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);
101 std::map<std::string, boost::shared_ptr<FeatureOpenMS> >
features_;
108 template <
typename SpectrumT,
typename TransitionT>
125 return trgroup_.size();
130 std::vector<std::string> result;
131 for (std::size_t i = 0; i < this->size(); i++)
133 result.push_back(trgroup_.getChromatograms()[i].getNativeID());
140 trgroup_.getLibraryIntensity(intensities);
151 template <
typename PeakT>
158 double sn_win_len_,
unsigned int sn_bin_count_) :
159 chromatogram_(chromat), sn_()
162 snt_parameters.
setValue(
"win_len", sn_win_len_);
163 snt_parameters.
setValue(
"bin_count", sn_bin_count_);
164 sn_.setParameters(snt_parameters);
165 sn_.init(chromatogram_);
171 return sn_.getSignalToNoise(*it);
TransitionGroupOpenMS(MRMTransitionGroup< SpectrumT, TransitionT > &trgroup)
Definition: MRMFeatureAccessOpenMS.h:114
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:176
const OpenMS::MSSpectrum< PeakT > & chromatogram_
Definition: MRMFeatureAccessOpenMS.h:175
Feature * feature_
Definition: MRMFeatureAccessOpenMS.h:77
std::vector< std::string > getNativeIDs()
Definition: MRMFeatureAccessOpenMS.h:128
const MRMTransitionGroup< SpectrumT, TransitionT > & trgroup_
Definition: MRMFeatureAccessOpenMS.h:144
An implementation of the OpenSWATH Transition Group Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:109
Iterator MZBegin(CoordinateType mz)
Binary search for peak range begin.
Definition: MSSpectrum.h:506
Definition: ITransition.h:65
std::map< std::string, boost::shared_ptr< FeatureOpenMS > > features_
Definition: MRMFeatureAccessOpenMS.h:101
std::size_t size()
Definition: MRMFeatureAccessOpenMS.h:123
Definition: ITransition.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:152
void getLibraryIntensities(std::vector< double > &intensities)
Definition: MRMFeatureAccessOpenMS.h:138
SignalToNoiseOpenMS(OpenMS::MSSpectrum< PeakT > &chromat, double sn_win_len_, unsigned int sn_bin_count_)
Definition: MRMFeatureAccessOpenMS.h:157
An LC-MS feature.
Definition: Feature.h:66
Management and storage of parameters / INI files.
Definition: Param.h:69
Definition: ITransition.h:56
const MRMFeature & mrmfeature_
Definition: MRMFeatureAccessOpenMS.h:100
~TransitionGroupOpenMS()
Definition: MRMFeatureAccessOpenMS.h:119
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
double getValueAtRT(double RT)
Definition: MRMFeatureAccessOpenMS.h:168
Definition: ITransition.h:73
An implementation of the OpenSWATH MRM Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:84