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);
}
public EmassCalculator(string filename)
{
if (!File.Exists(filename))
{
throw new FileNotFoundException(filename);
}
IsotopicMap = new ElemMap();
using (StreamReader f = new StreamReader(filename))
{
sad.Clear();
IsotopicMap.Clear();
string line;
int elemindex = 0;
int state = 0;
while ((line = f.ReadLine()) != null)
{
string element;
switch (state)
{
case 0: // new element
var m0 = eleReg.Match(line);
element = m0.Groups[1].Value;
IsotopicMap[element] = elemindex;
var pkl = new Pattern();
var sal = new SuperAtomList();
sal.Add(pkl);
sad.Add(sal);
elemindex++;
state = 1;
break;
case 1: // isotope
var m1 = eleReg.Match(line);
if (m1.Success)
{
Peak p = new Peak();
p.Mz = MyConvert.ToDouble(m1.Groups[1].Value);
p.Intensity = MyConvert.ToDouble(m1.Groups[2].Value);
Pattern idist = sad.Last().First();
// fill the gaps in the patterns with zero abundancy peaks
if (idist.Count > 0)
{
double prevmass = idist.Last().Mz;
for (int i = 0; i < (int)(p.Mz - prevmass - 0.5); i++)
{
Peak filler = new Peak();
filler.Mz = DUMMY_MASS;
filler.Intensity = 0;
idist.Add(filler);
}
}
// insert the peak
idist.Add(p);
}
else
{
state = 0;
}
break;
}
}
}
}
