Spectra.cs

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namespace CandidateSearch.util
{
    public class Spectrum
    {
        public double[] mz { get; }
        public double[] intensity { get; }
        public int scanNumber { get; }
 
        public Spectrum(double[] Mz, double[] Intensity, int ScanNumber) 
        {
            mz = Mz;
            intensity = Intensity;
            scanNumber = ScanNumber;
            Array.Sort(mz, intensity);
        }
 
        public int[] getEncoding(int massRange = 5000, int massMultiplier = 100)
        {
            var encoding = new List<int>();
 
            for (int i = 0; i < mz.Length; i++)
            {
                if (mz[i] < massRange)
                {
                    encoding.Add((int) Math.Round(mz[i] * massMultiplier));
                }
            }
 
            return encoding.Distinct().OrderBy(x => x).ToArray();
        }
    }
 
    public static class MGFReader
    {
        public static List<Spectrum> readMGF(string filename)
        { 
            var MSAMANDA_spectra = MSAMANDA_MGFPARSER.MGFParser.ParseNextSpectra(filename);
 
            var spectra = new List<Spectrum>();
 
            foreach(var spectrum in MSAMANDA_spectra)
            {
                var mz = new List<double>();
                var intensity = new List<double>();
 
                foreach (var peak in spectrum.FragmentsPeaks)
                {
                    mz.Add(peak.Position);
                    intensity.Add(peak.Intensity);
                }
 
                spectra.Add(new Spectrum(mz.ToArray(), intensity.ToArray(), spectrum.ScanNumber));
            }
 
            return spectra;
        }
    }
}