, including all inherited members.
| check_defaults_ | DefaultParamHandler | [protected] |
| checkForRequiredUserParams_(FeatureMap<> &features) | PrecursorIonSelection | [private] |
| convertPeptideIdScores_(std::vector< PeptideIdentification > &pep_ids) | PrecursorIonSelection | [private] |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | [protected] |
| defaultsToParam_() | DefaultParamHandler | [protected] |
| DEX enum value | PrecursorIonSelection | |
| DOWNSHIFT enum value | PrecursorIonSelection | |
| error_name_ | DefaultParamHandler | [protected] |
| filterPeptideIds_(std::vector< PeptideIdentification > &pep_ids) | PrecursorIonSelection | [private] |
| filterProtIds_(std::vector< ProteinIdentification > &prot_ids) | PrecursorIonSelection | [private] |
| fraction_counter_ | PrecursorIonSelection | [private] |
| getDefaults() const | DefaultParamHandler | |
| getLPSolver() | PrecursorIonSelection | [inline] |
| getMaxScore() const | PrecursorIonSelection | |
| getName() const | DefaultParamHandler | |
| getNextPrecursors(FeatureMap<> &features, FeatureMap<> &next_features, UInt number) | PrecursorIonSelection | |
| getNextPrecursors(std::vector< Int > &solution_indices, std::vector< PSLPFormulation::IndexTriple > &variable_indices, std::set< Int > &measured_variables, FeatureMap<> &features, FeatureMap<> &new_features, UInt step_size, PSLPFormulation &ilp) | PrecursorIonSelection | |
| getNextPrecursorsSeq(FeatureMap<> &features, FeatureMap<> &next_features, UInt number, DoubleReal &rt) | PrecursorIonSelection | |
| getParameters() const | DefaultParamHandler | |
| getPeptideProteinCounter() | PrecursorIonSelection | [inline] |
| getSubsections() const | DefaultParamHandler | |
| ILP_IPS enum value | PrecursorIonSelection | |
| IPS enum value | PrecursorIonSelection | |
| max_iteration_ | PrecursorIonSelection | [private] |
| max_score_ | PrecursorIonSelection | [private] |
| min_pep_ids_ | PrecursorIonSelection | [private] |
| mz_tolerance_ | PrecursorIonSelection | [private] |
| mz_tolerance_unit_ | PrecursorIonSelection | [private] |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | [virtual] |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | [virtual] |
| param_ | DefaultParamHandler | [protected] |
| PrecursorIonSelection() | PrecursorIonSelection | |
| PrecursorIonSelection(const PrecursorIonSelection &source) | PrecursorIonSelection | |
| prot_id_counter_ | PrecursorIonSelection | [private] |
| rescore(FeatureMap<> &features, std::vector< PeptideIdentification > &new_pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, bool check_meta_values=true) | PrecursorIonSelection | |
| rescore_(FeatureMap<> &features, std::vector< PeptideIdentification > &new_pep_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, PSProteinInference &protein_inference) | PrecursorIonSelection | [private] |
| reset() | PrecursorIonSelection | |
| setLPSolver(LPWrapper::SOLVER solver) | PrecursorIonSelection | [inline] |
| setMaxScore(const DoubleReal &max_score) | PrecursorIonSelection | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| shiftDown_(FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc) | PrecursorIonSelection | [private] |
| shiftUp_(FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc) | PrecursorIonSelection | [private] |
| simulateILPBasedIPSRun_(FeatureMap<> &features, MSExperiment<> &experiment, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String output_path, String precursor_path="") | PrecursorIonSelection | [private] |
| simulateRun(FeatureMap<> &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, MSExperiment<> &experiment, String precursor_path="") | PrecursorIonSelection | |
| simulateRun_(FeatureMap<> &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, String precursor_path="") | PrecursorIonSelection | [private] |
| solver_ | PrecursorIonSelection | [private] |
| sortByTotalScore(FeatureMap<> &features) | PrecursorIonSelection | [inline] |
| SPS enum value | PrecursorIonSelection | |
| subsections_ | DefaultParamHandler | [protected] |
| Type enum name | PrecursorIonSelection | |
| type_ | PrecursorIonSelection | [private] |
| updateMembers_() | PrecursorIonSelection | [private, virtual] |
| UPSHIFT enum value | PrecursorIonSelection | |
| warn_empty_defaults_ | DefaultParamHandler | [protected] |
| x_variable_number_ | PrecursorIonSelection | [private] |
| ~DefaultParamHandler() | DefaultParamHandler | [virtual] |
| ~PrecursorIonSelection() | PrecursorIonSelection | |