// TODO what about charge 2 isotopes, etc. if tolerance is low enough, we can check for them too
void PeakList::calculateIsotopicLevels(mass_t tolerance,
vector<float>& isotopicLevels) const
{
const mass_t isotopicTolerance = (tolerance<0.2 ? tolerance : 0.2);
const int lastPeakIndex = numPeaks_-1;
isotopicLevels.clear();
isotopicLevels.resize(numPeaks_,0);
int i;
for (i=0; i<lastPeakIndex; i++)
{
if (isotopicLevels[i]>0)
continue;
// look for +1 peak
int idx1 = findPeakWithMaxIntensity(peaks_[i].mass + MASS_PROTON, isotopicTolerance);
if (idx1<0)
continue;
const float oneOverIntensity = 1.0 / peaks_[i].intensity;
float ratio1 = peaks_[idx1].intensity * oneOverIntensity;
// ignore strong +1
if ( ratio1 > 3.0)
continue;
// examine ratios
vector<float> expectedPeakRatios, observedPeakRatios, relativeRatios;
vector<int> isotopicIndexs;
observedPeakRatios.resize(6);
observedPeakRatios[0]=1.0;
observedPeakRatios[1]= ratio1;
isotopicIndexs.resize(6);
isotopicIndexs[0]=i;
isotopicIndexs[1]=idx1; // peak index at +1 position
// find additional peaks
int j;
for (j=2; j<=5; j++)
{
int idx = findPeakWithMaxIntensity(peaks_[i].mass + j*MASS_ISO, isotopicTolerance);
if (idx<0)
break;
observedPeakRatios[j] = peaks_[idx].mass * oneOverIntensity;
isotopicIndexs[j]=idx;
}
const int lastIsotopicPosition = j-1;
// get expected iso ratios
calc_expected_iso_ratios(peaks_[i].mass,expectedPeakRatios,j);
// calc ratios between observed and expected
relativeRatios.clear();
relativeRatios.resize(6,0);
relativeRatios[0]=1.0;
for (j=1; j<=lastIsotopicPosition; j++)
if (expectedPeakRatios[j]>0)
relativeRatios[j]=observedPeakRatios[j] / expectedPeakRatios[j];
float levelDiscount=1.0; // as we move farther from the monoisotopic peak, the rates down
for (j=1; j<= lastIsotopicPosition; j++)
{
float isotopicLevel;
if (relativeRatios[j]>= 0.75 && relativeRatios[j]<=1.333)
{
isotopicLevel=2.0;
}
else if (relativeRatios[j] >= 0.5 && relativeRatios[j] <=2.0)
{
isotopicLevel=1.3333;
}
else if (relativeRatios[j] >= 0.3333 && relativeRatios[j] <=3.0)
{
isotopicLevel=0.6666;
}
else if (relativeRatios[j] >= 0.25 && relativeRatios[j] <= 4.0)
{
isotopicLevel=0.3333;
}
else
break;
isotopicLevels[isotopicIndexs[j]] = isotopicLevels[isotopicIndexs[j-1]] +
levelDiscount * isotopicLevel;
levelDiscount *= 0.5;
}
}
}
/**************************************************************
Sets the iso_level for each peak. Iso level 0 means that there
is no evidence that this peaks is an isotopic peak. The higher
the level, the more this looks like an isotopic peak
***************************************************************/
void Spectrum::calc_isotope_levels()
{
int i;
const mass_t iso_tolerance = (config_->getTolerance()<0.2) ?
config_->getTolerance() : 0.2;
const int last_peak_idx = numPeaks_-1;
isotopicLevels_.clear();
isotopicLevels_.resize(numPeaks_,0);
for (i=0; i<last_peak_idx; i++)
{
if (isotopicLevels_[i]>0)
continue;
// look for +1 peak
int idx1 = findPeakWithMaxIntensity(peaks_[i].mass + MASS_PROTON, iso_tolerance);
if (idx1<0)
continue;
float one_over_intensity = 1.0 / peaks_[i].intensity;
float ratio1 = peaks_[idx1].intensity * one_over_intensity;
// ignore strong +1
if ( ratio1 > 3)
continue;
// examine ratios
vector<float> expected_ratios, observed_ratios, relative_ratios;
vector<int> iso_idxs;
observed_ratios.resize(6);
observed_ratios[0]=1.0;
observed_ratios[1]= ratio1;
iso_idxs.resize(6);
iso_idxs[0]=i;
iso_idxs[1]=idx1;
// find additional peaks
int j;
for (j=2; j<=5; j++)
{
int idx = findPeakWithMaxIntensity(peaks_[i].mass + j, iso_tolerance);
if (idx<0)
break;
observed_ratios[j] = peaks_[idx].mass * one_over_intensity;
iso_idxs[j]=idx;
}
int last_iso = j-1;
// get expected iso ratios
calc_expected_iso_ratios(peaks_[i].mass,expected_ratios,j);
// calc ratios between observed and expected
relative_ratios.resize(j);
relative_ratios[0]=1;
for (j=1; j<=last_iso; j++)
relative_ratios[j]=observed_ratios[j] / expected_ratios[j];
float level_mul=1.0;
for (j=1; j<= last_iso; j++)
{
float iso_level;
if (relative_ratios[j]>= 0.75 && relative_ratios[j]<=1.333)
{
iso_level=2.0;
}
else if (relative_ratios[j] >= 0.5 && relative_ratios[j] <=2)
{
iso_level=1.3333;
}
else if (relative_ratios[j] >= 0.3333 && relative_ratios[j] <=3)
{
iso_level=0.6666;
}
else if (relative_ratios[j] >= 0.25 && relative_ratios[j] <= 4)
{
iso_level=0.3333;
}
else
break;
// if (relative_ratios[j] / relative_ratios[j-1] > 3)
// break;
isotopicLevels_[iso_idxs[j]] = isotopicLevels_[iso_idxs[j-1]] + level_mul * iso_level;
// peaks[iso_idxs[j]].IsotopicLevel = peaks[iso_idxs[j-1]].IsotopicLevel +
// level_mul * iso_level;
level_mul *= 0.5;
}
}
vector<rank_pair> mono_pairs, iso_pairs;
for (i=0; i<numPeaks_; i++)
{
rank_pair p;
p.idx=i;
p.inten = peaks_[i].intensity;
if (isotopicLevels_[i] <= 0)
{
mono_pairs.push_back(p);
}
else
iso_pairs.push_back(p);
}
sort(mono_pairs.begin(),mono_pairs.end());
sort(iso_pairs.begin(),iso_pairs.end());
/* ranked_mono_peaks.resize(numPeaks_);
for (i=0; i<mono_pairs.size(); i++)
ranked_mono_peaks[i]=mono_pairs[i].idx;
for (i=0; i<iso_pairs.size(); i++)
ranked_mono_peaks[mono_pairs.size()+i]=iso_pairs[i].idx;
*/
}
