////////////////////////////////////////////////////////////////////////////////
// print all monositopic peak cluster along the LC profile:
void LCElutionPeak::createConsensIsotopPattern()
{
//////////////
// go through the different isotopes and
// constructe a consensus patterns:
isotopePattern = new ConsensusIsotopePattern();
multimap<int, MSPeak>::iterator R = intens_signals.begin();
while (R != intens_signals.end())
{
MSPeak * peak = &(*R).second;
// map<double, double> isotopeCluster; // unused variable
vector<CentroidPeak>::iterator p = peak->get_isotopic_peaks_start();
while (p != peak->get_isotopic_peaks_end())
{
isotopePattern->addIsotopeTrace((*p).getMass(), (*p).getFittedIntensity());
++p;
}
++R;
}
// create the pattern:
isotopePattern->constructConsusPattern();
}
////////////////////////////////////////////////////////
// function to add the elution profile to the feature:
void FTPeakDetectController::addLCelutionProfile(SHFeature * inF, LCElutionPeak * PEAK)
{
////////////////////////////////
// get parameters of the peak:
// apex:
int apex_scan = PEAK->get_scan_apex();
double apex_MZ = PEAK->get_apex_MZ();
double apex_TR = PEAK->get_apex_retention_time();
float apex_Intensity = (float) PEAK->get_apex_intensity();
// peak shape:
float peak_area = (float) PEAK->get_total_peak_area();
int charge_state = PEAK->get_charge_state();
// create the class:
FeatureLCProfile * myProfile = new FeatureLCProfile(apex_MZ, apex_TR, apex_Intensity, apex_scan, charge_state,
peak_area);
// add the raw individual mono isotopic peaks peaks:
SIGNAL_iterator P = PEAK->get_signal_list_start();
while (P != PEAK->get_signal_list_end())
{
MSPeak * MSpeak = &(*P).second;
myProfile->addMS1elutionSignal(MSpeak->get_MZ(), MSpeak->get_intensity(), MSpeak->get_scan_number(),
MSpeak->get_charge_state(), MSpeak->get_retention_time());
P++;
}
inF->setLCelutionProfile(myProfile);
myProfile = NULL;
}
//////////////////////////////////////////////////////////////////
// determine the intensity background baseline based on S/N
// value:
void LCElutionPeak::setSNIntensityThreshold()
{
fSignalToNoise = 0;
fSNIntensityThreshold = 0;
double TotArea = 0;
SIGNAL_iterator P = get_signal_list_start();
while (P != get_signal_list_end())
{
MSPeak * peak = &(P->second);
fSignalToNoise += peak->getSignalToNoise() * peak->get_intensity();
fSNIntensityThreshold += peak->get_intensity() * (peak->get_intensity() / peak->getSignalToNoise());
TotArea += peak->get_intensity();
P++;
}
// set the signal to noise:
fSignalToNoise /= TotArea;
// set the noise threshold:
fSNIntensityThreshold /= TotArea;
}
//////////////////////////////////////////////////////////////////
// Compute a varietiy of parameters for the LC elution peak
void LCElutionPeak::computeLCElutionPeakParameters()
{
double TOT_AREA = 0;
double apexScan = 0;
double apexTr = 0;
MSPeak * endPeak = NULL;
MSPeak * startPeak = NULL;
// find the first peaks above the background intensity:
SIGNAL_iterator P = get_signal_list_start();
fScanNumberStart = (*P).second.get_scan_number();
fStartTR = (*P).second.get_retention_time();
// set start et first scan in the LC_peak:
while (P != get_signal_list_end())
{
if ((*P).second.get_intensity() >= fSNIntensityThreshold)
{
break;
}
P++;
}
// FLO: On windows, there is an error when we try to de-reference P when
// P refers to get_signal_list_end() - the case is quite obvious when we
// see that P is incremented afterwards. Without knowing I just introduce
// a check whether P is equal to get_signal_list_end().
if (P != get_signal_list_end())
{
startPeak = &((*P).second);
// to compute some other parameters at the same time:
update_CHRGMAP(&(*P).second);
P++;
}
// go through all peaks in the LC elution profile:
while (P != get_signal_list_end())
{
if ((*P).second.get_intensity() >= fSNIntensityThreshold)
{
if (startPeak != NULL)
{
endPeak = &((*P).second);
}
else
{
startPeak = &((*P).second);
}
}
else
{
endPeak = NULL;
startPeak = NULL;
}
if ((endPeak != NULL) && (startPeak != NULL))
{
// to compute some other parameters at the same time:
update_CHRGMAP(endPeak);
///////////////////////////////////////////////////
// compute an area between local start / end ms peak:
double area = compute_delta_area(startPeak->get_retention_time(),
startPeak->get_intensity() - fSNIntensityThreshold, endPeak->get_retention_time(),
endPeak->get_intensity() - fSNIntensityThreshold);
TOT_AREA += area;
apexScan += (double) (P->first) * area;
apexTr += startPeak->get_retention_time() * area;
// next scan:
startPeak = endPeak;
}
P++;
}
// if contained only one peak!
if (get_nb_ms_peaks() == 1)
{
TOT_AREA = startPeak->get_intensity();
fScanNumberEnd = fScanNumberStart;
fEndTR = startPeak->get_retention_time();
}
else
{
P--;
fScanNumberEnd = (*P).second.get_scan_number();
fEndTR = (*P).second.get_retention_time();
fpeak_area = TOT_AREA;
apexScan /= TOT_AREA;
apexTr /= TOT_AREA;
fRT = apexTr;
}
// set the apex ms peak:
MSPeak * APEX = find_true_peak((float) apexScan); // TODO : this may be a bug, maybe this should not declare a new APEX
if (!APEX->getExtraPeakInfo().empty())
{
setElutionPeakExtraInfo(APEX->getExtraPeakInfo());
}
// find retention time and intensity of apex:
fScanNumberApex = APEX->get_scan_number();
fapex_intensity = APEX->get_intensity();
}
