public static PSM getPSM_BySpectra(Spectra spec)
{
PSM psm = new PSM(0, spec.Title, "", "", 0.0, spec.Pepmass, 0.0, 0.0, 0.0, 0.0, ' ', "0", true, "", 0);
psm.Charge = spec.Charge;
psm.Spectra_mass = spec.Pepmass * spec.Charge - Config_Help.massZI * (spec.Charge - 1);
return(psm);
}
private void translateCharge(int j, Spectra out_spectra, int charge)
{
double mass = this.Peaks[j].Mass;
mass *= charge;
mass -= ((charge - 1) * Config_Help.massZI);
PEAK peak = new PEAK(mass, this.Peaks[j].Intensity);
out_spectra.Peaks.Add(peak);
}
private bool deisotpeChargeHCD(int j, Spectra out_spectra, int charge, List <int> PeaksTag, double ppm_me, double da_me, bool isNeed_translate = true)
{
double deviation = Config_Help.mass_ISO / charge;
double lfCurrentVal = this.Peaks[j].Mass + deviation;
double d1 = calc(ppm_me, da_me, this.Peaks[j].Mass);
SortedSet <int> PeakR = new SortedSet <int>();
bool tag = false;
for (int k = j + 1; k < this.Peaks.Count; ++k)
{
double d2 = calc(ppm_me, da_me, this.Peaks[k].Mass);
double d = (d1 + d2) / 2;
if (this.Peaks[k].Mass >= lfCurrentVal - d && this.Peaks[k].Mass <= lfCurrentVal + d)
{
lfCurrentVal = this.Peaks[k].Mass + deviation;
d1 = d2;
PeaksTag[k] = charge;
PeaksTag[j] = charge;
PeakR.Add(k);
PeakR.Add(j);
tag = true;
}
else if (this.Peaks[k].Mass > lfCurrentVal + d)
{
break;
}
}
if (tag)
{
bool flag = false;
foreach (int i in PeakR)
{
if (flag && this.Peaks[i].Intensity < this.Peaks[PeakR.First()].Intensity)
{
continue;
}
if (isNeed_translate)
{
translateCharge(i, out_spectra, charge);
}
else
{
translateCharge(i, out_spectra, 1);
}
flag = true;
}
return(true);
}
return(false);
}
private void delete_isotope(double ppm_me, double da_me, bool isNeed_translate = true) //去同位素峰并转化成单电荷
{
Spectra out_spectra = new Spectra();
List <int> PeaksTag = new List <int>();
for (int j = 0; j < this.Peaks.Count; ++j)
{
PeaksTag.Add(0);
}
for (int j = 0; j < this.Peaks.Count; ++j)
{
if (PeaksTag[j] > 0)
{
continue;
}
for (int c = this.Charge; c >= 1; --c)
{
if (deisotpeChargeHCD(j, out_spectra, c, PeaksTag, ppm_me, da_me, isNeed_translate))
{
break;
}
}
if (PeaksTag[j] == 0)
{
if (isNeed_translate)
{
translateCharge(j, out_spectra, 1);
translateCharge(j, out_spectra, 2);
}
else
{
translateCharge(j, out_spectra, 1);
}
}
}
List <PEAK> peaks = new List <PEAK>(out_spectra.Peaks);
peaks.Sort();
this.Peaks = new ObservableCollection <PEAK>(peaks);
}
public Pnovo_Help(string mgf_path, string output_path, Spectra spectra)
{
this.mgf_path = mgf_path;
this.output_path = output_path;
this.spectra = spectra;
}