private static double GetUncalibratedSilacMass(SilacCluster sc, SilacType type, IsotopeCluster[] isotopeClusters,
double[] centerMz, float[] intensities)
{
return
(GetUncalibratedFullIsotopePatternMassEstimate(sc.GetIsotopeClusterIndices(type), sc.GetIsotopePatternStarts(type),
sc.GetMassDiffs(type), isotopeClusters, centerMz, intensities));
}
public SilacMatchEvidence(int silacId, int rawFileIndex, SilacCluster silacCluster,
int charge, double intensity0, double intensity1,
double intensity2, double calibRT, MascotPeptide peptide)
:
base(silacId, rawFileIndex, silacCluster, charge, intensity0,
intensity1, intensity2, calibRT)
{
massErrPpm = (silacCluster.Mass - peptide.Mass) / peptide.Mass * 1e6;
}
private static double GetCalibratedSilacMassStat(SilacCluster sc, double[,] mzCalibrationPar,
double[,] intensityCalibrationPar,
SilacType type, IsotopeCluster[] isotopeCluster, IPeakList peakList,
float[] intensities)
{
int dummy;
return
(GetFullIsotopePatternMassEstimateNoBootstrapStat(sc.GetIsotopeClusterIndices(type), sc.GetIsotopePatternStarts(type),
sc.GetMassDiffs(type), mzCalibrationPar, intensityCalibrationPar,
true,
out dummy, isotopeCluster, peakList, intensities));
}
public static double[] CalcSilacClusterProfile(SilacCluster cl, out int minIndex, SilacType type,
IsotopeCluster[] isotopeClusters, IPeakList peakList,
float[] intensities)
{
int[] m = cl.GetIsotopeClusterIndices(type);
int n = m.Length;
if (n == 1)
{
return(T03SilacAssembly.CalcIsotopeClusterProfile(isotopeClusters[m[0]], out minIndex, peakList));
}
double[][] profiles = new double[n][];
int[] mins = new int[n];
int[] ends = new int[n];
double[] intens = new double[n];
for (int i = 0; i < n; i++)
{
if (m[i] == -1)
{
continue;
}
IsotopeCluster ic = isotopeClusters[m[i]];
profiles[i] = T03SilacAssembly.CalcIsotopeClusterProfile(ic, out mins[i], peakList);
intens[i] = T03SilacAssembly.GetIsotopeClusterIntensity(ic, intensities);
ends[i] = mins[i] + profiles[i].Length;
}
minIndex = ArrayUtil.Min(mins);
int maxEnd = ArrayUtil.Max(ends);
int len = maxEnd - minIndex;
double[] result = new double[len];
double norm = 0;
for (int i = 0; i < n; i++)
{
if (m[i] == -1)
{
continue;
}
norm += intens[i];
for (int j = 0; j < profiles[i].Length; j++)
{
result[j + mins[i] - minIndex] += profiles[i][j] * intens[i];
}
}
for (int i = 0; i < len; i++)
{
result[i] /= norm;
}
return(result);
}
public static int[][] FindChargePairs(int nsilac, SilacType silacType, double matchPpm,
double silacTimeCorrelationThreshold, SilacCluster[] silacClusters,
IsotopeCluster[] isotopeClusters, IPeakList peakList, float[] intensities,
double[] centerMz)
{
double[] m = new double[nsilac];
for (int i = 0; i < m.Length; i++)
{
SilacCluster si = silacClusters[i];
m[i] = GetUncalibratedSilacMass(si, silacType, isotopeClusters, centerMz, intensities);
}
int[] o = ArrayUtil.Order(m);
m = ArrayUtil.SubArray(m, o);
List <int[]> pairs = new List <int[]>();
for (int i = 0; i < m.Length; i++)
{
SilacCluster si = silacClusters[o[i]];
int chargei = isotopeClusters[si.IsotopeClusterindex1].Charge;
double m1 = m[i];
int ind1 = ArrayUtil.CeilIndex(m, m1 - matchPpm * 1e-6 * m1);
for (int j = ind1; j < i; j++)
{
SilacCluster sj = silacClusters[o[j]];
int chargej = isotopeClusters[sj.IsotopeClusterindex1].Charge;
if (chargei == chargej)
{
continue;
}
int mini;
double[] pi = CalcSilacClusterProfile(si, out mini, silacType, isotopeClusters, peakList,
intensities);
int minj;
double[] pj = CalcSilacClusterProfile(sj, out minj, silacType, isotopeClusters, peakList,
intensities);
if (T03SilacAssembly.Correlate(pi, mini, pj, minj) > silacTimeCorrelationThreshold)
{
pairs.Add(new int[] { o[i], o[j] });
}
}
}
return(pairs.ToArray());
}
protected SilacEvidence(int silacId, int rawFileIndex, SilacCluster silacCluster, int charge,
double intensity0, double intensity1, double intensity2, double calibRT)
: base(rawFileIndex, (float)silacCluster.ElutionTime, (float)calibRT, charge)
{
this.silacId = silacId;
ratio10 = (float)silacCluster.Ratio10;
ratio20 = (float)silacCluster.Ratio20;
ratio21 = (float)silacCluster.Ratio21;
normalizedRatio10 = (float)silacCluster.NormalizedRatio10;
normalizedRatio20 = (float)silacCluster.NormalizedRatio20;
normalizedRatio21 = (float)silacCluster.NormalizedRatio21;
ratioSignificanceA10 = (float)Math.Log(silacCluster.RatioSignificanceA10);
ratioSignificanceA20 = (float)Math.Log(silacCluster.RatioSignificanceA20);
ratioSignificanceA21 = (float)Math.Log(silacCluster.RatioSignificanceA21);
ratioSignificanceB10 = (float)Math.Log(silacCluster.RatioSignificanceB10);
ratioSignificanceB20 = (float)Math.Log(silacCluster.RatioSignificanceB20);
ratioSignificanceB21 = (float)Math.Log(silacCluster.RatioSignificanceB21);
this.intensity0 = (float)intensity0;
this.intensity1 = (float)intensity1;
this.intensity2 = (float)intensity2;
calibratedMass = silacCluster.Mass;
uncalibratedMass = silacCluster.UncalibratedMass;
}
public static void RecalibrateImpl(SilacType silacType, int nranges, int[] iranges, int[][] chargePairs,
SilacCluster[] silacClusters, ref double[,] mzCalibrationParams,
ref double[,] intensityCalibrationParams, double massErrorNormalization,
IsotopeCluster[] isotopeCluster, IPeakList peakList, float[] intensities)
{
double[] x = new double[chargePairs.Length];
double[] y = new double[chargePairs.Length];
double[] sig = new double[chargePairs.Length];
for (int i = 0; i < chargePairs.Length; i++)
{
x[i] = i;
int ind1 = chargePairs[i][0];
int ind2 = chargePairs[i][1];
SilacCluster sc1 = silacClusters[ind1];
SilacCluster sc2 = silacClusters[ind2];
sig[i] = Math.Sqrt(sc1.GetMassError(massErrorNormalization) * sc1.GetMassError(massErrorNormalization) +
sc2.GetMassError(massErrorNormalization) * sc2.GetMassError(massErrorNormalization));
}
intensityCalibrationParams = new double[nranges, nparamsIntensityFit];
double[,] icp = intensityCalibrationParams;
Funcs2 f = delegate(double x1, double[] aa) {
int ind = (int)Math.Round(x1);
int ind1 = chargePairs[ind][0];
int ind2 = chargePairs[ind][1];
double[,] mzAa = new double[nranges, nparamsMzFit];
int c = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzAa[iranges[j], i] = aa[c++];
}
}
double y1 = GetCalibratedSilacMassStat(silacClusters[ind1], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double y2 = GetCalibratedSilacMassStat(silacClusters[ind2], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double yy = y1 - y2;
return(yy);
};
double chisq;
double[] a = new double[nparamsMzFit * iranges.Length];
int county = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
a[county++] = startValsMzFit[i];
}
}
NumUtil.FitNonlin(x, y, sig, a, out chisq, f);
mzCalibrationParams = new double[nranges, nparamsMzFit];
int s = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzCalibrationParams[iranges[j], i] = a[s++];
}
}
double[,] mcp = mzCalibrationParams;
f = delegate(double x1, double[] aa) {
int ind = (int)Math.Round(x1);
int ind1 = chargePairs[ind][0];
int ind2 = chargePairs[ind][1];
double[,] intensityAa = new double[nranges, nparamsIntensityFit];
int c = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsIntensityFit; i++)
{
intensityAa[iranges[j], i] = aa[c++];
}
}
double y1 = GetCalibratedSilacMassStat(silacClusters[ind1], mcp, intensityAa, silacType, isotopeCluster, peakList,
intensities);
double y2 = GetCalibratedSilacMassStat(silacClusters[ind2], mcp, intensityAa, silacType, isotopeCluster, peakList,
intensities);
double yy = y1 - y2;
return(yy);
};
a = new double[nparamsIntensityFit * iranges.Length];
NumUtil.FitNonlin(x, y, sig, a, out chisq, f);
s = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsIntensityFit; i++)
{
intensityCalibrationParams[iranges[j], i] = a[s++];
}
}
icp = intensityCalibrationParams;
f = delegate(double x1, double[] aa) {
int ind = (int)Math.Round(x1);
int ind1 = chargePairs[ind][0];
int ind2 = chargePairs[ind][1];
double[,] mzAa = new double[nranges, nparamsMzFit];
int c = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzAa[iranges[j], i] = aa[c++];
}
}
double y1 = GetCalibratedSilacMassStat(silacClusters[ind1], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double y2 = GetCalibratedSilacMassStat(silacClusters[ind2], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double yy = y1 - y2;
return(yy);
};
a = new double[nparamsMzFit * iranges.Length];
county = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
a[county++] = mzCalibrationParams[iranges[j], i];
}
}
NumUtil.FitNonlin(x, y, sig, a, out chisq, f);
s = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzCalibrationParams[iranges[j], i] = a[s++];
}
}
}
public SilacMassEvidence(int silacId, int fileIndex, SilacCluster silacCluster, int charge, double intensity0,
double intensity1, double intensity2, double rt)
: base(silacId, fileIndex, silacCluster, charge, intensity0,
intensity1, intensity2, rt)
{
}
public SilacMsmsEvidence(int silacId, int rawFileIndex, SilacCluster silacCluster, int charge, double intensity0,
double intensity1, double intensity2, double calibRT)
:
base(silacId, rawFileIndex, silacCluster, charge, intensity0, intensity1, intensity2, calibRT)
{
}
