convert the features, and make a map, so that we can re-adjust the aligned values later.
var map = FeatureDataConverters.MapFeature(umcLights);
progData.StepRange(10, "Setting alignee features.");
// Set features
OnStatus("Setting alignee features.");
alignmentProcessor.SetAligneeDatasetFeatures(filteredFeatures);
progData.StepRange(90, "Performing alignment warping.");
// Find alignment
OnStatus("Performing alignment warping.");
alignmentProcessor.PerformAlignmentToMsFeatures(localProgress);
progData.StepRange(95);
// Extract alignment function
alignmentData.AlignmentFunction = alignmentProcessor.GetAlignmentFunction();
progData.StepRange(100);
// Extract the NET value for every scan
_scanToNETMap = alignmentProcessor.GetScanToNETMapping();
// Correct the features (updates NetAligned and MassMonoisotopicAligned)
OnStatus("Applying alignment function to all features.");
progData.Status = "Applying alignment function to all features.";
umcLights = alignmentProcessor.ApplyNetMassFunctionToAligneeDatasetFeatures(umcLights);
progData.Report(100);
// Find min/max scan for meta-data
var minScanBaseline = int.MaxValue;
var maxScanBaseline = int.MinValue;
foreach (var feature in umcLights)
{
maxScanBaseline = Math.Max(maxScanBaseline, feature.Scan);
minScanBaseline = Math.Min(minScanBaseline, feature.Scan);
}
// Update the scan and NET ranges
alignmentData.MinScanBaseline = minScanBaseline;
alignmentData.MaxScanBaseline = maxScanBaseline;
alignmentData.MinMTDBNET = (float)alignmentProcessor.MinReferenceNet;
alignmentData.MaxMTDBNET = (float)alignmentProcessor.MaxReferenceNet;
// Cache the matching features
alignmentData.FeatureMatches = alignmentProcessor.FeatureMatches;
// Pull out the heat maps...
OnStatus("Retrieving alignment data.");
progData.Status = "Retrieving alignment data.";
alignmentData.HeatScores = alignmentProcessor.GetAlignmentHeatMap(alignmentOptions.StandardizeHeatScores);
// Mass and net error histograms!
alignmentData.MassErrorHistogram = alignmentProcessor.GetMassErrorHistogram(alignmentOptions.MassBinSize);
alignmentData.NetErrorHistogram = alignmentProcessor.GetNetErrorHistogram(alignmentOptions.NetBinSize);
alignmentData.DriftErrorHistogram = alignmentProcessor.GetDriftErrorHistogram(alignmentOptions.DriftTimeBinSize);
// Get the residual data from the warp.
alignmentData.ResidualData = alignmentProcessor.GetResidualData();
alignmentData.NETIntercept = alignmentProcessor.NetIntercept;
alignmentData.NETRsquared = alignmentProcessor.NetRsquared;
alignmentData.NETSlope = alignmentProcessor.NetSlope;
alignmentData.MassMean = alignmentProcessor.MassMu;
alignmentData.MassStandardDeviation = alignmentProcessor.MassStd;
alignmentData.NETMean = alignmentProcessor.NetMu;
alignmentData.NETStandardDeviation = alignmentProcessor.NetStd;
alignmentData.BaselineIsAmtDB = _options.AlignToMassTagDatabase;
return(alignmentData);
}
