public Pattern Calculate(FormMap fm, double limit, long charge)
{
Pattern tmp = new Pattern();
Pattern result = new Pattern();
result.Add(new Peak()
{
Mz = 0.0, Intensity = 1.0
});
foreach (var i in fm)
{
int atom_index = i.Key;
SuperAtomList sal = sad[atom_index];
int n = i.Value;
int j = 0;
while (n > 0)
{
int sz = sal.Count;
if (j == sz)
{
sal.Add(new Pattern());
convolute_basic(sal[j], sal[j - 1], sal[j - 1]);
Prune(sal[j], limit);
}
if ((n & 1) == 1)
{ // digit is 1, convolute result
convolute_basic(tmp, result, sal[j]);
Prune(tmp, limit);
result.Clear();
result.AddRange(tmp);
}
n >>= 1;
j++;
}
}
// take charge into account
foreach (var p in result)
{
if (charge > 0)
{
p.Mz = p.Mz / Math.Abs(charge) - ELECTRON_MASS;
}
else if (charge < 0)
{
p.Mz = p.Mz / Math.Abs(charge) + ELECTRON_MASS;
}
}
if (result.Count == 0)
{
throw new Exception("Calculate profile failed");
}
return(result);
}
