, including all inherited members.
| 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 | [protected, virtual] |
| warn_empty_defaults_ | DefaultParamHandler | [protected] |
| windowMower_(PeakSpectrum &spec, DoubleReal windowsize, Size no_peaks) | CompNovoIdentificationBase | [protected] |
| zhang_ | CompNovoIdentificationBase | [protected] |
| ~CompNovoIdentificationBase() | CompNovoIdentificationBase | [virtual] |
| ~DefaultParamHandler() | DefaultParamHandler | [virtual] |