/// <summary>
/// Function to search bigest peak in spectra around MZ mass, interval of search is specified in ppm by Error parameter
/// </summary>
/// <param name="MZ">Mass, to search around of</param>
/// <param name="Error">Interval of +/- ppm to be searched in</param>
/// <returns>If found returns data point, otherwise returns zero data point</returns>
public MZData FindBiggestPeak(double MZ, double Error)
{
double LowerMass = MZPlusPPM(MZ, -Error);
double UpperMass = MZPlusPPM(MZ, Error);
int LowerIndex = FindMassAbove(LowerMass);
int UpperIndex = FindMassBelow(UpperMass);
if (LowerIndex > UpperIndex || LowerIndex == -1) //if nothing if found - return zero data point
{
return(MZData.CreateZero(Scan));
}
double MaxInt = Data[LowerIndex].Intensity;
int MaxIndex = LowerIndex;
LowerIndex++;
while (LowerIndex <= UpperIndex) //if there are more then one data point - return most intensive
{
if (Data[LowerIndex].Intensity > MaxInt)
{
MaxInt = Data[LowerIndex].Intensity;
MaxIndex = LowerIndex;
}
LowerIndex++;
}
return(Data[MaxIndex]);
}
/// <summary>
/// Function to search nearest peak in spectra around MZ mass, interval of search is specified in ppm by Error parameter
/// </summary>
/// <param name="MZ">Mass, to search around of</param>
/// <param name="Error">Interval of +/- ppm to be searched in</param>
/// <returns>If found returns data point, otherwise returns zero data point</returns>
public MZData FindNearestPeak(double MZ, double Error)
{
double LowerMass = MZPlusPPM(MZ, -Error);
double UpperMass = MZPlusPPM(MZ, Error);
int LowerIndex = FindMassAbove(LowerMass);
int UpperIndex = FindMassBelow(UpperMass);
if (LowerIndex > UpperIndex || LowerIndex == -1) //if nothing if found - return zero data point
{
return(MZData.CreateZero(Scan));
}
while (LowerIndex < UpperIndex) //if there are more then one data point - return closest by mass
//Console.WriteLine("Warning: Two peaks at distanse of {0} ppm in scan {1} mass {2}",
// ((Data[LowerIndex].Mass - Data[LowerIndex+1].Mass) * 500000.0) / (Data[LowerIndex].Mass + Data[LowerIndex+1].Mass),
// Scan, Data[LowerIndex].Mass);
{
if (LowerIndex == Data.GetLength(0) - 1 ||
Math.Abs(MZ - Data[LowerIndex].Mass) < Math.Abs(MZ - Data[LowerIndex + 1].Mass))
{
break;
}
LowerIndex++;
}
return(Data[LowerIndex]);
}
/// <summary>
/// Creates zero intesity fake data point
/// That is necessary for chromatograms leading/trailing zeroes and so on
/// </summary>
public static MZData CreateZero(int Scan)
{
MZData Res = new MZData();
Res.Mass = 0.0;
Res.Intensity = 0.0;
Res.Scan = Scan;
return(Res);
}
/* 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;
}
