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