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 | |
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 |
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 | virtual |
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, 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 |
zhang_ | CompNovoIdentificationBase | protected |
~CompNovoIdentificationBase() override | CompNovoIdentificationBase | |
~DefaultParamHandler() | DefaultParamHandler | virtual |