private void Normalize()
{
foreach (var groupParameter in GroupParameter.GetAllFragmentGroupParameters(_maxCharge))
{
if (!RatioProbDictionary.ContainsKey(groupParameter))
{
RatioProbDictionary[groupParameter] = new Dictionary <Tuple <IonType, IonType>, Dictionary <int, double> >();
}
if (!_allNumberDictionary.ContainsKey(groupParameter))
{
_allNumberDictionary[groupParameter] = 1.0;
}
if (!NoIonProbDictionary.ContainsKey(groupParameter))
{
NoIonProbDictionary[groupParameter] = 1.0;
}
NoIonProbDictionary[groupParameter] = NoIonProbDictionary[groupParameter] /
Math.Max(_allNumberDictionary[groupParameter], 1.0);
var sr = RatioProbDictionary[groupParameter];
foreach (var ionType in _ionTypes[groupParameter])
{
foreach (var ionType2 in _ionTypes[groupParameter])
{
var sum = 0.0;
var ionTypes = new Tuple <IonType, IonType> (ionType, ionType2);
if (!sr.ContainsKey(ionTypes))
{
sr[ionTypes] = new Dictionary <int, double>();
}
var ssr = sr[ionTypes];
foreach (var ratio in FeatureEdge.GetAllRatioIndices())
{
if (!ssr.ContainsKey(ratio))
{
ssr[ratio] = 1.0;
}
sum = sum + ssr[ratio];
}
var keys = new List <int> (ssr.Keys);
foreach (var ratio in keys)
{
ssr[ratio] = Math.Max(Double.MinValue, ssr[ratio] / sum);
}
}
}
}
}
public void Train()
{
foreach (var spectrum in _spectra)
{
var annotation = spectrum.Annotation;
for (var cutNumber = 1; cutNumber < annotation.Count; cutNumber++)
{
var groupParameter = spectrum.GetGroupParameter(annotation, cutNumber);
var ionTypes = _ionTypes[groupParameter];
var explainedPeaks = spectrum.GetExplainedPeaks(annotation, cutNumber, ionTypes, _tolerance);
if (!RatioProbDictionary.ContainsKey(groupParameter))
{
RatioProbDictionary[groupParameter] = new Dictionary <Tuple <IonType, IonType>, Dictionary <int, double> >();
}
if (!_allNumberDictionary.ContainsKey(groupParameter))
{
_allNumberDictionary[groupParameter] = 0.0;
}
if (!NoIonProbDictionary.ContainsKey(groupParameter))
{
NoIonProbDictionary[groupParameter] = 0.0;
}
_allNumberDictionary[groupParameter] = _allNumberDictionary[groupParameter] + 1;
var s = RatioProbDictionary[groupParameter];
/*var writeNoIon = true;
* foreach (var peak in explainedPeaks)
* {
* if (peak.Intensity > 0)
* {
* writeNoIon = false;
* break;
* }
* }*/
//if (writeNoIon)
NoIonProbDictionary[groupParameter] = NoIonProbDictionary[groupParameter] + 1;
for (var i = 0; i < ionTypes.Count; i++)
{
for (var j = 0; j < ionTypes.Count; j++)
{
//if (i == j) continue; //TODO THis is for precursor but there is not precursor ion in mgf file..
var ionPair = new Tuple <IonType, IonType>(ionTypes[i], ionTypes[j]);
if (!s.ContainsKey(ionPair))
{
s[ionPair] = new Dictionary <int, double>();
}
var t = s[ionPair];
//if (explainedPeaks[i].Intensity <= 0 || explainedPeaks[j].Intensity <= 0)
//{
// continue;
//}
var ratio = FeatureEdge.GetRatioIndex(explainedPeaks[i].Intensity, explainedPeaks[j].Intensity);
if (!t.ContainsKey(ratio))
{
t[ratio] = 0;
}
t[ratio] = t[ratio] + 1;
}
}
}
}
Normalize();
Console.WriteLine(RatioProbDictionary.Count);
}