/// <summary>
/// Gets the spectral matches
/// </summary>
/// <param name="baselineFeatures"></param>
/// <param name="aligneeFeatures"></param>
/// <returns></returns>
private List <SpectralMatch> GetSpectralMatches(List <UMCLight> baselineFeatures,
List <UMCLight> aligneeFeatures,
double comparisonCutoff)
{
var matches = new List <SpectralMatch>();
var baselineSpectra = GetSpectra(baselineFeatures);
var aligneeSpectra = GetSpectra(aligneeFeatures);
// Optimizes the loading of a spectra...
var map = new Dictionary <int, MSSpectra>();
var filter = SpectrumFilterFactory.CreateFilter(SpectraFilters.TopPercent);
var comparer = SpectralComparerFactory.CreateSpectraComparer(SpectralComparison.CosineDotProduct);
var percent = .2;
var mzTolerance = .5;
double maxScanDiff = 1500;
foreach (var baselineSpectrum in baselineSpectra)
{
baselineSpectrum.Peaks = filter.Threshold(baselineSpectrum.Peaks, percent);
baselineSpectrum.Peaks = XYData.Bin(baselineSpectrum.Peaks, 0, 2000, mzTolerance);
foreach (var aligneeSpectrum in aligneeSpectra)
{
// Only consider spectra that are near each other in mass.
var diff = Math.Abs(baselineSpectrum.PrecursorMz - aligneeSpectrum.PrecursorMz);
if (diff >= mzTolerance)
{
continue;
}
// Only consider spectra that are within some range of another.
var scanDiff = Math.Abs(aligneeSpectrum.Scan - baselineSpectrum.Scan);
if (scanDiff > maxScanDiff)
{
continue;
}
// Bin and threshold the spectra
aligneeSpectrum.Peaks = filter.Threshold(aligneeSpectrum.Peaks, percent);
aligneeSpectrum.Peaks = XYData.Bin(aligneeSpectrum.Peaks, 0, 2000, mzTolerance);
// Compare the spectra
var value = comparer.CompareSpectra(baselineSpectrum, aligneeSpectrum);
if (double.IsNaN(value))
{
continue;
}
if (value > comparisonCutoff)
{
var match = new SpectralMatch();
match.Alignee = aligneeSpectrum;
match.Baseline = baselineSpectrum;
match.Similarity = value;
matches.Add(match);
}
}
}
return(matches);
}
/// <summary>
/// Gets the spectral matches
/// </summary>
/// <param name="baselineFeatures"></param>
/// <param name="aligneeFeatures"></param>
/// <returns></returns>
private List<SpectralMatch> GetSpectralMatches(List<UMCLight> baselineFeatures,
List<UMCLight> aligneeFeatures,
double comparisonCutoff)
{
var matches = new List<SpectralMatch>();
var baselineSpectra = GetSpectra(baselineFeatures);
var aligneeSpectra = GetSpectra(aligneeFeatures);
// Optimizes the loading of a spectra...
var map = new Dictionary<int, MSSpectra>();
var filter = SpectrumFilterFactory.CreateFilter(SpectraFilters.TopPercent);
var comparer = SpectralComparerFactory.CreateSpectraComparer(SpectralComparison.CosineDotProduct);
var percent = .2;
var mzTolerance = .5;
double maxScanDiff = 1500;
foreach (var baselineSpectrum in baselineSpectra)
{
baselineSpectrum.Peaks = filter.Threshold(baselineSpectrum.Peaks, percent);
baselineSpectrum.Peaks = XYData.Bin(baselineSpectrum.Peaks, 0, 2000, mzTolerance);
foreach (var aligneeSpectrum in aligneeSpectra)
{
// Only consider spectra that are near each other in mass.
var diff = Math.Abs(baselineSpectrum.PrecursorMz - aligneeSpectrum.PrecursorMz);
if (diff >= mzTolerance)
continue;
// Only consider spectra that are within some range of another.
var scanDiff = Math.Abs(aligneeSpectrum.Scan - baselineSpectrum.Scan);
if (scanDiff > maxScanDiff)
continue;
// Bin and threshold the spectra
aligneeSpectrum.Peaks = filter.Threshold(aligneeSpectrum.Peaks, percent);
aligneeSpectrum.Peaks = XYData.Bin(aligneeSpectrum.Peaks, 0, 2000, mzTolerance);
// Compare the spectra
var value = comparer.CompareSpectra(baselineSpectrum, aligneeSpectrum);
if (double.IsNaN(value))
continue;
if (value > comparisonCutoff)
{
var match = new SpectralMatch();
match.Alignee = aligneeSpectrum;
match.Baseline = baselineSpectrum;
match.Similarity = value;
matches.Add(match);
}
}
}
return matches;
}
