/// <summary>
/// Aligns a dataset to a mass tag database
/// </summary>
/// <param name="massTagDatabase"></param>
/// <param name="features"></param>
/// <param name="progress"></param>
/// <returns></returns>
public AlignmentData Align(MassTagDatabase massTagDatabase,
IEnumerable <UMCLight> features,
IProgress <ProgressData> progress = null)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor(_options);
alignmentProcessor.Progress += AlignmentProcessor_Progress;
var umcLights = features as IList <UMCLight> ?? features.ToList();
var featureTest = umcLights.ToList().Find(x => x.DriftTime > 0);
if (featureTest != null && !massTagDatabase.DoesContainDriftTime)
{
OnStatus("Warning! Data contains drift time information and the database does not.");
}
OnStatus("Configuring features as mass tags.");
OnStatus("Setting reference features using mass tags.");
alignmentProcessor.SetReferenceDatasetFeatures(massTagDatabase.MassTags);
var data = AlignFeatures(alignmentProcessor,
umcLights,
_options,
progress);
return(data);
}
/// <summary>
/// Align a dataset to a baseline dataset
/// </summary>
/// <param name="baselineFeatures">baseline dataset features</param>
/// <param name="features">alignee dataset features</param>
/// <param name="progress"></param>
/// <returns></returns>
public AlignmentData Align(IEnumerable <UMCLight> baselineFeatures,
IEnumerable <UMCLight> features,
IProgress <ProgressData> progress = null)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor(_options);
alignmentProcessor.Progress += AlignmentProcessor_Progress;
OnStatus("Setting features from baseline dataset.");
var umcLights = baselineFeatures as List <UMCLight> ?? baselineFeatures.ToList();
var filteredFeatures = FilterFeaturesByAbundance(umcLights, _options);
alignmentProcessor.SetReferenceDatasetFeatures(filteredFeatures);
var alignmentData = AlignFeatures(alignmentProcessor,
features,
_options,
progress);
var minScanReference = int.MaxValue;
var maxScanReference = int.MinValue;
foreach (var feature in umcLights)
{
minScanReference = Math.Min(minScanReference, feature.Scan);
maxScanReference = Math.Max(maxScanReference, feature.Scan);
}
alignmentData.MaxMTDBNET = maxScanReference;
alignmentData.MinMTDBNET = minScanReference;
return(alignmentData);
}
/// <summary>
/// Align a UMCLight Enumerable to a MassTagLight enumerable.
/// The MassTagLight Enumerable is used as the baseline to align the
/// UMCLight enumerable.
/// </summary>
/// <param name="baseline">Base dataset or AMT tags to align to</param>
/// <param name="features">LC-MS Features to align to the baseline</param>
/// <param name="progress"></param>
/// <returns></returns>
public AlignmentData Align(IEnumerable <MassTagLight> baseline, IEnumerable <UMCLight> features,
IProgress <ProgressData> progress = null)
{
var alignmentProcessor = new LcmsWarpAlignmentProcessor(_options);
alignmentProcessor.Progress += AlignmentProcessor_Progress;
var baselineMassTags = baseline as List <MassTagLight> ?? baseline.ToList();
var aligneeFeatures = features as List <UMCLight> ?? features.ToList();
var featureTest = aligneeFeatures.Find(x => x.DriftTime > 0);
var massTagTest = baselineMassTags.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(baselineMassTags);
var data = AlignFeatures(alignmentProcessor, aligneeFeatures, _options, progress);
return(data);
}