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 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)
{
return(First);
}
MSMatch Ret;
if (Charge > 1)
{
Ret = FindMatch(Scan, HighMZ, Charge - 1);
if (Ret.Score != 0.0 && Ret.SecondIsotope > 0.0)
{
First.LowerCharges = Ret;
}
}
Ret = FindMatch(Scan, LowMZ, Charge + 1);
if (Ret.Score != 0.0 && Ret.SecondIsotope > 0.0)
{
First.UpperCharges = Ret;
}
return(First);
}
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;
LongESICoef = Match.LongESICoef;
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 void LoadMSMatches(List <QPeptide> Peptides)
{
iLog.Log("Loading Peak Shapes");
iLog.RepProgress(0);
for (int f = 0; f < Peptides[0].Matches.GetLength(0); f++)
{
int FileNumber = FileNumbers[f];
SQLiteCommand Select = new SQLiteCommand(
"Select FileNumber, MascotScan, Charge, Score, MZ, RT, FirstIsotope, SecondIsotope, TimeCoeff " +
String.Format("From MSMatches Where FileNumber = {0} ", FileNumber) +
"Order by MascotScan,RT ", con);
SQLiteDataReader Reader = Select.ExecuteReader();
MSMatch[] Charges = new MSMatch[12];
bool flag = true;
Reader.Read();
iLog.RepProgress(f * 100 / Peptides[0].Matches.GetLength(0));
for (int i = 0; i < Peptides.Count; i++)
{
while (Reader.GetInt32(1) < Peptides[i].MascotScan)
{
flag = Reader.Read();
if (!flag)
{
break;
}
}
if (!flag)
{
break;
}
while (Reader.GetInt32(1) == Peptides[i].MascotScan)
{
for (int j = 0; j < 12; j++)
{
Charges[j] = null;
}
FileNumber = Reader.GetInt32(0);
double RT = Reader.GetDouble(5);
while (Reader.GetInt32(0) == FileNumber &&
Reader.GetInt32(1) == Peptides[i].MascotScan &&
RT == Reader.GetDouble(5))
{
int Charge = Reader.GetInt32(2);
Charges[Charge] = new MSMatch();
Charges[Charge].Score = Reader.GetDouble(3);
Charges[Charge].MZ = Reader.GetDouble(4);
Charges[Charge].RT = Reader.GetDouble(5);
Charges[Charge].FirstIsotope = Reader.GetDouble(6);
Charges[Charge].SecondIsotope = Reader.GetDouble(7);
Charges[Charge].TimeCoeff = Reader.GetDouble(8);
flag = Reader.Read();
if (!flag)
{
break;
}
}
if (Charges[Peptides[i].Charge - 1] != null)
{
Charges[Peptides[i].Charge].LowerCharges = Charges[Peptides[i].Charge - 1];
}
if (Charges[Peptides[i].Charge + 1] != null)
{
Charges[Peptides[i].Charge].LowerCharges = Charges[Peptides[i].Charge + 1];
}
Peptides[i].Matches[f].MSMatches.Add(Charges[Peptides[i].Charge]);
if (!flag)
{
break;
}
}
if (!flag)
{
break;
}
}
}
}
public void LoadMSMatches(List <QPeptide> Peptides)
{
iLog.Log("Loading Peak Shapes");
iLog.RepProgress(0);
int FileNumber;
int BandID = -1;
int SampleID = 0;
if (Bands < 0)
{
FileNumber = FileNumbers.Count;
}
else
{
FileNumber = BandList.GetLength(0) * BandList.GetLength(1);
}
for (int f = 0; f < FileNumber; f++)
{
int FileID;
if (Bands < 0)
{
FileID = FileNumbers[f];
SampleID = f;
}
else
{
FileID = f;
BandID = f / SampleNumber;
SampleID = f % SampleNumber;
}
SQLiteCommand Select = new SQLiteCommand(
"Select FileNumber, MascotScan, Charge, Score, MZ, RT, FirstIsotope, SecondIsotope, TimeCoeff " +
String.Format("From MSMatches Where FileNumber = {0} ", FileID) +
"Order by MascotScan,RT ", con);
SQLiteDataReader Reader = Select.ExecuteReader();
MSMatch[] Charges = new MSMatch[12];
bool flag = true;
Reader.Read();
if (!Reader.HasRows)
{
break;
}
iLog.RepProgress(f, FileNumber);
for (int i = 0; i < Peptides.Count; i++)
{
while (Peptides[i].BandID != BandID)
{
i++;
flag = (i < Peptides.Count);
if (!flag)
{
break;
}
}
if (!flag)
{
break;
}
while (Reader.GetInt32(1) < Peptides[i].MascotScan)
{
flag = Reader.Read();
if (!flag)
{
break;
}
}
if (!flag)
{
break;
}
while (Reader.GetInt32(1) == Peptides[i].MascotScan)
{
for (int j = 0; j < 12; j++)
{
Charges[j] = null;
}
//FileNumber = Reader.GetInt32(0);
double RT = Reader.GetDouble(5);
while (//Reader.GetInt32(0) == FileNumber &&
Reader.GetInt32(1) == Peptides[i].MascotScan &&
RT == Reader.GetDouble(5))
{
int Charge = Reader.GetInt32(2);
Charges[Charge] = new MSMatch();
Charges[Charge].Score = Reader.GetDouble(3);
Charges[Charge].MZ = Reader.GetDouble(4);
Charges[Charge].RT = Reader.GetDouble(5);
Charges[Charge].FirstIsotope = Reader.GetDouble(6);
Charges[Charge].SecondIsotope = Reader.GetDouble(7);
Charges[Charge].TimeCoeff = Reader.GetDouble(8);
flag = Reader.Read();
if (!flag)
{
break;
}
}
if (Charges[Peptides[i].Charge - 1] != null)
{
Charges[Peptides[i].Charge].LowerCharges = Charges[Peptides[i].Charge - 1];
}
if (Charges[Peptides[i].Charge + 1] != null)
{
//порпавить в версии 2.6 - должно быть:
Charges[Peptides[i].Charge].UpperCharges = Charges[Peptides[i].Charge + 1];
}
//Charges[Peptides[i].Charge].LowerCharges = Charges[Peptides[i].Charge+1];
Peptides[i].Matches[SampleID].MSMatches.Add(Charges[Peptides[i].Charge]);
if (!flag)
{
break;
}
}
if (!flag)
{
break;
}
}
}
}
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 (Settings.Default.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)
{
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)
{
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 (Settings.Default.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)
{
Res.MSMatches.Add(First);
break;
}
fs = First.SecondIsotope / First.FirstIsotope;
//включаем здесь контроль по соотношению изотопов
//if (fs < IsoRatio*0.5 || fs > IsoRatio * 2 ){
// break;
//}
Res.MSMatches.Add(First);
}
//берем сплошную область вокруг Best - назад
for (Scan = IndexRev[BestIndex]; Scan > 0; Scan = IndexRev[Scan])
{
if (Settings.Default.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)
{
Res.MSMatches.Add(First);
break;
}
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);
}
Res.Estimate(IsoRatio);
Res.CleanUp();
return(Res);
}
public MSMatch FindMatch(int Scan, double MZ, int Charge)
{
MSMatch ret = new MSMatch();
ret.Score = 0.0;
ret.FirstIsotope = 0.0;
ret.SecondIsotope = 0.0;
ret.TimeCoeff = RTCorrection?TimeCoefs[Scan]:1;
double maxs = 0.0, curs, bestd, tk10low, tk10high;
int i, t;
int cur = ms2index[Scan];
//ворота по массе
double mmi = MZ * ((1000000.0 - Convert.ToDouble(Settings.Default.MassError)) / 1000000.0);
double mma = MZ * ((1000000.0 + Convert.ToDouble(Settings.Default.MassError)) / 1000000.0);
RawData Peaks = RawSpectra[cur];
ret.RT = Peaks.RT;
//Если сразу ясно что мы за пределами поиска
int LowerIndex = FindMassAbove(Peaks, mmi);
int UpperIndex = FindMassBelow(Peaks, mma);
if (UpperIndex == -1 || LowerIndex == -1 || LowerIndex > UpperIndex)
{
return(ret);
}
while (LowerIndex <= UpperIndex) //for all masses that match
{
if (hasPreviousIsotope(Peaks, LowerIndex, Charge)) //skip this mass if Seq turns out Seq's a part of another peak
{
LowerIndex++;
continue;
}
curs = Peaks.Data[LowerIndex].Intensity;
tk10low = 0.0; tk10high = 0.0;
for (i = 1; i < 3; ++i)
{
double maxs2 = Peaks.Data[LowerIndex].Mass + (1.003 / (double)Charge) * (double)i;
double mmi2 = maxs2 * ((1000000.0 - Convert.ToDouble(Settings.Default.MassError)) / 1000000.0);
double mma2 = maxs2 * ((1000000.0 + Convert.ToDouble(Settings.Default.MassError)) / 1000000.0);
int LowerIndex2 = FindMassAbove(Peaks, mmi2);
int UpperIndex2 = FindMassBelow(Peaks, mma2);
if (LowerIndex2 > UpperIndex2 || LowerIndex2 == -1) //ничего не нашли - ничего и не делаем
{
continue;
}
bestd = maxs2;
while (LowerIndex2 < UpperIndex2) //если больше одного - ищем самый близкий к целевой массе
{
if (Math.Abs(maxs2 - Peaks.Data[LowerIndex2].Mass) < bestd)
{
bestd = Math.Abs(maxs2 - Peaks.Data[LowerIndex2].Mass);
t = LowerIndex2;
}
LowerIndex2++;
}
if (i == 1)
{
tk10low = curs;
tk10high = Peaks.Data[LowerIndex2].Intensity;
}
curs += Peaks.Data[LowerIndex2].Intensity;
}
if (maxs < curs)
{
maxs = curs;
ret.Score = curs;
ret.MZ = Peaks.Data[LowerIndex].Mass;
ret.RT = Peaks.RT;
ret.FirstIsotope = tk10low;
ret.SecondIsotope = tk10high;
}
LowerIndex++;
}
if (RTCorrection)
{
ret.Score *= TimeCoefs[Scan];
}
if (ESICorrection)
{
ret.Score = ret.Score / ESICurrents[Scan];
}
if (ret.SecondIsotope == 0.0)
{
ret.Score = 0.0;
}
return(ret);
}