Commit ca63d566 authored by Olivier Langella's avatar Olivier Langella
Browse files

remove trying to detect on real MSMS observations (bad results in benchmark)

parent f82cceeb
......@@ -43,7 +43,7 @@ void MapQuanti::operator()(QuantiItemBase * p_currentSearchItem)
qDebug() << " MapQuanti::operator begin";
try {
pappso::pappso_double rt_target = -1;
std::vector<MsMsRtIntensity> rt_list;
//std::vector<MsMsRtIntensity> rt_list;
PeptideRt * p_peptide_rt = p_currentSearchItem->getPeptideRtSp().get();
......@@ -55,23 +55,6 @@ void MapQuanti::operator()(QuantiItemBase * p_currentSearchItem)
throw mcqError(QObject::tr("Error in MapQuanti::operator() isnan(rt_target) %1")
.arg(p_currentSearchItem->getQuantiItemId()));
}
switch (_matching_mode) {
case McqMatchingMode::realxic_or_mean:
if (p_peptide_rt->isObservedIn(_p_msrun)) {
if(_quantificator->isInMissedQuantiItem(_p_msrun, p_currentSearchItem)) {
}
else {
return;
}
}
break;
case McqMatchingMode::post_matching:
case McqMatchingMode::real_or_mean:
rt_list = p_currentSearchItem->getPeptide()->getPeptideRtSp()->getObservedRtList(_p_msrun);
break;
default:
break;
}
}
if (rt_target == -1) {
......@@ -96,26 +79,13 @@ void MapQuanti::operator()(QuantiItemBase * p_currentSearchItem)
qDebug() << " MapQuanti::operator begin 3 rt_target=" << rt_target;
XicTraceBase * p_xic_trace = nullptr;
if (rt_list.size() > 0) {
//MSMS observed
//idea : add weighted mean retention time to the list ?
p_xic_trace = p_currentSearchItem->newXicTrace(_quantificator, _p_msrun, "MSMS");
//only take an rt reference to match peak
p_xic_trace = p_currentSearchItem->newXicTrace(_quantificator, _p_msrun, "target");
XicFilterDetectMatchRealRt filter_detect_match_real_xic(p_xic_trace, _monitor, _p_xic_filter, _p_detection, _quantificator, _matching_mode);
XicFilterDetectMatch filter_detect_match(p_xic_trace, _monitor, _p_xic_filter, _p_detection, _matching_mode) ;
filter_detect_match.filterDetectQuantify(*(_p_xic.get()), rt_target, p_currentSearchItem, _p_msrun);
filter_detect_match_real_xic.filterDetectQuantify(_p_xic.get(), &rt_list, p_currentSearchItem, _p_msrun);
}
else {
//only take an rt reference to match peak
p_xic_trace = p_currentSearchItem->newXicTrace(_quantificator, _p_msrun, "target");
XicFilterDetectMatch filter_detect_match(p_xic_trace, _monitor, _p_xic_filter, _p_detection, _matching_mode) ;
filter_detect_match.filterDetectQuantify(*(_p_xic.get()), rt_target, p_currentSearchItem, _p_msrun);
}
if (p_xic_trace != nullptr) {
p_xic_trace->setAlignedRtTarget(_p_msrun->getAlignedRtByOriginalRt(rt_target));
......
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