| 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 |  | 
  | 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 |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | error_name_ | DefaultParamHandler | protected | 
  | estimatePrecursorWeight_(const PeakSpectrum &ETD_spec, Size &charge) | CompNovoIdentificationBase | 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, DoubleReal prefix=0.0, DoubleReal suffix=0.0) | CompNovoIdentificationBase | protected | 
  | getCIDSpectrumLight_(PeakSpectrum &spec, const String &sequence, DoubleReal prefix, DoubleReal suffix) | CompNovoIdentificationBase | protected | 
  | getDecompositions_(std::vector< MassDecomposition > &decomps, DoubleReal mass, bool no_caching=false) | CompNovoIdentificationBase | protected | 
  | getDefaults() const | DefaultParamHandler |  | 
  | 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 | protected | 
  | 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 | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | permute_(String prefix, String s, std::set< String > &permutations) | CompNovoIdentificationBase | protected | 
  | permute_cache_ | CompNovoIdentificationBase | protected | 
  | residue_to_name_ | CompNovoIdentificationBase | protected | 
  | selectPivotIons_(std::vector< Size > &pivots, Size left, Size right, Map< DoubleReal, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, DoubleReal 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_() | CompNovoIdentificationBase | protectedvirtual | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | windowMower_(PeakSpectrum &spec, DoubleReal windowsize, Size no_peaks) | CompNovoIdentificationBase | protected | 
  | zhang_ | CompNovoIdentificationBase | protected | 
  | ~CompNovoIdentificationBase() | CompNovoIdentificationBase | virtual | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual |