public static Spectra Import(string filenameMSMS, string filenameTracks, DBOptions dbOptions)
{
Spectra spectra = new Spectra();
vsCSV csv = new vsCSV(filenameMSMS);
if (csv.LINES_LIST.Count == 0 || csv.LINES_LIST[0].CompareTo(ProductSpectrum.TITLE) != 0)
{
return(null);
}
for (int i = 1; i < csv.LINES_LIST.Count; i++)
{
string[] splits = csv.LINES_LIST[i].Split(vsCSV._Generic_Separator);
double mz = double.Parse(splits[3]);
int charge = int.Parse(splits[5]);
int nbPeaks = int.Parse(splits[9]);
GraphML_List <MsMsPeak> peaks = new GraphML_List <MsMsPeak>(nbPeaks);
i++;
for (int j = 0; j < nbPeaks; i++, j++)
{
try
{
string[] splitPeaks = csv.LINES_LIST[i].Split('\t');
if (splitPeaks.Length > 2)
{
peaks.Add(new MsMsPeak(double.Parse(splitPeaks[0]), double.Parse(splitPeaks[1]), int.Parse(splitPeaks[2])));
}
else
{
peaks.Add(new MsMsPeak(double.Parse(splitPeaks[0]), double.Parse(splitPeaks[1]), 0));
}
}
catch (Exception)
{
dbOptions.ConSole.WriteLine("Error parsing line : " + csv.LINES_LIST[i]);
}
}
spectra.AddMSMS(new ProductSpectrum(int.Parse(splits[0]), double.Parse(splits[1]), splits[2], mz, double.Parse(splits[4]), charge, Proteomics.Utilities.Numerics.MassFromMZ(mz, charge), peaks, double.Parse(splits[8]), double.Parse(splits[10]), double.Parse(splits[11])));
}
if (!string.IsNullOrEmpty(filenameTracks))
{
spectra.tracks = Tracks.Import(filenameTracks, dbOptions);
}
return(spectra);
}
