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| PSLPFormulation () |
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virtual | ~PSLPFormulation () |
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void | createAndSolveILPForKnownLCMSMapFeatureBased (const FeatureMap &features, const PeakMap &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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void | createAndSolveCombinedLPForKnownLCMSMapFeatureBased (const FeatureMap &features, const PeakMap &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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void | getXIC_ (const std::vector< std::pair< Size, Size > > &end_points, std::vector< double > &weights, const PeakMap &experiment, const bool normalize) |
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void | calculateXICs_ (std::vector< std::vector< double > > &xics, const FeatureMap &features, const PeakMap &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< double > > &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< double > > &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< double > >::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.