| a_ion_losses_cd_ | PILISModel | protected | 
  | a_ion_losses_cr_ | PILISModel | protected | 
  | addPeaks_(DoubleReal mz, int charge, DoubleReal mz_offset, DoubleReal intensity, RichPeakSpectrum &spectrum, const IsotopeDistribution &id, const String &name) | PILISModel | protected | 
  | b2_ion_losses_cd_ | PILISModel | protected | 
  | b2_ion_losses_cr_ | PILISModel | protected | 
  | b_ion_losses_cd_ | PILISModel | protected | 
  | b_ion_losses_cr_ | PILISModel | protected | 
  | check_defaults_ | DefaultParamHandler | protected | 
  | DefaultParamHandler(const String &name) | DefaultParamHandler |  | 
  | DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | error_name_ | DefaultParamHandler | protected | 
  | evaluate() | PILISModel |  | 
  | getAvailableBackboneCharge_(const AASequence &ion, Residue::ResidueType res_type, int charge) | PILISModel | protected | 
  | getDefaults() const | DefaultParamHandler |  | 
  | getInitialTransitionProbabilities_(std::vector< DoubleReal > &bb_init, std::vector< DoubleReal > &cr_init, std::vector< DoubleReal > &sc_init, DoubleReal &precursor_init, const std::vector< DoubleReal > &bb_charges, const std::vector< DoubleReal > &sc_charges, const AASequence &peptide) | PILISModel | protected | 
  | getName() const | DefaultParamHandler |  | 
  | getParameters() const | DefaultParamHandler |  | 
  | getSpectrum(RichPeakSpectrum &spec, const AASequence &peptide, UInt charge) | PILISModel |  | 
  | getSubsections() const | DefaultParamHandler |  | 
  | hmm_ | PILISModel | protected | 
  | init(bool generate_models=true) | PILISModel |  | 
  | operator=(const PILISModel &mode) | PILISModel |  | 
  | OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | parseHMMModel_(const TextFile::ConstIterator &begin, const TextFile::ConstIterator &end, HiddenMarkovModel &hmm, Param ¶m) | PILISModel | protected | 
  | peaks_ | PILISModel | protected | 
  | PILISModel() | PILISModel |  | 
  | PILISModel(const PILISModel &model) | PILISModel |  | 
  | precursor_model_cd_ | PILISModel | protected | 
  | precursor_model_cr_ | PILISModel | protected | 
  | prot_dist_ | PILISModel | protected | 
  | readFromFile(const String &filename) | PILISModel |  | 
  | setName(const String &name) | DefaultParamHandler |  | 
  | setParameters(const Param ¶m) | DefaultParamHandler |  | 
  | spectra_aligner_ | PILISModel | protected | 
  | subsections_ | DefaultParamHandler | protected | 
  | train(const RichPeakSpectrum &, const AASequence &peptide, UInt charge) | PILISModel |  | 
  | tsg_ | PILISModel | protected | 
  | updateMembers_() | PILISModel | protectedvirtual | 
  | valid_ | PILISModel | protected | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | writeGraphMLFile(const String &filename) | PILISModel |  | 
  | writeParameters_(std::ostream &os, const Param ¶m) | PILISModel | protected | 
  | writeToFile(const String &filename) | PILISModel |  | 
  | y_ion_losses_cd_ | PILISModel | protected | 
  | y_ion_losses_cr_ | PILISModel | protected | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~PILISModel() | PILISModel | virtual |