| AVERAGE enum value | XTandemInfile |  | 
  | batch_size_ | XTandemInfile | protected | 
  | cleavage_site_ | XTandemInfile | protected | 
  | convertModificationSet_(const std::set< ModificationDefinition > &mods) const | XTandemInfile | protected | 
  | DALTONS enum value | XTandemInfile |  | 
  | default_parameters_file_ | XTandemInfile | protected | 
  | enforced_encoding_ | XMLFile | protected | 
  | enforceEncoding_(const String &encoding) | XMLFile | protected | 
  | ErrorUnit enum name | XTandemInfile |  | 
  | fragment_lower_mz_ | XTandemInfile | protected | 
  | fragment_mass_error_unit_ | XTandemInfile | protected | 
  | fragment_mass_tolerance_ | XTandemInfile | protected | 
  | fragment_mass_type_ | XTandemInfile | protected | 
  | getDefaultParametersFilename() const | XTandemInfile |  | 
  | getFragmentMassErrorUnit() const | XTandemInfile |  | 
  | getFragmentMassTolerance() const | XTandemInfile |  | 
  | getInputFilename() const | XTandemInfile |  | 
  | getMaxPrecursorCharge() const | XTandemInfile |  | 
  | getMaxValidEValue() const | XTandemInfile |  | 
  | getModifications() const | XTandemInfile |  | 
  | getNumberOfMissedCleavages() const | XTandemInfile |  | 
  | getNumberOfThreads() const | XTandemInfile |  | 
  | getOutputFilename() const | XTandemInfile |  | 
  | getPrecursorErrorType() const | XTandemInfile |  | 
  | getPrecursorMassErrorUnit() const | XTandemInfile |  | 
  | getPrecursorMassToleranceMinus() const | XTandemInfile |  | 
  | getPrecursorMassTolerancePlus() const | XTandemInfile |  | 
  | getTaxon() const | XTandemInfile |  | 
  | getTaxonomyFilename() const | XTandemInfile |  | 
  | getVersion() const | XMLFile |  | 
  | input_filename_ | XTandemInfile | protected | 
  | isRefining() const | XTandemInfile |  | 
  | isValid(const String &filename, std::ostream &os=std::cerr) | XMLFile |  | 
  | load(const String &filename) | XTandemInfile |  | 
  | MassType enum name | XTandemInfile |  | 
  | max_precursor_charge_ | XTandemInfile | protected | 
  | max_valid_evalue_ | XTandemInfile | protected | 
  | modifications_ | XTandemInfile | protected | 
  | MONOISOTOPIC enum value | XTandemInfile |  | 
  | notes_ | XTandemInfile | protected | 
  | number_of_missed_cleavages_ | XTandemInfile | protected | 
  | number_of_threads_ | XTandemInfile | protected | 
  | operator=(const XTandemInfile &rhs) | XTandemInfile | protected | 
  | output_filename_ | XTandemInfile | protected | 
  | parse_(const String &filename, XMLHandler *handler) | XMLFile | protected | 
  | PPM enum value | XTandemInfile |  | 
  | precursor_lower_mz_ | XTandemInfile | protected | 
  | precursor_mass_error_unit_ | XTandemInfile | protected | 
  | precursor_mass_tolerance_minus_ | XTandemInfile | protected | 
  | precursor_mass_tolerance_plus_ | XTandemInfile | protected | 
  | precursor_mass_type_ | XTandemInfile | protected | 
  | refine_ | XTandemInfile | protected | 
  | refine_max_valid_evalue_ | XTandemInfile | protected | 
  | save_(const String &filename, XMLHandler *handler) const | XMLFile | protected | 
  | schema_location_ | XMLFile | protected | 
  | schema_version_ | XMLFile | protected | 
  | semi_cleavage_ | XTandemInfile | protected | 
  | setDefaultParametersFilename(const String &filename) | XTandemInfile |  | 
  | setFragmentMassErrorUnit(ErrorUnit unit) | XTandemInfile |  | 
  | setFragmentMassTolerance(double tolerance) | XTandemInfile |  | 
  | setInputFilename(const String &input_file) | XTandemInfile |  | 
  | setMaxPrecursorCharge(Int max_charge) | XTandemInfile |  | 
  | setMaxValidEValue(double value) | XTandemInfile |  | 
  | setModifications(const ModificationDefinitionsSet &mods) | XTandemInfile |  | 
  | setNumberOfMissedCleavages(UInt missed_cleavages) | XTandemInfile |  | 
  | setNumberOfThreads(UInt threads) | XTandemInfile |  | 
  | setOutputFilename(const String &output) | XTandemInfile |  | 
  | setPrecursorErrorType(MassType mono_isotopic) | XTandemInfile |  | 
  | setPrecursorMassErrorUnit(ErrorUnit unit) | XTandemInfile |  | 
  | setPrecursorMassToleranceMinus(double tol) | XTandemInfile |  | 
  | setPrecursorMassTolerancePlus(double tol) | XTandemInfile |  | 
  | setRefine(const bool refine) | XTandemInfile |  | 
  | setSemiCleavage(const bool semi_cleavage) | XTandemInfile |  | 
  | setTaxon(const String &taxon) | XTandemInfile |  | 
  | setTaxonomyFilename(const String &filename) | XTandemInfile |  | 
  | taxon_ | XTandemInfile | protected | 
  | taxonomy_file_ | XTandemInfile | protected | 
  | write(const String &filename) | XTandemInfile |  | 
  | writeNote_(std::ostream &os, const String &type, const String &label, const String &value) | XTandemInfile | protected | 
  | writeNote_(std::ostream &os, const String &type, const String &label, const char *value) | XTandemInfile | protected | 
  | writeNote_(std::ostream &os, const String &type, const String &label, bool value) | XTandemInfile | protected | 
  | writeTo_(std::ostream &os) | XTandemInfile | protected | 
  | XMLFile() | XMLFile |  | 
  | XMLFile(const String &schema_location, const String &version) | XMLFile |  | 
  | XTandemInfile() | XTandemInfile |  | 
  | XTandemInfile(const XTandemInfile &rhs) | XTandemInfile | protected | 
  | ~XMLFile() | XMLFile | virtual | 
  | ~XTandemInfile() | XTandemInfile | virtual |