public static Comb.mzI[] calFunction(Comb.mzI[] expData, fitDataStrt fitData)
{
double a = fitData.A;
double b = fitData.alpha;
double c = fitData.B;
Comb.mzI[] fdata = new Comb.mzI[expData.Length];
for (int i = 1; i <= expData.GetUpperBound(0); i++)
{
fdata[i].mz = expData[i].mz;
fdata[i].I = a + b * fdata[i].mz + c * fdata[i].mz * fdata[i].mz;
}
return(fdata);
}
public static fitDataStrt getInitialConditions(fitDataStrt initialConds,
Comb.mzI[] expData,
Comb.mzI[] intensities,
double sn_f,
int charge,
double deltaR)
{
double h0 = getMax(expData, intensities[0].mz + (initialConds.deltaMz - 1) / charge, intensities[0].mz + (initialConds.deltaMz + 1) / charge);
double hmark = getMax(expData, intensities[0].mz + (initialConds.deltaMz + 2 * deltaR - 1) / charge, intensities[0].mz + (initialConds.deltaMz + 2 * deltaR + 1) / charge);
double alpha = initialConds.alpha;
double sigma = initialConds.sigma;
double efficiency = initialConds.f;
double PI = Math.PI;
initialConds.B = hmark / ((1 - alpha) / (Math.Sqrt(2 * PI) * sigma) + alpha / (2 * sigma)) / intensities[0].I;
initialConds.A = h0 / ((1 - alpha) / (Math.Sqrt(2 * PI) * sigma) + alpha / (2 * sigma)) / intensities[0].I;
initialConds.signoise = averagef(expData, sn_f);
return(initialConds);
}
public static fitDataStrt getInitialConditions(fitDataStrt initialConds,
Comb.mzI[] expData,
Comb.mzI[] intensities,
double sn_f,
int charge,
double deltaR,
Resolution res)
{
if (res == Resolution.LOW)
{
double h0 = getMax(expData, intensities[0].mz + (initialConds.deltaMz - 1) / charge, intensities[0].mz + (initialConds.deltaMz + 1) / charge);
double hmark = getMax(expData, intensities[0].mz + (initialConds.deltaMz + 2 * deltaR - 1) / charge, intensities[0].mz + (initialConds.deltaMz + 2 * deltaR + 1) / charge);
double alpha = initialConds.alpha;
double sigma = initialConds.sigma;
double efficiency = initialConds.f;
double PI = Math.PI;
initialConds.B = hmark / ((1 - alpha) / (Math.Sqrt(2 * PI) * sigma) + alpha / (2 * sigma)) / intensities[0].I;
initialConds.A = h0 / ((1 - alpha) / (Math.Sqrt(2 * PI) * sigma) + alpha / (2 * sigma)) / intensities[0].I;
//initialConds.B = hmark / ((1 - alpha) + alpha / (2 * sigma)) / intensities[0].I;
//initialConds.A = h0 / ((1 - alpha) + alpha / (2 * sigma)) / intensities[0].I;
initialConds.signoise = averagef(expData, sn_f);
}
else
{
initialConds.A = 0;
// we just need to know the order of magnitude, so we don't need to know accurately the sum in A and B,
for (int peak = 0; peak < expData.Length; peak++)
{
initialConds.A += expData[peak].I;
}
initialConds.A = initialConds.A / 2;
initialConds.B = initialConds.A;
}
return(initialConds);
}
/// <summary>
/// Calculates the isotopic envelope.
/// </summary>
/// <param name="intensities">(Comb.mzI[])array of isotopic peaks</param>
/// <param name="expData">(Comb.mzI[])array of the experimental data</param>
/// <param name="fitData">(fitDataStr)Fit parameters</param>
/// <param name="charge">(int)Charge</param>
/// <param name="deltaR">(double)Shift due to the marking (in 18O, deltaR=2.004245778)</param>
/// <returns>(Comb.mzI[])array of intensities representing the envelope</returns>
public static Comb.mzI[] calEnvelope(Comb.mzI[] intensities, Comb.mzI[] expData, fitDataStrt fitData, int charge, double deltaR)
{
double A = fitData.A;
double B = fitData.B;
double f = fitData.f;
double deltaMz = fitData.deltaMz;
double alpha = fitData.alpha;
double sigma = fitData.sigma;
double signoise = fitData.signoise;
Comb.mzI[] envelope = new Comb.mzI[expData.Length];
double Coeff1 = A + B * (1 - f) * (1 - f);
double Coeff2 = 2 * B * f * (1 - f);
double Coeff3 = B * f * f;
//Modify this to obtain beatiful figures for your posters
//Coeff1 = 0;//A + B * (1 - f) * (1 - f);
//Coeff2 = 0;// 2 * B * f * (1 - f);
//Coeff3 = 0; //B * f * f;
//
int nGaussians = intensities.Length;
//int nGaussians = 4; //intensities.GetUpperBound(0);
//ADDED 30.nov.2006
Comb.mzI[] intensitiesCoeff1 = new Comb.mzI[intensities.Length];
Comb.mzI[] intensitiesCoeff2 = new Comb.mzI[intensities.Length];
Comb.mzI[] intensitiesCoeff3 = new Comb.mzI[intensities.Length];
for (int i = 0; i <= intensitiesCoeff1.GetUpperBound(0); i++)
{
intensitiesCoeff1[i].mz = intensities[i].mz;
intensitiesCoeff2[i].mz = intensities[i].mz + deltaR / charge;
intensitiesCoeff3[i].mz = intensities[i].mz + 2 * deltaR / charge;
}
for (int i = 0; i < nGaussians; i++)
{
intensitiesCoeff1[i].I = Coeff1 * intensities[i].I;
intensitiesCoeff2[i].I = Coeff2 * intensities[i].I;
intensitiesCoeff3[i].I = Coeff3 * intensities[i].I;
}
Comb.mzI[] intensitiesTotal = new Comb.mzI[intensities.Length + 4];
//First 4 peaks
intensitiesTotal[0].mz = intensitiesCoeff1[0].mz;
intensitiesTotal[0].I = intensitiesCoeff1[0].I;
intensitiesTotal[1].mz = intensitiesCoeff1[1].mz;
intensitiesTotal[1].I = intensitiesCoeff1[1].I;
intensitiesTotal[2].mz = intensitiesCoeff1[2].mz;
intensitiesTotal[2].I = intensitiesCoeff1[2].I + intensitiesCoeff2[0].I;
intensitiesTotal[3].mz = intensitiesCoeff1[3].mz;
intensitiesTotal[3].I = intensitiesCoeff1[3].I + intensitiesCoeff2[1].I;
//Peaks in the middle
for (int i = 4; i <= intensitiesTotal.GetUpperBound(0) - 4; i++)
{
intensitiesTotal[i].mz = intensitiesCoeff3[i - 4].mz;
intensitiesTotal[i].I = intensitiesCoeff1[i].I + intensitiesCoeff2[i - 2].I + intensitiesCoeff3[i - 4].I;
}
//Last 4 peaks
intensitiesTotal[intensitiesTotal.GetUpperBound(0) - 3].mz = intensitiesCoeff2[intensitiesCoeff2.GetUpperBound(0) - 1].mz;
intensitiesTotal[intensitiesTotal.GetUpperBound(0) - 3].I = intensitiesCoeff2[intensitiesCoeff2.GetUpperBound(0) - 1].I + intensitiesCoeff3[intensitiesCoeff3.GetUpperBound(0) - 3].I;
intensitiesTotal[intensitiesTotal.GetUpperBound(0) - 2].mz = intensitiesCoeff2[intensitiesCoeff2.GetUpperBound(0)].mz;
intensitiesTotal[intensitiesTotal.GetUpperBound(0) - 2].I = intensitiesCoeff2[intensitiesCoeff2.GetUpperBound(0)].I + intensitiesCoeff3[intensitiesCoeff3.GetUpperBound(0) - 2].I;
intensitiesTotal[intensitiesTotal.GetUpperBound(0) - 1].mz = intensitiesCoeff3[intensitiesCoeff3.GetUpperBound(0) - 1].mz;
intensitiesTotal[intensitiesTotal.GetUpperBound(0) - 1].I = intensitiesCoeff3[intensitiesCoeff3.GetUpperBound(0) - 1].I;
intensitiesTotal[intensitiesTotal.GetUpperBound(0)].mz = intensitiesCoeff3[intensitiesCoeff3.GetUpperBound(0)].mz;
intensitiesTotal[intensitiesTotal.GetUpperBound(0)].I = intensitiesCoeff3[intensitiesCoeff3.GetUpperBound(0)].I;
//search the positions (m/z) of the peaks on the experimental data
//Assuming that expData is sorted by m/z!!!
double[] expmz = new double[expData.Length];
int[] intensitiesMzPos = new int[intensitiesTotal.Length];
for (int i = 0; i <= expData.GetUpperBound(0); i++)
{
expmz[i] = expData[i].mz;
}
for (int i = 0; i <= intensitiesTotal.GetUpperBound(0); i++)
{
intensitiesMzPos[i] = Utilities.find(expmz, intensitiesTotal[i].mz);
}
//Add background to theoretical envelope
for (int i = 0; i <= envelope.GetUpperBound(0); i++)
{
envelope[i].mz = expData[i].mz;
envelope[i].I = signoise;
}
double maxContribSigma = 3 * sigma;
for (int i = 0; i <= intensitiesTotal.GetUpperBound(0); i++)
{
double diff = 0;
int idx = 0;
while (diff < maxContribSigma && intensitiesMzPos[i] + idx < envelope.Length) //Meter el parámetro a la hoja XML de parámetros
{
double contrib;
contrib = intensitiesTotal[i].I * gaussDblExp(envelope[intensitiesMzPos[i] + idx].mz, intensitiesTotal[i].mz, sigma, alpha).I;
envelope[intensitiesMzPos[i] + idx].I += contrib;
//diff = contrib / (envelope[intensitiesMzPos[i] + idx].I+0.00001);
diff = Math.Abs(envelope[intensitiesMzPos[i] + idx].mz - envelope[intensitiesMzPos[i]].mz);
idx++;
}
diff = 0;
idx = 1;
while (diff < maxContribSigma && intensitiesMzPos[i] - idx > 0) //Meter el parámetro a la hoja XML de parámetros
{
double contrib;
contrib = intensitiesTotal[i].I * gaussDblExp(envelope[intensitiesMzPos[i] - idx].mz, intensitiesTotal[i].mz, sigma, alpha).I;
envelope[intensitiesMzPos[i] - idx].I += contrib;
//diff = contrib / (envelope[intensitiesMzPos[i] - idx].I+0.0001);
diff = Math.Abs(envelope[intensitiesMzPos[i] - idx].mz - envelope[intensitiesMzPos[i]].mz);
idx++;
}
}
//Correct deltaMZ
//Comb.mzI[] envelopeCorrected = (Comb.mzI[])envelope.Clone();
Comb.mzI[] envelopeCorrected = new Comb.mzI[envelope.Length];
for (int i = 1; i <= envelopeCorrected.GetUpperBound(0); i++)
{
envelopeCorrected[i].mz = envelope[i].mz;
envelopeCorrected[i].I = signoise; //signoise
}
int deltaMZpos = 0;
double deltaMZq = 0;
double initPos = expData[deltaMZpos + 1].mz;
while ((double)deltaMZq < Math.Abs(deltaMz))
{
deltaMZq = expData[deltaMZpos + 1].mz - initPos;
deltaMZpos++;
}
if (deltaMz < 0)
{
deltaMZpos = -deltaMZpos;
}
if (Math.Sign(deltaMZpos) >= 0)
{
for (int i = 1; i <= envelopeCorrected.GetUpperBound(0) - deltaMZpos; i++)
{
envelopeCorrected[i + deltaMZpos].I = envelope[i].I;
}
}
else
{
for (int i = -deltaMZpos; i <= envelopeCorrected.GetUpperBound(0) + deltaMZpos; i++)
{
envelopeCorrected[i + deltaMZpos + 1].I = envelope[i].I;
}
}
//ADDED_END
//DEPRECATED 30.nov.2006
/*
* for (int i = 0; i <= expData.GetUpperBound(0); i++)
* {
* envelope[i].mz=expData[i].mz;
* envelope[i].I += signoise;
*
* for (int j = 0; j < nGaussians; j++){
*
* envelope[i].I += Coeff1 * gaussDblExp(expData[i].mz, intensities[j].mz + deltaMz, sigma, alpha).I * intensities[j].I;
* envelope[i].I += Coeff2 * gaussDblExp(expData[i].mz, intensities[j].mz + deltaMz + deltaR / charge, sigma, alpha).I * intensities[j].I;
* envelope[i].I += Coeff3 * gaussDblExp(expData[i].mz, intensities[j].mz + deltaMz + 2 * deltaR / charge, sigma, alpha).I * intensities[j].I;
*
* }
* }
*/
//DEPRECATED_END
return(envelopeCorrected);
}
/// <summary>
/// Calculates the isotopic envelope.
/// </summary>
/// <param name="intensities">(Comb.mzI[])array of isotopic peaks</param>
/// <param name="expData">(Comb.mzI[])array of the experimental data</param>
/// <param name="fitData">(fitDataStr)Fit parameters</param>
/// <param name="charge">(int)Charge</param>
/// <param name="deltaR">(double)Shift due to the labeling (in 18O, deltaR=2.004245778)</param>
/// <returns>(Comb.mzI[])array of intensities representing the envelope</returns>
///
//#region normal distribution
// public static double normalDistribution(double x, double mean, double std, bool cumulative)
// {
// if (cumulative)
// {
// return Phi(x, mean, std);
// }
// else
// {
// double tmp = 1 / ((Math.Sqrt(2 * Math.PI) * std));
// return tmp * Math.Exp(-.5 * Math.Pow((x - mean) / std, 2));
// }
// }
// //from http://www.cs.princeton.edu/introcs/...Math.java.html
// // fractional error less than 1.2 * 10 ^ -7.
// static double erf(double z)
// {
// double t = 1.0 / (1.0 + 0.5 * Math.Abs(z));
// // use Horner's method
// double ans = 1 - t * Math.Exp(-z * z - 1.26551223 +
// t * (1.00002368 +
// t * (0.37409196 +
// t * (0.09678418 +
// t * (-0.18628806 +
// t * (0.27886807 +
// t * (-1.13520398 +
// t * (1.48851587 +
// t * (-0.82215223 +
// t * (0.17087277))))))))));
// if (z >= 0) return ans;
// else return -ans;
// }
// // cumulative normal distribution
// static double Phi(double z)
// {
// return 0.5 * (1.0 + erf(z / (Math.Sqrt(2.0))));
// }
// // cumulative normal distribution with mean mu and std deviation sigma
// static double Phi(double z, double mu, double sigma)
// {
// return Phi((z - mu) / sigma);
// }
// #endregion
public static Comb.mzI[] calEnvelope(Comb.mzI[] intensities,
Comb.mzI[] expData,
fitDataStrt fitData,
int charge,
double label,
Resolution res)
{
double A = fitData.A;
double B = fitData.B;
double f = fitData.f;
double deltaMz = fitData.deltaMz;
double alpha = fitData.alpha;
double sigma = fitData.sigma;
double signoise = fitData.signoise;
double Coeff1 = A + B * (1 - f) * (1 - f);
double Coeff2 = 2 * B * f * (1 - f);
double Coeff3 = B * f * f;
//Modify this to obtain beatiful figures for your posters
//Coeff1 = 0;//A + B * (1 - f) * (1 - f);
//Coeff2 = 0;// 2 * B * f * (1 - f);
//Coeff3 = 0; //B * f * f;
//
int nGaussians = intensities.Length;
Comb.mzI[] intensitiesCoeff1 = new Comb.mzI[nGaussians];
Comb.mzI[] intensitiesCoeff2 = new Comb.mzI[nGaussians];
Comb.mzI[] intensitiesCoeff3 = new Comb.mzI[nGaussians];
double ddd = 0;
for (int i = 0; i <= intensitiesCoeff1.GetUpperBound(0); i++)
{
intensitiesCoeff1[i].mz = intensities[i].mz;
intensitiesCoeff2[i].mz = intensities[i].mz + label / charge;
intensitiesCoeff3[i].mz = intensities[i].mz + 2 * label / charge;
ddd = (intensitiesCoeff2[i].mz - intensitiesCoeff1[i].mz) * 2;
}
for (int i = 0; i < nGaussians; i++)
{
intensitiesCoeff1[i].I = Coeff1 * intensities[i].I;
intensitiesCoeff2[i].I = Coeff2 * intensities[i].I;
intensitiesCoeff3[i].I = Coeff3 * intensities[i].I;
}
// 13July2009 Pedro : Modification for SILAC (and generalization for all isotopic labelings)
int maxNumOfPeaks = (int)Math.Floor(2 * label) + nGaussians;
Comb.mzI[] intensitiesTotal = new Comb.mzI[maxNumOfPeaks];
int beginCoeff1 = 0;
int beginCoeff2 = (int)Math.Floor(label);
int beginCoeff3 = (int)Math.Floor(2 * label);
for (int i = 0; i < maxNumOfPeaks; i++)
{
intensitiesTotal[i].I = 0;
}
for (int i = 0; i < nGaussians; i++)
{
intensitiesTotal[i + beginCoeff1].mz = intensitiesCoeff1[i].mz;
intensitiesTotal[i + beginCoeff2].mz = intensitiesCoeff2[i].mz;
intensitiesTotal[i + beginCoeff3].mz = intensitiesCoeff3[i].mz;
intensitiesTotal[i + beginCoeff1].I += intensitiesCoeff1[i].I;
intensitiesTotal[i + beginCoeff2].I += intensitiesCoeff2[i].I;
intensitiesTotal[i + beginCoeff3].I += intensitiesCoeff3[i].I;
}
ddd = (intensitiesTotal[0].mz - intensitiesTotal[2].mz) * 2;
if (res == Resolution.HIGH)
{
int counter = 0;
for (int k = 0; k < intensitiesTotal.Length; k++)
{
if (intensitiesTotal[k].mz != 0)
{
counter++;
}
}
//If the labeling distance is high, then we must clean empty peak positions
Comb.mzI[] intensitiesTotalClean = new Comb.mzI[counter];
counter = 0;
for (int k = 0; k < intensitiesTotal.Length; k++)
{
if (intensitiesTotal[k].mz != 0)
{
intensitiesTotalClean[counter].mz = intensitiesTotal[k].mz;
intensitiesTotalClean[counter].I = intensitiesTotal[k].I;
counter++;
}
}
return(intensitiesTotalClean);
}
Comb.mzI[] envelope = new Comb.mzI[expData.Length];
//search the positions (m/z) of the peaks on the experimental data
//Assuming that expData is sorted by m/z!!!
double[] expmz = new double[expData.Length];
int[] intensitiesMzPos = new int[intensitiesTotal.Length];
for (int i = 0; i <= expData.GetUpperBound(0); i++)
{
expmz[i] = expData[i].mz;
}
for (int i = 0; i <= intensitiesTotal.GetUpperBound(0); i++)
{
intensitiesMzPos[i] = Utilities.find(expmz, intensitiesTotal[i].mz);
}
//Add background to theoretical envelope
for (int i = 0; i <= envelope.GetUpperBound(0); i++)
{
envelope[i].mz = expData[i].mz;
envelope[i].I = signoise;
}
double maxContribSigma = 3 * sigma;
for (int i = 0; i <= intensitiesTotal.GetUpperBound(0); i++)
{
if (intensitiesTotal[i].I != 0)
{
double diff = 0;
int idx = 0;
// calculation for the right side of the gaussian
while (diff < maxContribSigma + Math.Abs(deltaMz) && intensitiesMzPos[i] + idx < envelope.Length) //Meter el parámetro a la hoja XML de parámetros
{
double contrib;
contrib = intensitiesTotal[i].I * gaussDblExp(envelope[intensitiesMzPos[i] + idx].mz - deltaMz,
intensitiesTotal[i].mz, sigma, alpha).I;
envelope[intensitiesMzPos[i] + idx].I += contrib;
//diff = contrib / (envelope[intensitiesMzPos[i] + idx].I+0.00001);
diff = Math.Abs(envelope[intensitiesMzPos[i] + idx].mz - envelope[intensitiesMzPos[i]].mz);
idx++;
}
diff = 0;
idx = 1;
// calculation for the left side of the gaussian
while (diff < maxContribSigma + Math.Abs(deltaMz) && intensitiesMzPos[i] - idx > 0) //Meter el parámetro a la hoja XML de parámetros
{
double contrib;
contrib = intensitiesTotal[i].I * gaussDblExp(envelope[intensitiesMzPos[i] - idx].mz - deltaMz,
intensitiesTotal[i].mz, sigma, alpha).I;
envelope[intensitiesMzPos[i] - idx].I += contrib;
//diff = contrib / (envelope[intensitiesMzPos[i] - idx].I+0.0001);
diff = Math.Abs(envelope[intensitiesMzPos[i] - idx].mz - envelope[intensitiesMzPos[i]].mz);
idx++;
}
}
}
////Correct deltaMZ
////Comb.mzI[] envelopeCorrected = (Comb.mzI[])envelope.Clone();
//Comb.mzI[] envelopeCorrected =new Comb.mzI[envelope.Length];
//for (int i = 0; i <= envelopeCorrected.GetUpperBound(0); i++)
//{
// envelopeCorrected[i].mz = envelope[i].mz;
// envelopeCorrected[i].I = signoise; //signoise
//}
//int deltaMZpos = 0;
//double deltaMZq = 0;
//double initPos = expData[deltaMZpos].mz;
//while ((double)deltaMZq < Math.Abs(deltaMz))
//{
// deltaMZpos++;
// deltaMZq = expData[deltaMZpos].mz - initPos;
//}
//if (deltaMZq > Math.Abs(deltaMz) * 2 && deltaMZpos == 1)
// deltaMZpos = 0;
//if (deltaMz < 0)
// deltaMZpos = -deltaMZpos;
//if (deltaMZpos >= 0)
//{
// // bug warning! nothing is copied before deltaMSpos ****
// for (int i = 0; i <= envelopeCorrected.GetUpperBound(0) - deltaMZpos; i++)
// {
// envelopeCorrected[i + deltaMZpos].I = envelope[i].I;
// }
//}
//else
//{
// // bug warning! nothing is copied from deltaMZpos to the end ****
// for (int i = -deltaMZpos; i <= envelopeCorrected.GetUpperBound(0) + deltaMZpos; i++)
// {
// envelopeCorrected[i + deltaMZpos].I = envelope[i].I;
// }
//}
return(envelope);// Corrected;
}
