OpenMS
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)PSLPFormulationprotected
addPrecursorAcquisitionNumberConstraint_(std::vector< IndexTriple > &variable_indices, Size number_of_features, UInt number_of_msms_per_precursor)PSLPFormulationprotected
addProteinCoverageConstraint_(std::vector< IndexTriple > &variable_indices, PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, Size > protein_variable_index_map)PSLPFormulationprotected
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)PSLPFormulationprotected
addRTBinCapacityConstraint_(std::vector< IndexTriple > &variable_indices, Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order=false)PSLPFormulationprotected
addStepSizeConstraint_(std::vector< IndexTriple > &variable_indices, UInt step_size)PSLPFormulationprotected
assembleInclusionListForProteinBasedLP_(std::vector< IndexTriple > &variable_indices, FeatureMap &precursors, std::vector< int > &solution_indices, PrecursorIonSelectionPreprocessing &preprocessing)PSLPFormulationprotected
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)PSLPFormulationprotected
check_defaults_DefaultParamHandlerprotected
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)PSLPFormulationprotected
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)PSLPFormulationprotected
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
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
getDefaults() constDefaultParamHandler
getLPSolver()PSLPFormulationinline
getName() constDefaultParamHandler
getNumberOfPrecsInSpectrum_(Int constr_idx)PSLPFormulationprotected
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
getXIC_(const std::vector< std::pair< Size, Size > > &end_points, std::vector< double > &weights, const PeakMap &experiment, const bool normalize)PSLPFormulationprotected
model_PSLPFormulationprotected
operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
PSLPFormulation()PSLPFormulation
setLPSolver(LPWrapper::SOLVER solver)PSLPFormulationinline
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
solveILP(std::vector< int > &solution_indices)PSLPFormulation
solver_PSLPFormulationprotected
subsections_DefaultParamHandlerprotected
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_()DefaultParamHandlerprotectedvirtual
updateObjFunction_(const String &acc, FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices)PSLPFormulationprotected
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_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~PSLPFormulation() overridePSLPFormulation