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OpenMS
2.6.0
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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
138 std::vector<std::string> result;
139 for (std::size_t i = 0; i < this->
size(); i++)
159 template <
typename ContainerT>
166 double sn_win_len_,
unsigned int sn_bin_count_,
bool write_log_messages) :
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");
192 typename ContainerT::const_iterator iter =
chromatogram_.MZEnd(RT);
200 typename ContainerT::const_iterator prev = iter;
206 if (std::fabs(prev->getMZ() - RT) < std::fabs(iter->getMZ() - RT) )
std::map< std::string, boost::shared_ptr< FeatureOpenMS > > features_
Definition: MRMFeatureAccessOpenMS.h:108
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
virtual void init(const Container &c)
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimat...
Definition: SignalToNoiseEstimator.h:100
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
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
TransitionGroupOpenMS(MRMTransitionGroup< SpectrumT, TransitionT > &trgroup)
Definition: MRMFeatureAccessOpenMS.h:122
SignalToNoiseOpenMS(ContainerT &chromat, double sn_win_len_, unsigned int sn_bin_count_, bool write_log_messages)
Definition: MRMFeatureAccessOpenMS.h:165
~TransitionGroupOpenMS() override
Definition: MRMFeatureAccessOpenMS.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
virtual double getSignalToNoise(const Size index) const
Definition: SignalToNoiseEstimator.h:108
Feature * feature_
Definition: MRMFeatureAccessOpenMS.h:76
const MRMTransitionGroup< SpectrumT, TransitionT > & trgroup_
Definition: MRMFeatureAccessOpenMS.h:152
An implementation of the OpenSWATH MRM Feature Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:83
OpenMS::SignalToNoiseEstimatorMedian< ContainerT > sn_
Definition: MRMFeatureAccessOpenMS.h:221
void getLibraryIntensities(std::vector< double > &intensities) const override
Definition: MRMFeatureAccessOpenMS.h:146
void setParameters(const Param ¶m)
Sets the parameters.
Definition: ITransition.h:46
const Param & getParameters() const
Non-mutable access to the parameters.
const ContainerT & chromatogram_
Definition: MRMFeatureAccessOpenMS.h:220
Definition: ITransition.h:69
const MRMFeature & mrmfeature_
Definition: MRMFeatureAccessOpenMS.h:107
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:73
An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:160
An implementation of the OpenSWATH Transition Group Access interface using OpenMS.
Definition: MRMFeatureAccessOpenMS.h:117
Definition: ITransition.h:77
std::size_t size() const override
Definition: MRMFeatureAccessOpenMS.h:131
std::vector< ChromatogramType > & getChromatograms()
Definition: MRMTransitionGroup.h:174
void getLibraryIntensity(std::vector< double > &result) const
Definition: MRMTransitionGroup.h:320
double getValueAtRT(double RT) override
Definition: MRMFeatureAccessOpenMS.h:186
Size size() const
Definition: MRMTransitionGroup.h:125
Definition: ITransition.h:56