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OpenMS
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This is the complete list of members for ProSEAlgorithm, including all inherited members.
| annotate_psm_ | ProSEAlgorithm | protected |
| calibration_enabled_ | ProSEAlgorithm | protected |
| calibration_min_psms_ | ProSEAlgorithm | protected |
| calibration_subset_ratio_ | ProSEAlgorithm | protected |
| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| computeModMatchTolerance_() const | ProSEAlgorithm | inlineprotected |
| current_logger_ | ProgressLogger | mutableprotected |
| decoy_prefix_ | ProSEAlgorithm | protected |
| decoys_ | ProSEAlgorithm | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| endProgress(UInt64 bytes_processed=0) const | ProgressLogger | |
| enzyme_ | ProSEAlgorithm | protected |
| error_name_ | DefaultParamHandler | protected |
| ExitCodes enum name | ProSEAlgorithm | |
| fdr_protein_ | ProSEAlgorithm | protected |
| fdr_psm_ | ProSEAlgorithm | protected |
| fragment_mass_tolerance_ | ProSEAlgorithm | protected |
| fragment_mass_tolerance_unit_ | ProSEAlgorithm | protected |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| isOpenSearchMode_() const | ProSEAlgorithm | inlineprotected |
| last_calibration_result_ | ProSEAlgorithm | mutableprotected |
| last_invoke_ | ProgressLogger | mutableprotected |
| last_mod_match_tolerance_used_ | ProSEAlgorithm | mutableprotected |
| logModificationAnalysisSummary_(const SearchResult &result, const String &output_base_name) const | ProSEAlgorithm | protected |
| logSearchDiagnostics_(const PeakMap &spectra, const std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids) const | ProSEAlgorithm | protected |
| LogType enum name | ProgressLogger | |
| modifications_fixed_ | ProSEAlgorithm | protected |
| modifications_max_variable_mods_per_peptide_ | ProSEAlgorithm | protected |
| modifications_variable_ | ProSEAlgorithm | protected |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| peptide_enzyme_specificity_ | ProSEAlgorithm | protected |
| peptide_max_size_ | ProSEAlgorithm | protected |
| peptide_min_size_ | ProSEAlgorithm | protected |
| peptide_missed_cleavages_ | ProSEAlgorithm | protected |
| peptide_motif_ | ProSEAlgorithm | protected |
| postProcessHits_(const PeakMap &exp, std::vector< std::vector< ProSEAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, Size top_hits, const StringList &modifications_fixed, const StringList &modifications_variable, Int peptide_missed_cleavages, double precursor_mass_tolerance, double fragment_mass_tolerance, const String &precursor_mass_tolerance_unit_ppm, const String &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const String &enzyme, const String &database_name) const | ProSEAlgorithm | protected |
| precursor_isotopes_ | ProSEAlgorithm | protected |
| precursor_mass_tolerance_lower_ | ProSEAlgorithm | mutableprotected |
| precursor_mass_tolerance_unit_ | ProSEAlgorithm | protected |
| precursor_mass_tolerance_upper_ | ProSEAlgorithm | mutableprotected |
| precursor_max_charge_ | ProSEAlgorithm | protected |
| precursor_min_charge_ | ProSEAlgorithm | protected |
| prepareContext(const std::vector< FASTAFile::FASTAEntry > &fasta_db) const | ProSEAlgorithm | |
| preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm) | ProSEAlgorithm | protectedstatic |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProSEAlgorithm() | ProSEAlgorithm | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| report_top_hits_ | ProSEAlgorithm | protected |
| runCalibrationPass_(PeakMap &spectra, FragmentIndex &fragment_index, const std::vector< FASTAFile::FASTAEntry > &db) const | ProSEAlgorithm | protected |
| search(const String &in_spectra, const String &in_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const | ProSEAlgorithm | |
| search(PeakMap &spectra, const std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const | ProSEAlgorithm | |
| search(PeakMap &spectra, SearchContext &ctx, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const | ProSEAlgorithm | |
| searchWithModificationAnalysis(const String &in_spectra, const String &in_db, const String &output_base_name="") const | ProSEAlgorithm | |
| searchWithModificationAnalysis(PeakMap &spectra, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const String &output_base_name="") const | ProSEAlgorithm | |
| searchWithModificationAnalysis(const std::vector< String > &in_spectra_files, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const std::vector< String > &output_base_names={}, const String &aggregate_base_name="") const | ProSEAlgorithm | |
| searchWithModificationAnalysis(const std::vector< String > &in_spectra_files, const String &in_db, const std::vector< String > &output_base_names={}, const String &aggregate_base_name="") const | ProSEAlgorithm | |
| setLogger(ProgressLoggerImpl *logger) | ProgressLogger | |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| subsections_ | DefaultParamHandler | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() override | ProSEAlgorithm | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.8 