27 class IsoLayeredGenerator;
28 class IsoThresholdGenerator;
29 class IsoOrderedGenerator;
205 const std::vector<int>& atomCounts,
206 const std::vector<std::vector<double> >& isotopeMasses,
207 const std::vector<std::vector<double> >& isotopeProbabilities,
222 double getMass() final;
223 double getIntensity() final;
224 double getLogIntensity() final;
227 std::unique_ptr<
IsoSpec::IsoLayeredGenerator> ILG;
270 const std::vector<int>& atomCounts,
271 const std::vector<std::vector<double> >& isotopeMasses,
272 const std::vector<std::vector<double> >& isotopeProbabilities,
289 double getMass() final;
290 double getIntensity() final;
291 double getLogIntensity() final;
295 std::unique_ptr<
IsoSpec::IsoThresholdGenerator> ITG;
328 const std::vector<int>& atomCounts,
329 const std::vector<std::vector<double> >& isotopeMasses,
330 const std::vector<std::vector<double> >& isotopeProbabilities);
344 inline
double getMass() final;
345 inline
double getIntensity() final;
346 inline
double getLogIntensity() final;
349 std::unique_ptr<
IsoSpec::IsoOrderedGenerator> IOG;
395 const std::vector<int>& atomCounts,
396 const std::vector<std::vector<double> >& isotopeMasses,
397 const std::vector<std::vector<double> >& isotopeProbabilities,
399 bool do_p_trim =
false);
415 std::unique_ptr<
IsoSpec::IsoLayeredGenerator> ILG;
416 const
double target_prob;
417 const
bool do_p_trim;
459 const std::vector<int>& atomCounts,
460 const std::vector<std::vector<double> >& isotopeMasses,
461 const std::vector<std::vector<double> >& isotopeProbabilities,
478 std::unique_ptr<
IsoSpec::IsoThresholdGenerator> ITG;
Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra.
Definition: IsoSpecWrapper.h:63
virtual Peak1D getConf()=0
Obtain the current isotopologue.
virtual bool nextConf()=0
Move the generator to a next isotopologue.
virtual ~IsoSpecGeneratorWrapper()=default
Destructor.
virtual double getIntensity()=0
Obtain the intensity (probability, relative peak height) of the current configuration.
virtual double getLogIntensity()=0
Obtain the natural logarithm of the intensity (probability, relative peak height) of the current conf...
virtual double getMass()=0
Obtain the mass of the current isotopologue.
Generate the stream of configurations, ordered from most likely to least likely.
Definition: IsoSpecWrapper.h:316
~IsoSpecOrderedGeneratorWrapper()
bool nextConf() final
Move the generator to a next isotopologue.
IsoSpecOrderedGeneratorWrapper(const EmpiricalFormula &formula)
Setup the algorithm to run on an EmpiricalFormula.
IsoSpecOrderedGeneratorWrapper(const IsoSpecOrderedGeneratorWrapper &)=delete
IsoSpecOrderedGeneratorWrapper(const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities)
Constructor.
Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than...
Definition: IsoSpecWrapper.h:252
IsoSpecThresholdGeneratorWrapper(const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities, double threshold, bool absolute)
Constructor.
IsoSpecThresholdGeneratorWrapper(const IsoSpecThresholdGeneratorWrapper &)=delete
bool nextConf() final
Move the generator to a next isotopologue.
IsoSpecThresholdGeneratorWrapper(const EmpiricalFormula &formula, double threshold, bool absolute)
Setup the algorithm to run on an EmpiricalFormula.
~IsoSpecThresholdGeneratorWrapper()
A non-generator version of IsoSpecThresholdGeneratorWrapper.
Definition: IsoSpecWrapper.h:441
IsoSpecThresholdWrapper(const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities, double threshold, bool absolute)
Constructor.
~IsoSpecThresholdWrapper()
IsotopeDistribution run() final
Run the algorithm.
IsoSpecThresholdWrapper(const EmpiricalFormula &formula, double threshold, bool absolute)
Setup the algorithm to run on an EmpiricalFormula.
IsoSpecThresholdWrapper(const IsoSpecThresholdWrapper &)=delete
Generate a p-set of configurations for a given p (that is, a set of configurations such that their pr...
Definition: IsoSpecWrapper.h:189
IsoSpecTotalProbGeneratorWrapper(const IsoSpecTotalProbGeneratorWrapper &)=delete
delete copy constructor
~IsoSpecTotalProbGeneratorWrapper()
IsoSpecTotalProbGeneratorWrapper(const EmpiricalFormula &formula, double p)
Setup the algorithm to run on an EmpiricalFormula.
bool nextConf() final
Move the generator to a next isotopologue.
IsoSpecTotalProbGeneratorWrapper(const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities, double p)
Constructor.
Create a p-set of configurations for a given p (that is, a set of configurations such that their prob...
Definition: IsoSpecWrapper.h:378
IsoSpecTotalProbWrapper(const IsoSpecTotalProbWrapper &)=delete
IsotopeDistribution run() final
Run the algorithm.
IsoSpecTotalProbWrapper(const EmpiricalFormula &formula, double p, bool do_p_trim=false)
Setup the algorithm to run on an EmpiricalFormula.
~IsoSpecTotalProbWrapper()
IsoSpecTotalProbWrapper(const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities, double p, bool do_p_trim=false)
Constructor.
A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classe...
Definition: IsoSpecWrapper.h:130
virtual IsotopeDistribution run()=0
Run the algorithm.
virtual ~IsoSpecWrapper()=default
Definition: IsotopeDistribution.h:39
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:28
Definition: IsoSpecWrapper.h:26
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22