| aa_to_weight_ | CompNovoIdentificationBase | protected |
| check_defaults_ | DefaultParamHandler | protected |
| compareSpectra_(const PeakSpectrum &s1, const PeakSpectrum &s2) | CompNovoIdentificationBase | protected |
| CompNovoIdentificationBase() | CompNovoIdentificationBase | |
| CompNovoIdentificationBase(const CompNovoIdentificationBase &source) | CompNovoIdentificationBase | |
| CompNovoIdentificationCID() | CompNovoIdentificationCID | |
| CompNovoIdentificationCID(const CompNovoIdentificationCID &source) | CompNovoIdentificationCID | |
| countMissedCleavagesTryptic_(const String &peptide) const | CompNovoIdentificationBase | protected |
| decomp_cache_ | CompNovoIdentificationBase | protected |
| decomp_weights_precision_ | CompNovoIdentificationBase | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| error_name_ | DefaultParamHandler | protected |
| filterDecomps_(std::vector< MassDecomposition > &decomps) | CompNovoIdentificationBase | protected |
| filterPermuts_(std::set< String > &permut) | CompNovoIdentificationBase | protected |
| fragment_mass_tolerance_ | CompNovoIdentificationBase | protected |
| getCIDSpectrum_(PeakSpectrum &spec, const String &sequence, Size charge, double prefix=0.0, double suffix=0.0) | CompNovoIdentificationBase | protected |
| getCIDSpectrumLight_(PeakSpectrum &spec, const String &sequence, double prefix, double suffix) | CompNovoIdentificationBase | protected |
| getDecompositions_(std::vector< MassDecomposition > &decomps, double mass, bool no_caching=false) | CompNovoIdentificationBase | protected |
| getDecompositionsDAC_(std::set< String > &sequences, Size left, Size right, double peptide_weight, const PeakSpectrum &CID_orig_spec, Map< double, IonScore > &CID_nodes) | CompNovoIdentificationCID | protected |
| getDefaults() const | DefaultParamHandler | |
| getETDSpectrum_(PeakSpectrum &spec, const String &sequence, Size, double prefix=0.0, double suffix=0.0) | CompNovoIdentificationBase | protected |
| getIdentification(PeptideIdentification &id, const PeakSpectrum &CID_spec) | CompNovoIdentificationCID | |
| getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp) override | CompNovoIdentificationCID | virtual |
| getModifiedAASequence_(const String &sequence) | CompNovoIdentificationBase | protected |
| getModifiedStringFromAASequence_(const AASequence &sequence) | CompNovoIdentificationBase | protected |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| initIsotopeDistributions_() | CompNovoIdentificationBase | protected |
| IonScore typedef | CompNovoIdentificationCID | |
| isotope_distributions_ | CompNovoIdentificationBase | private |
| IsotopeType typedef | CompNovoIdentificationCID | |
| mass_decomp_algorithm_ | CompNovoIdentificationBase | protected |
| max_decomp_weight_ | CompNovoIdentificationBase | protected |
| max_isotope_ | CompNovoIdentificationBase | protected |
| max_mz_ | CompNovoIdentificationBase | protected |
| max_number_aa_per_decomp_ | CompNovoIdentificationBase | protected |
| max_number_pivot_ | CompNovoIdentificationBase | protected |
| max_subscore_number_ | CompNovoIdentificationBase | protected |
| min_aa_weight_ | CompNovoIdentificationBase | protected |
| min_mz_ | CompNovoIdentificationBase | protected |
| name_to_residue_ | CompNovoIdentificationBase | protected |
| operator=(const CompNovoIdentificationCID &source) | CompNovoIdentificationCID | |
| OpenMS::CompNovoIdentificationBase::operator=(const CompNovoIdentificationBase &source) | CompNovoIdentificationBase | |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| Permut typedef | CompNovoIdentificationCID | |
| permute_(const String &prefix, String s, std::set< String > &permutations) | CompNovoIdentificationBase | protectedstatic |
| permute_cache_ | CompNovoIdentificationBase | protected |
| precursor_mass_tolerance_ | CompNovoIdentificationCID | protected |
| reducePermuts_(std::set< String > &permuts, const PeakSpectrum &CID_orig_spec, double prefix, double suffix) | CompNovoIdentificationCID | protected |
| residue_to_name_ | CompNovoIdentificationBase | protected |
| selectPivotIons_(std::vector< Size > &pivots, Size left, Size right, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, double precursor_weight, bool full_range=false) | CompNovoIdentificationBase | protected |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| subsections_ | DefaultParamHandler | protected |
| subspec_to_sequences_ | CompNovoIdentificationBase | protected |
| tryptic_only_ | CompNovoIdentificationBase | protected |
| updateMembers_() override | CompNovoIdentificationCID | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| windowMower_(PeakSpectrum &spec, double windowsize, Size no_peaks) | CompNovoIdentificationBase | protected |
| zhang_ | CompNovoIdentificationBase | protected |
| ~CompNovoIdentificationBase() override | CompNovoIdentificationBase | |
| ~CompNovoIdentificationCID() override | CompNovoIdentificationCID | |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
1.8.16