public double CheckIsotope(RawData Peaks, double MZ, int Charge, int Isotope)
{
double TargetMass = MZ + (1.003 / (double)Charge) * (double)Isotope;
MZData Peak = Peaks.FindNearestPeak(TargetMass, MassError);
return(Peak.Intensity);
}
bool hasPreviousIsotope(RawData Peaks, MZData Peak, int Charge)
{
double expectedMass = Peak.Mass - (1.003 / (double)Charge);
MZData Candidate = Peaks.FindBiggestPeak(expectedMass, MassError);
if (Candidate.Mass != 0.0 && Candidate.Intensity > 0.5 * Peak.Intensity)
{
return(true);
}
return(false);
}
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 MZData[] PeakDetect(MZData[] Data ){
PeakDetecting.PeakDetector pd = new PeakDetecting.PeakDetector();
PeakDetecting.peakinside[] Peaks = new PeakDetecting.peakinside[1];
pd.PeaksDetecting(ref Data, ref Peaks);
MZData[] OutData = new MZData[Peaks.GetLength(0)];
for (int i = 0 ; i < Peaks.GetLength(0) ; i++){
OutData[i].Intensity = Peaks[i].Value;
OutData[i].Mass = Peaks[i].Center;
}
return OutData;
}*/
public MZData[] Centroid(MZData[] Data,int Len, bool StickMode /* former "in" */)
{
int total = 0, u;
int o = 0, i = 0, count = Len;
double sumIi, sumI, last = 0.0;
double du = 0.0;
bool goingdown = false;
MZData[] OutData;
if (StickMode) {
//считаем пока не начнутся нули или пока следующий не станет меньше помассе
for ( i = 1 ; i<count ; i++){
if (Data[i].Mass < Data[i-1].Mass || Data[i].Mass == 0){
break;
}
}
OutData = new MZData[i];
count = i;
for (i=0; i<count ; i++){
OutData[i].Intensity = Data[i].Intensity;
OutData[i].Mass = Data[i].Mass;
}
return OutData;
}
//пропуск начальных нулей
while(i < count && Data[i].Intensity == 0.0) ++i;
//считает области больше нуля
while(i < count)
{
while(i < count && Data[i].Intensity != 0.0)
{
if(last > Data[i].Intensity) {
goingdown = true;
}else{
if(goingdown) {
++total;
goingdown = false;
}
}
last = Data[i].Intensity;
++i;
}
last = 0.0;
goingdown = false;
while(i < count && Data[i].Intensity == 0.0)
i++;
total++;
}
//запасает память на подсчитанные области
OutData = new MZData[total];
i = 0; o = 0; total = 0; last = 0.0; goingdown = false;
while(i < count && Data[i].Intensity == 0.0) i++;
while(i < count)
{
sumIi = sumI = 0.0;
o = i -1;
while(i < count && Data[i].Intensity != 0.0){
//если пошло на спад
if(last > Data[i].Intensity) {
goingdown = true;
}else{
if(goingdown) {
u = Convert.ToInt32((sumIi / sumI)/* + 0.5*/);
OutData[total].Intensity = sumI;
OutData[total].Mass = Data[o+u].Mass;
++total;
sumIi = sumI = 0.0;
o = i -1;
goingdown = false;
}
}
sumIi += Data[i].Intensity*(i-o);
sumI += Data[i].Intensity;
last = Data[i].Intensity;
i++;
}
u = Convert.ToInt32((sumIi / sumI) /*+0.5*/ );
du = sumIi / sumI - (double)u;
//интенсивность по интегралу
OutData[total].Intensity = sumI;
//сентроид - по апексу
//OutData[total].Mass = Data[o+u].Mass;
//центроид по центру
OutData[total].Mass = Data[o+u].Mass*(1-du) + Data[o+u+1].Mass*du;
last = 0.0;
goingdown = false;
while(i < count && Data[i].Intensity == 0.0)
i++;
total++;
}
return OutData;
}
/* public MZData[] PeakDetect(MZData[] Data ){
*
* PeakDetecting.PeakDetector pd = new PeakDetecting.PeakDetector();
* PeakDetecting.peakinside[] Peaks = new PeakDetecting.peakinside[1];
* pd.PeaksDetecting(ref Data, ref Peaks);
* MZData[] OutData = new MZData[Peaks.GetLength(0)];
* for (int i = 0 ; i < Peaks.GetLength(0) ; i++){
* OutData[i].Intensity = Peaks[i].Value;
* OutData[i].Mass = Peaks[i].Center;
* }
* return OutData;
* }*/
public MZData[] Centroid(MZData[] Data, int Len, bool StickMode /* former "in" */)
{
int total = 0, u;
int o = 0, i = 0, count = Len;
double sumIi, sumI, last = 0.0;
double du = 0.0;
bool goingdown = false;
MZData[] OutData;
if (StickMode)
{
//считаем пока не начнутся нули или пока следующий не станет меньше помассе
for (i = 1; i < count; i++)
{
if (Data[i].Mass < Data[i - 1].Mass || Data[i].Mass == 0)
{
break;
}
}
OutData = new MZData[i];
count = i;
for (i = 0; i < count; i++)
{
OutData[i].Intensity = Data[i].Intensity;
OutData[i].Mass = Data[i].Mass;
}
return(OutData);
}
//пропуск начальных нулей
while (i < count && Data[i].Intensity == 0.0)
{
++i;
}
//считает области больше нуля
while (i < count)
{
while (i < count && Data[i].Intensity != 0.0)
{
if (last > Data[i].Intensity)
{
goingdown = true;
}
else
{
if (goingdown)
{
++total;
goingdown = false;
}
}
last = Data[i].Intensity;
++i;
}
last = 0.0;
goingdown = false;
while (i < count && Data[i].Intensity == 0.0)
{
i++;
}
total++;
}
//запасает память на подсчитанные области
OutData = new MZData[total];
i = 0; o = 0; total = 0; last = 0.0; goingdown = false;
while (i < count && Data[i].Intensity == 0.0)
{
i++;
}
while (i < count)
{
sumIi = sumI = 0.0;
o = i - 1;
while (i < count && Data[i].Intensity != 0.0)
{
//если пошло на спад
if (last > Data[i].Intensity)
{
goingdown = true;
}
else
{
if (goingdown)
{
u = Convert.ToInt32((sumIi / sumI) /* + 0.5*/);
OutData[total].Intensity = sumI;
OutData[total].Mass = Data[o + u].Mass;
++total;
sumIi = sumI = 0.0;
o = i - 1;
goingdown = false;
}
}
sumIi += Data[i].Intensity * (i - o);
sumI += Data[i].Intensity;
last = Data[i].Intensity;
i++;
}
u = Convert.ToInt32((sumIi / sumI) /*+0.5*/);
du = sumIi / sumI - (double)u;
//интенсивность по интегралу
OutData[total].Intensity = sumI;
//сентроид - по апексу
//OutData[total].Mass = Data[o+u].Mass;
//центроид по центру
OutData[total].Mass = Data[o + u].Mass * (1 - du) + Data[o + u + 1].Mass * du;
last = 0.0;
goingdown = false;
while (i < count && Data[i].Intensity == 0.0)
{
i++;
}
total++;
}
return(OutData);
}
