////////////////////////////////////////////////////////
// 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;
}
/////////////////////////////////////////////////////////////////////////////
// merge the target to the search feature
void MS1FeatureMerger::mergeFeatures(SHFeature * target, SHFeature * toMerge)
{
double TOT_AREA = target->get_peak_area() + toMerge->get_peak_area();
// merge the m/z:
target->set_MZ(
(target->get_peak_area() * target->get_MZ() + toMerge->get_peak_area() * toMerge->get_MZ()) / TOT_AREA);
// merge S/N:
target->setSignalToNoise(
(target->getSignalToNoise() * target->get_peak_area() + toMerge->getSignalToNoise() * toMerge->get_peak_area())
/ TOT_AREA);
// merge score:
target->set_peak_score(
(target->get_peak_score() * target->get_peak_area() + toMerge->get_peak_score() * toMerge->get_peak_area())
/ TOT_AREA);
// merge first the elution profiles:
FeatureLCProfile * targetLC = target->getLCelutionProfile();
FeatureLCProfile * mergeLC = toMerge->getLCelutionProfile();
// add points of the toMerge to the target:
map<int, MS1Signal>::iterator LC = mergeLC->getLCelutionSignalsStart();
while (LC != mergeLC->getLCelutionSignalsEnd())
{
targetLC->addMS1elutionSignal(&(LC->second));
++LC;
}
// possible extra info:
if (target->getFeatureExtraInformation().empty())
{
target->setFeatureExtraInformation(toMerge->getFeatureExtraInformation());
}
// compute new parameters
computeNewMS1FeatureParameters(target);
// copy MS/MS information:
if (toMerge->get_MS2_info(-3.0))
{
target->add_MS2_info(toMerge->get_MS2_SCAN_MAP());
}
}
//////////////////////////////////////////////////////////////////
// Compute a varietiy of parameters for the LC elution peak
void MS1FeatureMerger::computeNewMS1FeatureParameters(SHFeature * in)
{
FeatureLCProfile * lcProfile = in->getLCelutionProfile();
// define the apex treshold:
double maxIntens = -1;
map<int, MS1Signal>::iterator LC = lcProfile->getLCelutionSignalsStart();
while (LC != lcProfile->getLCelutionSignalsEnd())
{
if (maxIntens < (*LC).second.intensity)
{
maxIntens = (*LC).second.intensity;
}
++LC;
}
// get the MS peak above noise to copmute:
double THRESHOLD = maxIntens / in->getSignalToNoise();
vector<MS1Signal *> computeMap;
LC = lcProfile->getLCelutionSignalsStart();
in->set_scan_start((*LC).second.scan);
in->set_retention_time_START((*LC).second.TR);
while (LC != lcProfile->getLCelutionSignalsEnd())
{
if ((*LC).second.intensity >= THRESHOLD)
{
computeMap.push_back(&(LC->second));
}
++LC;
}
--LC;
in->set_scan_end((*LC).second.scan);
in->set_retention_time_END((*LC).second.TR);
if (!computeMap.empty())
{
vector<MS1Signal *>::iterator P = computeMap.begin();
double TOT_AREA = 0;
double start_TR = 0;
double start_int = 0;
double apexScan = 0;
double apexTr = 0;
double end_TR = 0;
double end_int = 0;
start_TR = (*P)->TR;
start_int = (*P)->intensity;
++P;
// go through all peaks in the LC elution profile:
while (P != computeMap.end())
{
if ((*P)->intensity >= THRESHOLD)
{
end_TR = (*P)->TR;
end_int = (*P)->intensity;
// compute an area between local start / end ms peak:
double area = computeDeltaArea(start_TR, start_int - THRESHOLD, end_TR, end_int - THRESHOLD);
TOT_AREA += area;
apexScan += (double) ((*P)->scan) * area;
apexTr += start_TR * area;
// next scan:
start_TR = end_TR;
start_int = end_int;
}
++P;
}
// if contained only one peak!
if (computeMap.size() == 1)
{
in->set_peak_area((float) start_int);
in->set_retention_time(in->get_retention_time_START());
in->set_scan_number(in->get_scan_start());
}
else
{
in->set_peak_area((float) TOT_AREA);
apexScan /= TOT_AREA;
in->set_scan_number((int) apexScan);
apexTr /= TOT_AREA;
in->set_retention_time(apexTr);
}
// set the apex ms peak:
LC = lcProfile->getLCelutionSignalMap()->lower_bound(in->get_scan_number());
in->set_apex_peak_intensity((*LC).second.intensity);
}
else
{
// no good peak above threshold, so reset all the features parameters to remove the feature
in->set_peak_area(0);
in->set_scan_number(0);
in->set_retention_time(0);
}
}
//////////////////////////////////////////////////
// find to this feature the features which should be merged
vector<SHFeature *>::iterator MS1FeatureMerger::findFeaturesToMerge(SHFeature * search,
vector<SHFeature *>::iterator mapCurrent, vector<SHFeature *> * Fmap)
{
bool log10Intens = true;
// get the elution profile:
FeatureLCProfile * searchLC = search->getLCelutionProfile();
while (mapCurrent != Fmap->end())
{
// check absolute retention time difference:
bool toMerge = false;
SHFeature * mergedTarget = (*mapCurrent);
double deltaTr = fabs(search->get_retention_time() - mergedTarget->get_retention_time());
if (deltaTr <= SuperHirnParameters::instance()->getInitialTrTolerance())
{
// compare the end / start of the elution peak:
MS1Signal * start;
MS1Signal * end;
if (search->get_retention_time() < mergedTarget->get_retention_time())
{
start = &(searchLC->getLastLCelutionSignal()->second);
end = &(mergedTarget->getLCelutionProfile()->getLCelutionSignalsStart()->second);
}
else
{
end = &(mergedTarget->getLCelutionProfile()->getLastLCelutionSignal()->second);
start = &(searchLC->getLCelutionSignalsStart()->second);
}
double startIntens = start->intensity;
if (log10Intens)
{
startIntens = log10(startIntens);
}
double endIntens = end->intensity;
if (log10Intens)
{
endIntens = log10(endIntens);
}
double deltaIntens = fabs(startIntens - endIntens);
deltaIntens /= startIntens;
deltaTr = fabs(start->TR - end->TR);
if ((deltaTr <= SuperHirnParameters::instance()->getMs1FeatureMergingTrTolerance())
&& (deltaIntens <= SuperHirnParameters::instance()->getPercentageIntensityElutionBorderVariation()))
{
toMerge = true;
}
}
if (toMerge)
{
// search->show_info();(*mapCurrent)->show_info();
mergeFeatures(search, mergedTarget);
idsToRemove.push_back(mergedTarget->get_feature_ID());
mapCurrent = Fmap->erase(mapCurrent);
if (search->get_peak_area() == 0)
{
idsToRemove.push_back(search->get_feature_ID());
mapCurrent++;
break;
}
}
else
{
mapCurrent++;
}
}
return mapCurrent;
}
