, including all inherited members.
| 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 | [protected, virtual] |
| 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] |