/// <summary>
/// Aligns to a mass tag database. The baseline provider should be able to convert a mass tag sequence into a theoretical spectrum.
/// </summary>
/// <param name="baseline"></param>
/// <param name="alignee"></param>
/// <returns></returns>
public IEnumerable <SpectralAnchorPointMatch> Align(MassTagDatabase baseline,
IEnumerable <UMCLight> alignee, IProgress <ProgressData> progress = null)
{
OnProgress("Finding anchor point matches");
var finder = new SpectralAnchorPointFinder();
var matches = finder.FindAnchorPoints(BaselineSpectraProvider as ISpectraProvider,
AligneeSpectraProvider as ISpectraProvider,
SpectralComparer,
Filter,
Options);
OnProgress("Creating Alignment Functions");
var aligner = new SpectralAnchorPointAligner();
var spectralAnchorPointMatches = matches as SpectralAnchorPointMatch[] ?? matches.ToArray();
//TODO: Brian modified to test alignment using LCMSWarp regression code.
aligner.CreateAlignmentFunctions(spectralAnchorPointMatches);
OnProgress("Transforming sub-features");
foreach (var feature in alignee)
{
feature.NetAligned = feature.Net; // aligner.AlignNet(feature.Net);
}
return(spectralAnchorPointMatches);
}
/// <summary>
/// Aligns two feature datasets.
/// </summary>
/// <param name="baseline"></param>
/// <param name="alignee"></param>
/// <returns></returns>
public IEnumerable <SpectralAnchorPointMatch> Align(IEnumerable <UMCLight> baseline,
IEnumerable <UMCLight> alignee, IProgress <ProgressData> progress = null)
{
OnProgress("Finding anchor point matches");
var finder = new SpectralAnchorPointFinder();
var matches = finder.FindAnchorPoints(BaselineSpectraProvider as ISpectraProvider,
AligneeSpectraProvider as ISpectraProvider,
SpectralComparer,
Filter,
Options);
OnProgress("Creating Alignment Functions");
var aligner = new SpectralAnchorPointAligner(Bandwidth);
var spectralAnchorPointMatches = matches as SpectralAnchorPointMatch[] ?? matches.ToArray();
aligner.CreateAlignmentFunctions(spectralAnchorPointMatches);
OnProgress("Transforming sub-features");
foreach (var feature in alignee)
{
feature.NetAligned = aligner.AlignNet(feature.Net);
feature.Net = feature.NetAligned;
feature.MassMonoisotopicAligned = aligner.AlignMass(feature.MassMonoisotopic);
}
return(spectralAnchorPointMatches);
}