private static GraphML_List <MsMsPeak> Deisotopebkp(GraphML_List <MsMsPeak> peaks, int maxCharge, MassTolerance isotopicMzTolerance)
{
GraphML_List <MsMsPeak> new_peaks = new GraphML_List <MsMsPeak>(peaks);
peaks.Sort(MsMsPeak.AscendingMzComparison);
for (int lowMassIndex = 0; lowMassIndex < new_peaks.Count - 1; lowMassIndex++)
{
if (new_peaks[lowMassIndex].Charge > 0)
{
int toRemove = -1;
double bestMassError = isotopicMzTolerance.Value;
double aim = Numerics.IsotopicMassShift(1, new_peaks[lowMassIndex].Charge) + new_peaks[lowMassIndex].MZ;
int potentialIsotopeIndex = lowMassIndex + 1;
while (potentialIsotopeIndex < new_peaks.Count && new_peaks[potentialIsotopeIndex].MZ < aim + bestMassError)
{
if (new_peaks[lowMassIndex].Intensity > new_peaks[potentialIsotopeIndex].Intensity)
{
double massError = Math.Abs(Numerics.CalculateMassError(new_peaks[potentialIsotopeIndex].MZ, aim, isotopicMzTolerance.Units));
if (massError < bestMassError)
{
bestMassError = massError;
toRemove = potentialIsotopeIndex;
}
}
potentialIsotopeIndex++;
}
if (toRemove > 0)
{
new_peaks[lowMassIndex].Intensity += new_peaks[toRemove].Intensity;
new_peaks.RemoveAt(toRemove);
}
}
}
return(new_peaks);
}
private static GraphML_List <MsMsPeak> AssignChargeStatesAndDeisotope(GraphML_List <MsMsPeak> peaks, int maxCharge, MassTolerance isotopicMzTolerance)
{
GraphML_List <MsMsPeak> new_peaks = new GraphML_List <MsMsPeak>(peaks);
//peaks.Sort(MSPeak.AscendingMzComparison);
int[] bestIsotopes = new int[4];
int[] currentIsotopes = new int[4];
for (int lowMassIndex = 0; lowMassIndex < new_peaks.Count - 1; lowMassIndex++)
{
double bestChargeScore = 0;
int bestCharge = 0;
bestIsotopes[0] = 0; bestIsotopes[1] = 0; bestIsotopes[2] = 0; bestIsotopes[3] = 0;
for (int charge = maxCharge; charge > 0; charge--)
{
currentIsotopes[0] = 0; currentIsotopes[1] = 0; currentIsotopes[2] = 0; currentIsotopes[3] = 0;
double score = 0;
int potentialIsotopeIndex = lowMassIndex + 1;
for (int isotope = 1; isotope <= 4; isotope++)
{
double bestMassError = isotopicMzTolerance.Value;
double aim = Numerics.IsotopicMassShift(isotope, charge) + new_peaks[lowMassIndex].MZ;
while (potentialIsotopeIndex < new_peaks.Count && new_peaks[potentialIsotopeIndex].MZ < aim + bestMassError)
{
if (new_peaks[lowMassIndex].Intensity > new_peaks[potentialIsotopeIndex].Intensity)
{
double massError = Math.Abs(Numerics.CalculateMassError(new_peaks[potentialIsotopeIndex].MZ, aim, isotopicMzTolerance.Units));
if (massError < bestMassError)
{
bestMassError = massError;
currentIsotopes[isotope - 1] = potentialIsotopeIndex;
}
}
potentialIsotopeIndex++;
}
score += isotopicMzTolerance.Value - bestMassError;
if (score == 0)
{
break;
}
;
}
if (score > bestChargeScore)
{
bestIsotopes[0] = currentIsotopes[0];
bestIsotopes[1] = currentIsotopes[1];
bestIsotopes[2] = currentIsotopes[2];
bestIsotopes[3] = currentIsotopes[3];
bestChargeScore = score;
bestCharge = charge;
}
}
new_peaks[lowMassIndex].Charge = bestCharge;
for (int i = 3; i >= 0; i--)
{
if (bestIsotopes[i] > 0)
{
new_peaks[lowMassIndex].Intensity += new_peaks[bestIsotopes[i]].Intensity;
new_peaks.RemoveAt(bestIsotopes[i]);
}
}
}
return(new_peaks);
}