44 #include <boost/shared_ptr.hpp> 67 void getRT(std::vector<double>& rt)
const override;
69 void getIntensity(std::vector<double>& intens)
const override;
71 float getIntensity()
const override;
73 double getRT()
const override;
92 boost::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID)
override;
94 boost::shared_ptr<OpenSwath::IFeature> getPrecursorFeature(std::string nativeID)
override;
96 std::vector<std::string> getNativeIDs()
const override;
98 std::vector<std::string> getPrecursorIDs()
const override;
100 float getIntensity()
const override;
102 double getRT()
const override;
104 size_t size()
const override;
108 std::map<std::string, boost::shared_ptr<FeatureOpenMS> >
features_;
116 template <
typename SpectrumT,
typename TransitionT>
131 std::size_t
size()
const override 133 return trgroup_.size();
138 std::vector<std::string> result;
139 for (std::size_t i = 0; i < this->size(); i++)
141 result.push_back(trgroup_.getChromatograms()[i].getNativeID());
148 trgroup_.getLibraryIntensity(intensities);
159 template <
typename ContainerT>
166 double sn_win_len_,
unsigned int sn_bin_count_,
bool write_log_messages) :
167 chromatogram_(chromat), sn_()
170 snt_parameters.
setValue(
"win_len", sn_win_len_);
171 snt_parameters.
setValue(
"bin_count", sn_bin_count_);
173 if (write_log_messages)
175 snt_parameters.
setValue(
"write_log_messages",
"true");
179 snt_parameters.
setValue(
"write_log_messages",
"false");
182 sn_.setParameters(snt_parameters);
183 sn_.init(chromatogram_);
188 if (chromatogram_.empty()) {
return -1;}
192 typename ContainerT::const_iterator iter = chromatogram_.MZEnd(RT);
195 if (iter == chromatogram_.end())
200 typename ContainerT::const_iterator prev = iter;
201 if (prev != chromatogram_.begin() )
206 if (std::fabs(prev->getMZ() - RT) < std::fabs(iter->getMZ() - RT) )
209 return sn_.getSignalToNoise(*prev);
214 return sn_.getSignalToNoise(*iter);
TransitionGroupOpenMS(MRMTransitionGroup< SpectrumT, TransitionT > &trgroup)
Definition: MRMFeatureAccessOpenMS.h:122
std::vector< std::string > getNativeIDs() const override
Definition: MRMFeatureAccessOpenMS.h:136
An implementation of the OpenSWATH Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:58
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
~TransitionGroupOpenMS() override
Definition: MRMFeatureAccessOpenMS.h:127
Feature * feature_
Definition: MRMFeatureAccessOpenMS.h:76
const MRMTransitionGroup< SpectrumT, TransitionT > & trgroup_
Definition: MRMFeatureAccessOpenMS.h:152
SignalToNoiseOpenMS(ContainerT &chromat, double sn_win_len_, unsigned int sn_bin_count_, bool write_log_messages)
Definition: MRMFeatureAccessOpenMS.h:165
An implementation of the OpenSWATH Transition Group Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:117
OpenMS::SignalToNoiseEstimatorMedian< ContainerT > sn_
Definition: MRMFeatureAccessOpenMS.h:221
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::size_t size() const override
Definition: MRMFeatureAccessOpenMS.h:131
Definition: ITransition.h:68
std::map< std::string, boost::shared_ptr< FeatureOpenMS > > features_
Definition: MRMFeatureAccessOpenMS.h:108
Definition: ITransition.h:45
An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:160
An LC-MS feature.
Definition: Feature.h:70
std::map< std::string, boost::shared_ptr< FeatureOpenMS > > precursor_features_
Definition: MRMFeatureAccessOpenMS.h:109
Management and storage of parameters / INI files.
Definition: Param.h:74
Definition: ITransition.h:55
const MRMFeature & mrmfeature_
Definition: MRMFeatureAccessOpenMS.h:107
double getValueAtRT(double RT) override
Definition: MRMFeatureAccessOpenMS.h:186
const ContainerT & chromatogram_
Definition: MRMFeatureAccessOpenMS.h:220
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:49
void getLibraryIntensities(std::vector< double > &intensities) const override
Definition: MRMFeatureAccessOpenMS.h:146
Definition: ITransition.h:76
An implementation of the OpenSWATH MRM Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:83