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| | PSLPFormulation () |
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| virtual | ~PSLPFormulation () |
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| template<typename InputPeakType > |
| void | createAndSolveILPForKnownLCMSMapFeatureBased (const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< IndexTriple > &variable_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, std::vector< int > &solution_indices) |
| | Encode ILP formulation for a given LC-MS map, but unknown protein sample. More...
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| void | createAndSolveILPForInclusionListCreation (PrecursorIonSelectionPreprocessing &preprocessing, UInt ms2_spectra_per_rt_bin, UInt max_list_size, FeatureMap<> &precursors, bool solve_ILP=true) |
| | Find a set of precursors, so that the protein coverage is maximal and that the number of precursors per bin is not exceeded. More...
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| template<typename InputPeakType > |
| void | createAndSolveCombinedLPForKnownLCMSMapFeatureBased (const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< IndexTriple > &variable_indices, std::vector< int > &solution_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, Size step_size=0, bool sequential_order=false) |
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| void | updateStepSizeConstraint (Size iteration, UInt step_size) |
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| void | updateFeatureILPVariables (FeatureMap<> &new_features, std::vector< IndexTriple > &variable_indices, std::map< Size, std::vector< String > > &feature_constraints_map) |
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| void | updateRTConstraintsForSequentialILP (Size &rt_index, UInt ms2_spectra_per_rt_bin, Size max_rt_index) |
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| void | updateCombinedILP (FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices, std::vector< String > &new_protein_accs, std::vector< String > &protein_accs, PSProteinInference &prot_inference, Size &variable_counter, std::map< String, std::vector< Size > > &protein_feature_map, Feature &new_feature, std::map< String, Size > &protein_variable_index_map, std::map< String, std::set< String > > &prot_id_counter) |
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| void | solveILP (std::vector< int > &solution_indices) |
| | Solve the ILP. More...
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| void | setLPSolver (LPWrapper::SOLVER solver) |
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| LPWrapper::SOLVER | getLPSolver () |
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Public Member Functions inherited from DefaultParamHandler |
| | DefaultParamHandler (const String &name) |
| | Constructor with name that is displayed in error messages. More...
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| | DefaultParamHandler (const DefaultParamHandler &rhs) |
| | Copy constructor. More...
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| virtual | ~DefaultParamHandler () |
| | Destructor. More...
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| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| | Assignment operator. More...
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| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| | Equality operator. More...
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| void | setParameters (const Param ¶m) |
| | Sets the parameters. More...
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| const Param & | getParameters () const |
| | Non-mutable access to the parameters. More...
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| const Param & | getDefaults () const |
| | Non-mutable access to the default parameters. More...
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| const String & | getName () const |
| | Non-mutable access to the name. More...
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| void | setName (const String &name) |
| | Mutable access to the name. More...
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| const std::vector< String > & | getSubsections () const |
| | Non-mutable access to the registered subsections. More...
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| template<typename InputPeakType > |
| void | getXIC_ (const std::vector< std::pair< Size, Size > > &end_points, std::vector< DoubleReal > &weights, const MSExperiment< InputPeakType > &experiment, const bool normalize) |
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| template<typename InputPeakType > |
| void | calculateXICs_ (std::vector< std::vector< DoubleReal > > &xics, const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const bool normalize) |
| | Calculates the XICs for all features. More...
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| void | createAndSolveILP_ (const FeatureMap<> &features, std::vector< std::vector< DoubleReal > > &intensity_weights, std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::vector< IndexTriple > &variable_indices, std::vector< int > &solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans) |
| | Creates and solves the ILP. More...
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| void | createAndSolveCombinedLPFeatureBased_ (const FeatureMap<> &features, std::vector< std::vector< DoubleReal > > &intensity_weights, std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::vector< IndexTriple > &variable_indices, std::vector< Int > &solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans, Size step_size=0, bool sequential_order=false) |
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| void | addProteinToILP_ (PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, std::vector< DoubleReal > >::const_iterator map_iter, Size &counter, Size &pep_counter, Size &feature_counter, std::vector< IndexTriple > &variable_indices, std::map< String, Size > &protein_penalty_index_map, FeatureMap<> &precursors) |
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| void | addPrecursorAcquisitionNumberConstraint_ (std::vector< IndexTriple > &variable_indices, Size number_of_features, UInt number_of_msms_per_precursor) |
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| void | addMaxInclusionListSizeConstraints_ (std::vector< IndexTriple > &variable_indices, UInt max_list_size) |
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| void | addRTBinCapacityConstraint_ (std::vector< IndexTriple > &variable_indices, Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order=false) |
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| void | addProteinCoverageConstraint_ (std::vector< IndexTriple > &variable_indices, PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, Size > protein_variable_index_map) |
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| void | addStepSizeConstraint_ (std::vector< IndexTriple > &variable_indices, UInt step_size) |
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| void | assembleInclusionListForProteinBasedLP_ (std::vector< IndexTriple > &variable_indices, FeatureMap<> &precursors, std::vector< int > &solution_indices, PrecursorIonSelectionPreprocessing &preprocessing) |
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| void | updateObjFunction_ (String acc, FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices) |
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| Int | getNumberOfPrecsInSpectrum_ (Int constr_idx) |
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Protected Member Functions inherited from DefaultParamHandler |
| virtual void | updateMembers_ () |
| | This method is used to update extra member variables at the end of the setParameters() method. More...
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| void | defaultsToParam_ () |
| | Updates the parameters after the defaults have been set in the constructor. More...
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Implements ILP formulation of precursor selection problems.