| OpenMS 2.5.0

PSLPFormulation Member List

This is the complete list of members for PSLPFormulation, including all inherited members.

addMaxInclusionListSizeConstraints_(std::vector< IndexTriple > &variable_indices, UInt max_list_size) | PSLPFormulation | protected
addPrecursorAcquisitionNumberConstraint_(std::vector< IndexTriple > &variable_indices, Size number_of_features, UInt number_of_msms_per_precursor) | PSLPFormulation | protected
addProteinCoverageConstraint_(std::vector< IndexTriple > &variable_indices, PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, Size > protein_variable_index_map) | PSLPFormulation | protected
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) | PSLPFormulation | protected
addRTBinCapacityConstraint_(std::vector< IndexTriple > &variable_indices, Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order=false) | PSLPFormulation | protected
addStepSizeConstraint_(std::vector< IndexTriple > &variable_indices, UInt step_size) | PSLPFormulation | protected
assembleInclusionListForProteinBasedLP_(std::vector< IndexTriple > &variable_indices, FeatureMap &precursors, std::vector< int > &solution_indices, PrecursorIonSelectionPreprocessing &preprocessing) | PSLPFormulation | protected
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) | PSLPFormulation | protected
check_defaults_ | DefaultParamHandler | protected
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) | PSLPFormulation | protected
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) | PSLPFormulation |
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) | PSLPFormulation | protected
createAndSolveILPForInclusionListCreation(PrecursorIonSelectionPreprocessing &preprocessing, UInt ms2_spectra_per_rt_bin, UInt max_list_size, FeatureMap &precursors, bool solve_ILP=true) | PSLPFormulation |
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) | PSLPFormulation |
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
error_name_ | DefaultParamHandler | protected
getDefaults() const | DefaultParamHandler |
getLPSolver() | PSLPFormulation | inline
getName() const | DefaultParamHandler |
getNumberOfPrecsInSpectrum_(Int constr_idx) | PSLPFormulation | protected
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
getXIC_(const std::vector< std::pair< Size, Size > > &end_points, std::vector< double > &weights, const PeakMap &experiment, const bool normalize) | PSLPFormulation | protected
model_ | PSLPFormulation | protected
operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
param_ | DefaultParamHandler | protected
PSLPFormulation() | PSLPFormulation |
setLPSolver(LPWrapper::SOLVER solver) | PSLPFormulation | inline
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
solveILP(std::vector< int > &solution_indices) | PSLPFormulation |
solver_ | PSLPFormulation | protected
subsections_ | DefaultParamHandler | protected
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) | PSLPFormulation |
updateFeatureILPVariables(FeatureMap &new_features, std::vector< IndexTriple > &variable_indices, std::map< Size, std::vector< String > > &feature_constraints_map) | PSLPFormulation |
updateMembers_() | DefaultParamHandler | protected virtual
updateObjFunction_(String acc, FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices) | PSLPFormulation | protected
updateRTConstraintsForSequentialILP(Size &rt_index, UInt ms2_spectra_per_rt_bin, Size max_rt_index) | PSLPFormulation |
updateStepSizeConstraint(Size iteration, UInt step_size) | PSLPFormulation |
warn_empty_defaults_ | DefaultParamHandler | protected
~DefaultParamHandler() | DefaultParamHandler | virtual
~PSLPFormulation() override | PSLPFormulation |