/// <summary>
/// Uses a list of MassTagLights as a baseline for aligning a list of UMCLights to it, using
/// the passed in options for processor options as well as a boolean for whether to align based on
/// Drift Times as well.
/// Creates an LCMS Alignment processor to do the alignment, does the alignment, and then passes
/// back the alignment data to the caller.
/// </summary>
/// <param name="massTags"></param>
/// <param name="aligneeFeatures"></param>
/// <param name="options"></param>
/// <returns></returns>
private LcmsWarpAlignmentData AlignFeatures(List <MassTagLight> massTags, List <UMCLight> aligneeFeatures,
LcmsWarpAlignmentOptions options)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor
{
Options = options
};
alignmentProcessor.ApplyAlignmentOptions();
alignmentProcessor.Progress += alignmentProcessor_Progress;
var featureTest = aligneeFeatures.Find(x => x.DriftTime > 0);
var massTagTest = massTags.Find(x => x.DriftTime > 0);
if (featureTest != null && massTagTest == null)
{
Console.WriteLine("Warning! Data has drift time info, but the mass tags do not.");
}
alignmentProcessor.SetReferenceDatasetFeatures(massTags);
var data = AlignFeatures(alignmentProcessor, aligneeFeatures, options);
return(data);
}
/// <summary>
/// Uses a list of UMCLights as a baseline for aligning a second list of UMCLights to it, using
/// the passed in options for processor options
/// Creates an LCMS Alignment processor to do the alignment, does the alignment, and then passes
/// back the alignment data to the caller.
/// </summary>
/// <param name="baseline"></param>
/// <param name="aligneeFeatures"></param>
/// <param name="options"></param>
/// <returns></returns>
private LcmsWarpAlignmentData AlignFeatures(List <UMCLight> baseline, List <UMCLight> aligneeFeatures, LcmsWarpAlignmentOptions options)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor
{
Options = options
};
alignmentProcessor.ApplyAlignmentOptions();
alignmentProcessor.Progress += alignmentProcessor_Progress;
var filteredBaselineFeatures = FilterFeaturesByAbundance(baseline, options) as List <UMCLight>;
alignmentProcessor.SetReferenceDatasetFeatures(filteredBaselineFeatures);
return(AlignFeatures(alignmentProcessor, aligneeFeatures, options));
}
