| aa_to_weight_ | CompNovoIdentificationBase | protected |
| check_defaults_ | DefaultParamHandler | protected |
| compareSpectra_(const PeakSpectrum &s1, const PeakSpectrum &s2) const | CompNovoIdentificationBase | protected |
| CompNovoIdentificationBase() | CompNovoIdentificationBase | |
| CompNovoIdentificationBase(const CompNovoIdentificationBase &source) | CompNovoIdentificationBase | |
| 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) const | 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 |
| getDefaults() const | DefaultParamHandler | |
| getETDSpectrum_(PeakSpectrum &spec, const String &sequence, Size, double prefix=0.0, double suffix=0.0) | CompNovoIdentificationBase | protected |
| getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp)=0 | CompNovoIdentificationBase | pure 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 | CompNovoIdentificationBase | |
| isotope_distributions_ | CompNovoIdentificationBase | private |
| 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 CompNovoIdentificationBase &source) | CompNovoIdentificationBase | |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| permute_(const String &prefix, String s, std::set< String > &permutations) | CompNovoIdentificationBase | protectedstatic |
| permute_cache_ | CompNovoIdentificationBase | protected |
| residue_to_name_ | CompNovoIdentificationBase | protected |
| selectPivotIons_(std::vector< Size > &pivots, Size left, Size right, std::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 | CompNovoIdentificationBase | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| windowMower_(PeakSpectrum &spec, double windowsize, Size no_peaks) | CompNovoIdentificationBase | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| zhang_ | CompNovoIdentificationBase | protected |
| ~CompNovoIdentificationBase() override | CompNovoIdentificationBase | |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
1.9.1 
