public static void Train(string outFileName, List <MSMSSpectrum> spectra, Tolerance tolerance, int maxCharge)
{
var spectraTmp = new List <MSMSSpectrum>();
foreach (var spectrum in spectra)
{
if (spectrum.Charge <= maxCharge)
{
spectraTmp.Add(spectrum);
}
}
spectra = spectraTmp;
Console.WriteLine("Number of spectra: " + spectra.Count);
var ionTypeTrainer = new IonTypeTrainerUsingMgfFile(spectra, tolerance, maxCharge);
ionTypeTrainer.Train();
/*Console.WriteLine("Number of ion types: " + ionTypeTrainer.IonTypes.Count);
* foreach (var groupParameter in ionTypeTrainer.IonTypes.Keys)
* {
* Console.WriteLine(groupParameter.ToFileString());
* foreach (var ionType in ionTypeTrainer.IonTypes[groupParameter])
* {
* Console.WriteLine("\t" + ionType);
* }
* }*/
Console.WriteLine("Ion Type training Done");
// return;
var isotopeIntensityCorrelationScoreTrainerT = new IsotopeIntensityCorrelationScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
isotopeIntensityCorrelationScoreTrainerT.Train();
WriteIonTypes(outFileName, ionTypeTrainer);
Console.WriteLine("Isotope Training Done (Target)");
var ratioScoreTrainerT = new RatioScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
ratioScoreTrainerT.Train();
Write(outFileName, ionTypeTrainer, isotopeIntensityCorrelationScoreTrainerT, ratioScoreTrainerT, false);
Console.WriteLine("Ion Ratio Training Done (Target)");
foreach (var spectrum in spectra)
{
spectrum.Annotation = GetReversedSequence(spectrum.Annotation);
}
var isotopeIntensityCorrelationScoreTrainerD = new IsotopeIntensityCorrelationScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
isotopeIntensityCorrelationScoreTrainerD.Train();
Console.WriteLine("Isotope Training Done (Decoy)");
var ratioScoreTrainerD = new RatioScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
ratioScoreTrainerD.Train();
Write(outFileName, ionTypeTrainer, isotopeIntensityCorrelationScoreTrainerD, ratioScoreTrainerD, true);
Console.WriteLine("Ion Ratio Training Done (Decoy)");
}
private static void Write(string outFileName, IonTypeTrainerUsingMgfFile ionTypeTrainer, IsotopeIntensityCorrelationScoreTrainerUsingMgfFile isotopeIntensityCorrelationScoreTrainer, RatioScoreTrainerUsingMgfFile ratioScoreTrainer, bool isDecoy)
{
var writer = new StreamWriter(outFileName, true);
if(isDecoy) writer.WriteLine("###DECOY");
var isotope = isotopeIntensityCorrelationScoreTrainer.IsotopeIntensityCorrProbDictionary;
writer.Write("##ISOTOPE\n");
foreach (var groupParameter in isotope.Keys)
{
writer.Write("#G\t" + groupParameter + "\n");
var s = isotope[groupParameter];
var si = ionTypeTrainer.IonTypes[groupParameter];
foreach (var ionType in s.Keys)
{
writer.Write("#I\t" + si.IndexOf(ionType) + "\n");
var t = s[ionType];
foreach (var k in t.Keys)
{
writer.Write(k+","+t[k]+"\t");
}
writer.Write("\n");
}
}
var ratio = ratioScoreTrainer.RatioProbDictionary;
writer.Write("##RATIO\n");
foreach (var groupParameter in ratio.Keys)
{
writer.Write("#G\t" + groupParameter + "\n");
var s = ratio[groupParameter];
var si = ionTypeTrainer.IonTypes[groupParameter];
foreach (var ionTypes in s.Keys)
{
writer.Write("#I");
writer.Write("\t" + si.IndexOf(ionTypes.Item1) + "\t" + si.IndexOf(ionTypes.Item2));
writer.Write("\n");
var t = s[ionTypes];
foreach (var k in t.Keys)
{
writer.Write(k + "," + t[k] + "\t");
}
writer.Write("\n");
}
}
writer.Write("##NOION\n");
var noIon = ratioScoreTrainer.NoIonProbDictionary;
foreach (var groupParameter in noIon.Keys)
{
writer.Write("#G\t" + groupParameter + "\n");
writer.Write(noIon[groupParameter]+"\n");
}
writer.Close();
}
public static void Train(string outFileName, List<MSMSSpectrum> spectra, Tolerance tolerance, int maxCharge)
{
var spectraTmp = new List<MSMSSpectrum>();
foreach (var spectrum in spectra)
{
if (spectrum.Charge <= maxCharge) spectraTmp.Add(spectrum);
}
spectra = spectraTmp;
Console.WriteLine("Number of spectra: " + spectra.Count);
var ionTypeTrainer = new IonTypeTrainerUsingMgfFile(spectra, tolerance, maxCharge);
ionTypeTrainer.Train();
/*Console.WriteLine("Number of ion types: " + ionTypeTrainer.IonTypes.Count);
foreach (var groupParameter in ionTypeTrainer.IonTypes.Keys)
{
Console.WriteLine(groupParameter.ToFileString());
foreach (var ionType in ionTypeTrainer.IonTypes[groupParameter])
{
Console.WriteLine("\t" + ionType);
}
}*/
Console.WriteLine("Ion Type training Done");
// return;
var isotopeIntensityCorrelationScoreTrainerT = new IsotopeIntensityCorrelationScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
isotopeIntensityCorrelationScoreTrainerT.Train();
WriteIonTypes(outFileName, ionTypeTrainer);
Console.WriteLine("Isotope Training Done (Target)");
var ratioScoreTrainerT = new RatioScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
ratioScoreTrainerT.Train();
Write(outFileName, ionTypeTrainer, isotopeIntensityCorrelationScoreTrainerT, ratioScoreTrainerT, false);
Console.WriteLine("Ion Ratio Training Done (Target)");
foreach (var spectrum in spectra)
{
spectrum.Annotation = GetReversedSequence(spectrum.Annotation);
}
var isotopeIntensityCorrelationScoreTrainerD = new IsotopeIntensityCorrelationScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
isotopeIntensityCorrelationScoreTrainerD.Train();
Console.WriteLine("Isotope Training Done (Decoy)");
var ratioScoreTrainerD = new RatioScoreTrainerUsingMgfFile(spectra, ionTypeTrainer.IonTypes, tolerance, maxCharge);
ratioScoreTrainerD.Train();
Write(outFileName, ionTypeTrainer, isotopeIntensityCorrelationScoreTrainerD, ratioScoreTrainerD, true);
Console.WriteLine("Ion Ratio Training Done (Decoy)");
}
private static void Write(string outFileName, IonTypeTrainerUsingMgfFile ionTypeTrainer, IsotopeIntensityCorrelationScoreTrainerUsingMgfFile isotopeIntensityCorrelationScoreTrainer, RatioScoreTrainerUsingMgfFile ratioScoreTrainer, bool isDecoy)
{
var writer = new StreamWriter(outFileName, true);
if (isDecoy)
{
writer.WriteLine("###DECOY");
}
var isotope = isotopeIntensityCorrelationScoreTrainer.IsotopeIntensityCorrProbDictionary;
writer.Write("##ISOTOPE\n");
foreach (var groupParameter in isotope.Keys)
{
writer.Write("#G\t" + groupParameter + "\n");
var s = isotope[groupParameter];
var si = ionTypeTrainer.IonTypes[groupParameter];
foreach (var ionType in s.Keys)
{
writer.Write("#I\t" + si.IndexOf(ionType) + "\n");
var t = s[ionType];
foreach (var k in t.Keys)
{
writer.Write(k + "," + t[k] + "\t");
}
writer.Write("\n");
}
}
var ratio = ratioScoreTrainer.RatioProbDictionary;
writer.Write("##RATIO\n");
foreach (var groupParameter in ratio.Keys)
{
writer.Write("#G\t" + groupParameter + "\n");
var s = ratio[groupParameter];
var si = ionTypeTrainer.IonTypes[groupParameter];
foreach (var ionTypes in s.Keys)
{
writer.Write("#I");
writer.Write("\t" + si.IndexOf(ionTypes.Item1) + "\t" + si.IndexOf(ionTypes.Item2));
writer.Write("\n");
var t = s[ionTypes];
foreach (var k in t.Keys)
{
writer.Write(k + "," + t[k] + "\t");
}
writer.Write("\n");
}
}
writer.Write("##NOION\n");
var noIon = ratioScoreTrainer.NoIonProbDictionary;
foreach (var groupParameter in noIon.Keys)
{
writer.Write("#G\t" + groupParameter + "\n");
writer.Write(noIon[groupParameter] + "\n");
}
writer.Close();
}
