public QMatch(QMatch Match)
{
ApexRT = Match.ApexRT;
ApexScore = Match.ApexScore;
ApexMZ = Match.ApexMZ;
ApexIndex = Match.ApexIndex;
Score = Match.Score;
RTDisp = Match.RTDisp;
IsotopeRatio = Match.IsotopeRatio;
MaxConv = Match.MaxConv;
Shift = Match.Shift;
if (Match.MSMatches != null)
{
MSMatches = new List <MSMatch>();
MSMatch MS;
for (int i = 0; i < Match.MSMatches.Count; i++)
{
MS = new MSMatch(Match.MSMatches[i]);
MSMatches.Add(MS);
}
}
else
{
MSMatches = null;
}
}
public MSMatch FindMatchwithCharges(int Scan, double MZ, int Charge, double LowMZ, double HighMZ)
{
//double LowMZ = (MZ * Charge + (float) 1.007277) / (Charge + 1);
//double HighMZ = (MZ * Charge - 1.007277) / (Charge - 1);
MSMatch First = FindMatch(Scan, MZ, Charge);
if (First.Score == 0.0 || (First.SecondIsotope == 0.0 && !Program.Processor.MetaProfile))
{
return(First);
}
MSMatch Ret;
if (Charge > 1)
{
Ret = FindMatch(Scan, HighMZ, Charge - 1);
if (Ret.Score != 0.0 && (Ret.SecondIsotope > 0.0 || Program.Processor.MetaProfile))
{
First.LowerCharges = Ret;
}
}
Ret = FindMatch(Scan, LowMZ, Charge + 1);
if (Ret.Score != 0.0 && (Ret.SecondIsotope > 0.0 || Program.Processor.MetaProfile))
{
First.UpperCharges = Ret;
}
return(First);
}
public MSMatch(MSMatch MS)
{
Score = MS.Score;
MZ = MS.MZ;
RT = MS.RT;
FirstIsotope = MS.FirstIsotope;
SecondIsotope = MS.SecondIsotope;
TimeCoeff = MS.TimeCoeff;
if (LowerCharges != null)
{
LowerCharges = new MSMatch(MS.LowerCharges);
}
else
{
LowerCharges = null;
}
if (UpperCharges != null)
{
UpperCharges = new MSMatch(MS.UpperCharges);
}
else
{
UpperCharges = null;
}
}
public MSMatch FindMatch(int Scan, double MZ, int Charge)
{
MSMatch ret = new MSMatch();
ret.TimeCoeff = RTCorrection?TimeCoefs[Scan]:1;
RawData Peaks = RawSpectra[ms2index[Scan]];
MZData FirstPeak = Peaks.FindBiggestPeak(MZ, MassError);
if (hasPreviousIsotope(Peaks, FirstPeak, Charge)) //skip this mass if Seq turns out Seq's a part of another peak
{
return(ret);
}
ret.FirstIsotope = FirstPeak.Intensity;
if (Program.Processor.MetaProfile)
{
ret.Score = ret.FirstIsotope;
ret.SecondIsotope = 0.0;
}
else
{
ret.SecondIsotope = CheckIsotope(Peaks, FirstPeak.Mass, Charge, 1);
ret.Score = ret.FirstIsotope + ret.SecondIsotope;
if (ret.SecondIsotope != 0.0)
{
ret.Score += CheckIsotope(Peaks, FirstPeak.Mass, Charge, 2);
}
}
ret.MZ = FirstPeak.Mass;
ret.RT = Peaks.RT;
if (RTCorrection)
{
ret.Score *= TimeCoefs[Scan];
}
if (ret.SecondIsotope == 0.0 && !Program.Processor.MetaProfile)
{
ret.Score = 0.0;
}
return(ret);
}
public QMatch FindBestScore(double MZ, int Charge, double IsoRatio, double MinRT, double MaxRT)
{
MSMatch First = null, Best = null;
QMatch Res = new QMatch();
Res.Clean();
Res.MSMatches = new List <MSMatch>();
double FirstIso = 0.0, SecondIso = 0.0;
double BestScore = 0.0, fs = 0.0;
int BestIndex = 0;
int Scan = 0;
double AveRT = (MinRT + MaxRT) / 2;
RawFile.ScanNumFromRT(AveRT, ref Scan);
Scan = ms2index[Scan];
//отступаем до минимального времени RT в массиве спектров
double LowMZ = (MZ * Charge + (float)1.007277) / (Charge + 1);
double HighMZ;
if (Charge > 1)
{
HighMZ = (MZ * Charge - 1.007277) / (Charge - 1);
}
else
{
HighMZ = 0.0;
}
while (Scan > 0 && RawSpectra[Scan].RT >= MinRT)
{
Scan = IndexRev[Scan];
}
//цикл поиска лучшего
while (Scan != -1 && RawSpectra[Scan].RT <= MaxRT)
{
if (Program.Processor.Deconvolution) //прихватываем другие зарядовые состояния
{
First = FindMatchwithCharges(Scan, MZ, Charge, LowMZ, HighMZ);
}
else
{
First = FindMatch(Scan, MZ, Charge);
}
//если не найден сам пик или его первый изотоп - сбрасываем
if (First.Score == 0.0 || (First.SecondIsotope == 0.0 && !Program.Processor.MetaProfile))
{
Scan = IndexDir[Scan];
continue;
}
FirstIso = First.FirstIsotope +
(First.UpperCharges == null ? 0 : First.UpperCharges.FirstIsotope) +
(First.LowerCharges == null ? 0 : First.LowerCharges.FirstIsotope);
SecondIso = First.SecondIsotope +
(First.UpperCharges == null ? 0 : First.UpperCharges.SecondIsotope) +
(First.LowerCharges == null ? 0 : First.LowerCharges.SecondIsotope);
fs = SecondIso / FirstIso;
double CurrentScore = First.Score +
(First.UpperCharges == null ? 0 : First.UpperCharges.Score) +
(First.LowerCharges == null ? 0 : First.LowerCharges.Score);
//пик может распространяться за границы, но апекс должен быть внутри
if (CurrentScore > BestScore && ((fs > IsoRatio * 0.5 && fs < IsoRatio * 2) || Program.Processor.MetaProfile))
{
BestScore = CurrentScore;
BestIndex = Scan;
Best = First;
}
//переходим к следующему full-ms
Scan = IndexDir[Scan];
}
if (BestScore == 0.0)
{
return(null);
}
//если хоть что-то нашли
//добавляем наибольшее
LowMZ = (Best.MZ * Charge + (float)1.007277) / (Charge + 1);
if (Charge > 1)
{
HighMZ = (MZ * Charge - 1.007277) / (Charge - 1);
}
else
{
HighMZ = 0.0;
}
Res.ApexRT = Best.RT;
Res.MSMatches.Add(Best);
//берем сплошную область вокруг Best - вперед
for (Scan = IndexDir[BestIndex]; Scan > 0; Scan = IndexDir[Scan])
{
if (Program.Processor.Deconvolution)
{ //прихватываем другие зарядовые состояния
First = FindMatchwithCharges(Scan, Best.MZ, Charge, LowMZ, HighMZ);
}
else
{
First = FindMatch(Scan, Best.MZ, Charge);
}
if (First.Score == 0.0 || (First.SecondIsotope == 0.0 && !Program.Processor.MetaProfile))
{
Res.MSMatches.Add(First);
break;
}
//ограничение по уровню разрешения пика
if (Program.Processor.MetaProfile && First.Score <= Best.Score * (Program.Processor.RTRes / 100.0))
{
break;
}
//ограничение по ширине пика
if (Program.Processor.MetaProfile && Res.MSMatches[Res.MSMatches.Count - 1].RT - Res.MSMatches[0].RT > Program.Processor.MaxRTWidth)
{
return(null);
}
fs = First.SecondIsotope / First.FirstIsotope;
//включаем здесь контроль по соотношению изотопов
//if (fs < IsoRatio*0.5 || fs > IsoRatio * 2 ){
// break;
//}
//пик может распространяться за границы, но апекс должен быть внутри - по крайней мере для метаболитов
if (Program.Processor.MetaProfile && First.RT > MaxRT && First.Score > Best.Score * 1.1)
{
return(null);
}
Res.MSMatches.Add(First);
}
//берем сплошную область вокруг Best - назад
for (Scan = IndexRev[BestIndex]; Scan > 0; Scan = IndexRev[Scan])
{
if (Program.Processor.Deconvolution) //прихватываем другие зарядовые состояния
{
First = FindMatchwithCharges(Scan, Best.MZ, Charge, LowMZ, HighMZ);
}
else
{
First = FindMatch(Scan, Best.MZ, Charge);
}
if (First.Score == 0.0 || (First.SecondIsotope == 0.0 && !Program.Processor.MetaProfile))
{
Res.MSMatches.Insert(0, First);
break;
}
//ограничение по уровню разрешения пика
if (Program.Processor.MetaProfile && First.Score <= Best.Score * (Program.Processor.RTRes / 100.0))
{
break;
}
//ограничение по ширине пика
if (Program.Processor.MetaProfile && Res.MSMatches[Res.MSMatches.Count - 1].RT - Res.MSMatches[0].RT > Program.Processor.MaxRTWidth)
{
return(null);
}
fs = First.SecondIsotope / First.FirstIsotope;
//включаем здесь контроль по соотношению изотопов
//if (fs < IsoRatio*0.5 || fs > IsoRatio * 2 ){
// break;
//}
Res.MSMatches.Insert(0, First);
//пик может распространяться за границы, но апекс должен быть внутри - по крайней мере для метаболитов
if (Program.Processor.MetaProfile && First.RT < MinRT && First.Score > Best.Score * 1.1)
{
return(null);
}
}
if (Program.Processor.MetaProfile && Res.MSMatches[Res.MSMatches.Count - 1].RT - Res.MSMatches[0].RT < Program.Processor.MinRTWidth)
{
return(null);
}
Res.Estimate(IsoRatio);
Res.CleanUp();
return(Res);
}