35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_MRMFEATUREACCESSOPENMS_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_MRMFEATUREACCESSOPENMS_H
45 #include <boost/shared_ptr.hpp>
68 void getRT(std::vector<double>& rt);
70 void getIntensity(std::vector<double>& intens);
93 boost::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID);
95 boost::shared_ptr<OpenSwath::IFeature> getPrecursorFeature(std::string nativeID);
97 std::vector<std::string> getPrecursorIDs()
const;
107 std::map<std::string, boost::shared_ptr<FeatureOpenMS> >
features_;
115 template <
typename SpectrumT,
typename TransitionT>
132 return trgroup_.size();
137 std::vector<std::string> result;
138 for (std::size_t i = 0; i < this->size(); i++)
140 result.push_back(trgroup_.getChromatograms()[i].getNativeID());
147 trgroup_.getLibraryIntensity(intensities);
158 template <
typename PeakT>
165 double sn_win_len_,
unsigned int sn_bin_count_) :
166 chromatogram_(chromat), sn_()
169 snt_parameters.
setValue(
"win_len", sn_win_len_);
170 snt_parameters.
setValue(
"bin_count", sn_bin_count_);
171 sn_.setParameters(snt_parameters);
172 sn_.init(chromatogram_);
177 if (chromatogram_.empty()) {
return -1;}
184 if (iter == chromatogram_.end())
190 if (prev != chromatogram_.begin() )
195 if (std::fabs(prev->getMZ() - RT) < std::fabs(iter->getMZ() - RT) )
198 return sn_.getSignalToNoise(*prev);
203 return sn_.getSignalToNoise(*iter);
TransitionGroupOpenMS(MRMTransitionGroup< SpectrumT, TransitionT > &trgroup)
Definition: MRMFeatureAccessOpenMS.h:121
An implementation of the OpenSWATH Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:59
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > > sn_
Definition: MRMFeatureAccessOpenMS.h:210
const OpenMS::MSSpectrum< PeakT > & chromatogram_
Definition: MRMFeatureAccessOpenMS.h:209
Feature * feature_
Definition: MRMFeatureAccessOpenMS.h:77
std::vector< std::string > getNativeIDs()
Definition: MRMFeatureAccessOpenMS.h:135
const MRMTransitionGroup< SpectrumT, TransitionT > & trgroup_
Definition: MRMFeatureAccessOpenMS.h:151
An implementation of the OpenSWATH Transition Group Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:116
Iterator MZEnd(CoordinateType mz)
Binary search for peak range end (returns the past-the-end iterator)
Definition: MSSpectrum.h:560
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: ITransition.h:68
std::map< std::string, boost::shared_ptr< FeatureOpenMS > > features_
Definition: MRMFeatureAccessOpenMS.h:107
std::size_t size()
Definition: MRMFeatureAccessOpenMS.h:130
Definition: ITransition.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:159
void getLibraryIntensities(std::vector< double > &intensities)
Definition: MRMFeatureAccessOpenMS.h:145
SignalToNoiseOpenMS(OpenMS::MSSpectrum< PeakT > &chromat, double sn_win_len_, unsigned int sn_bin_count_)
Definition: MRMFeatureAccessOpenMS.h:164
An LC-MS feature.
Definition: Feature.h:70
std::map< std::string, boost::shared_ptr< FeatureOpenMS > > precursor_features_
Definition: MRMFeatureAccessOpenMS.h:108
Management and storage of parameters / INI files.
Definition: Param.h:75
Definition: ITransition.h:56
const MRMFeature & mrmfeature_
Definition: MRMFeatureAccessOpenMS.h:106
~TransitionGroupOpenMS()
Definition: MRMFeatureAccessOpenMS.h:126
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
double getValueAtRT(double RT)
Definition: MRMFeatureAccessOpenMS.h:175
Definition: ITransition.h:76
An implementation of the OpenSWATH MRM Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:84