private AlignmentResult getResultsForAlignment(clsAlignmentProcessor processor)
{
float[] scanLCValues = null;
float[] NETValues = null;
float[,] scores = null;
processor.GetAlignmentHeatMap(ref scores, ref scanLCValues, ref NETValues);
var result = new AlignmentResult();
result.ScanLCValues = scanLCValues;
result.NETValues = NETValues;
result.AlignmentHeatmapScores = scores;
//get massResiduals_vs_scan and massResiduals_vs_m/z
var residuals = processor.GetResidualData();
result.Mass_vs_scan_ResidualsBeforeAlignment = residuals.massError;
result.Mass_vs_scan_ResidualsAfterAlignment = residuals.massErrorCorrected;
result.Mass_vs_scan_ResidualsScanValues = residuals.scans;
result.Mass_vs_mz_ResidualsBeforeAlignment = residuals.mzMassError;
result.Mass_vs_mz_ResidualsAfterAlignment = residuals.mzMassErrorCorrected;
result.Mass_vs_mz_ResidualsMZValues = residuals.mz;
//get stats on variability
result.NETStDev = processor.GetNETStandardDeviation();
result.NETAverage = processor.GetNETMean();
result.MassAverage = processor.GetMassMean();
result.MassStDev = processor.GetMassStandardDeviation();
double[,] massHistogramData = null;
double[,] netHistogramData = null;
double[,] driftHistogramData = null;
processor.GetErrorHistograms(0.1, 0.002, 0.1, ref massHistogramData, ref netHistogramData, ref driftHistogramData);
result.massHistogramData = massHistogramData;
result.NETHistogramData = netHistogramData;
return(result);
}
public clsAlignmentFunction GetAlignment(List <TargetBase> massTagList, List <TargetedResultDTO> featuresToAlign)
{
var multialignMassTagDB = new clsMassTagDB();
//TODO: I might be able to dynamically update these values. Take my foundFeatures and calculate their avg PPMDiff. Then use that info here.
var alignmentOptions = new clsAlignmentOptions();
alignmentOptions.MassCalibrationWindow = this.AlignerParameters.MassCalibrationWindow; //note - it seems that 50 ppm is used as a default setting in VIPER.
alignmentOptions.ContractionFactor = this.AlignerParameters.ContractionFactor;
alignmentOptions.IsAlignmentBaselineAMasstagDB = this.AlignerParameters.IsAlignmentBaselineAMassTagDB;
alignmentOptions.MassBinSize = this.AlignerParameters.MassBinSize;
alignmentOptions.MassCalibrationLSQNumKnots = this.AlignerParameters.MassCalibrationLSQNumKnots;
alignmentOptions.MassCalibrationLSQZScore = this.AlignerParameters.MassCalibrationLSQZScore;
alignmentOptions.MassCalibrationMaxJump = this.AlignerParameters.MassCalibrationMaxJump;
alignmentOptions.MassCalibrationMaxZScore = this.AlignerParameters.MassCalibrationMaxZScore;
alignmentOptions.MassCalibrationNumMassDeltaBins = this.AlignerParameters.MassCalibrationNumMassDeltaBins;
alignmentOptions.MassCalibrationNumXSlices = this.AlignerParameters.MassCalibrationNumXSlices;
alignmentOptions.MassCalibrationUseLSQ = this.AlignerParameters.MassCalibrationUseLSQ;
alignmentOptions.MassCalibrationWindow = this.AlignerParameters.MassCalibrationWindow;
alignmentOptions.MassTolerance = this.AlignerParameters.MassToleranceForNETAlignment;
alignmentOptions.MaxPromiscuity = this.AlignerParameters.MaxPromiscuity;
alignmentOptions.MaxTimeJump = this.AlignerParameters.MaxTimeJump;
alignmentOptions.NETBinSize = this.AlignerParameters.NETBinSize;
alignmentOptions.NETTolerance = this.AlignerParameters.NETTolerance;
alignmentOptions.NumTimeSections = this.AlignerParameters.NumTimeSections;
alignmentOptions.UsePromiscuousPoints = this.AlignerParameters.UsePromiscuousPoints;
var processor = new clsAlignmentProcessor();
processor.AlignmentOptions = alignmentOptions;
var multiAlignMassTags = convertDeconToolsMassTagsToMultialignMassTags(massTagList);
multialignMassTagDB.AddMassTags(multiAlignMassTags);
processor.SetReferenceDatasetFeatures(multialignMassTagDB);
var multialignUMCs = convertDeconToolsLCMSFeaturesToMultialignFeatures(featuresToAlign);
processor.SetAligneeDatasetFeatures(multialignUMCs, alignmentOptions.MZBoundaries[0]);
processor.PerformAlignmentToMSFeatures();
this.Result = getResultsForAlignment(processor);
return(processor.GetAlignmentFunction());
}
public clsAlignmentFunction GetAlignment(List <MassTag> massTagList, List <TargetedResult> featuresToAlign)
{
clsMassTagDB multialignMassTagDB = new clsMassTagDB();
//TODO: figure out which options I need to parameterize in this class. For now, use defaults
clsAlignmentOptions alignmentOptions = new clsAlignmentOptions();
clsAlignmentProcessor processor = new clsAlignmentProcessor();
clsMassTag[] multiAlignMassTags = convertDeconToolsMassTagsToMultialignMassTags(massTagList);
multialignMassTagDB.AddMassTags(multiAlignMassTags);
processor.SetReferenceDatasetFeatures(multialignMassTagDB);
List <clsUMC> multialignUMCs = convertDeconToolsLCMSFeaturesToMultialignFeatures(featuresToAlign);
processor.SetAligneeDatasetFeatures(multialignUMCs, alignmentOptions.MZBoundaries[0]);
processor.PerformAlignmentToMSFeatures();
return(processor.GetAlignmentFunction());
}
