public void Create(string directory, SpectralComparison comparerType, double percent)
{
var comparer = SpectralComparerFactory.CreateSpectraComparer(comparerType, percent);
var spectra = new List <MSSpectra>();
var files = Directory.GetFiles(directory, "*.txt");
foreach (var file in files)
{
spectra.Add(ReadSpectrum(file));
}
var values = new List <double>();
for (var i = 0; i < spectra.Count; i++)
{
//for (int j = i + 1; j < spectra.Count; j++)
{
//double value = comparer.CompareSpectra(spectra[i], spectra[j]);
//values.Add(value);
Console.WriteLine("{0}", Path.GetFileNameWithoutExtension(files[i]));
// Path.GetFileNameWithoutExtension(files[j]));
DisplaySpectra(spectra[i], .15, newTitle: "MS/MS Spectra - ");
}
}
var baseName = Path.GetFileName(directory);
// Console.WriteLine("{0} - {1}", baseName, values.Average());
// values.ForEach(x => Console.WriteLine("\t{0}", x));
}
public void TestSpectralSimilarityScore(
string pathX, int scanX,
string pathY, int scanY,
SpectralComparison comparerType,
SpectraFilters filterType,
double percent,
double mzTolerance)
{
// Convert relative paths to absolute paths
pathX = GetPath(pathX);
pathY = GetPath(pathY);
var spectrumX = GetSpectrum(pathX, scanX);
var spectrumY = GetSpectrum(pathY, scanY);
var comparer = SpectralComparerFactory.CreateSpectraComparer(comparerType, percent);
var filter = SpectrumFilterFactory.CreateFilter(filterType);
spectrumX.Peaks = filter.Threshold(spectrumX.Peaks, percent);
spectrumY.Peaks = filter.Threshold(spectrumY.Peaks, percent);
spectrumX.Peaks = XYData.Bin(spectrumX.Peaks,
0,
2000,
mzTolerance);
spectrumY.Peaks = XYData.Bin(spectrumY.Peaks,
0,
2000,
mzTolerance);
var value = comparer.CompareSpectra(spectrumX, spectrumY);
var path = Path.GetDirectoryName(pathX);
var plotTitle = string.Format("comparison-{2}-{3}-{0}-{1}_{4:0.000}", scanX, scanY, comparerType, percent,
value);
var pathCompareImage = Path.Combine(path, plotTitle + ".png");
DisplayComparisonPlot(spectrumX, spectrumY, mzTolerance, pathCompareImage, plotTitle);
}
protected static SpectralAnalysis MatchDatasets(SpectralComparison comparerType,
ISpectraProvider readerX,
ISpectraProvider readerY,
SpectralOptions options,
AlignmentDataset datasetX,
AlignmentDataset datasetY,
List <string> names)
{
var peptideReader = PeptideReaderFactory.CreateReader(SequenceFileType.MSGF);
var finder = new SpectralAnchorPointFinder();
var validator = new SpectralAnchorPointValidator();
var comparer = SpectralComparerFactory.CreateSpectraComparer(comparerType);
var filter = SpectrumFilterFactory.CreateFilter(SpectraFilters.TopPercent);
var matches = finder.FindAnchorPoints(readerX,
readerY,
comparer,
filter,
options);
var peptidesX = peptideReader.Read(datasetX.PeptideFile);
var peptidesY = peptideReader.Read(datasetY.PeptideFile);
validator.ValidateMatches(matches,
peptidesX,
peptidesY,
options);
var analysis = new SpectralAnalysis
{
DatasetNames = names,
Matches = matches,
Options = options
};
return(analysis);
}
/// <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);
}
public SpectralAligner()
{
Options = new SpectralOptions();
Filter = SpectrumFilterFactory.CreateFilter(SpectraFilters.TopPercent);
SpectralComparer = SpectralComparerFactory.CreateSpectraComparer(SpectralComparison.CosineDotProduct);
}