| allow_isotope_error_ | XTandemInfile | protected |
| AVERAGE enum value | XTandemInfile | |
| batch_size_ | XTandemInfile | protected |
| cleavage_site_ | XTandemInfile | protected |
| convertModificationSet_(const std::set< ModificationDefinition > &mods, std::map< String, double > &affected_origins) 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 | |
| force_default_mods_ | XTandemInfile | protected |
| fragment_lower_mz_ | XTandemInfile | protected |
| fragment_mass_error_unit_ | XTandemInfile | protected |
| fragment_mass_tolerance_ | XTandemInfile | protected |
| fragment_mass_type_ | XTandemInfile | protected |
| getCleavageSite() const | XTandemInfile | |
| getDefaultParametersFilename() const | XTandemInfile | |
| getFragmentMassErrorUnit() const | XTandemInfile | |
| getFragmentMassTolerance() const | XTandemInfile | |
| getInputFilename() const | XTandemInfile | |
| getMaxPrecursorCharge() const | XTandemInfile | |
| getMaxValidEValue() const | XTandemInfile | |
| getModifications() const | XTandemInfile | |
| getNoiseSuppression() const | XTandemInfile | |
| getNumberOfMissedCleavages() const | XTandemInfile | |
| getNumberOfThreads() const | XTandemInfile | |
| getOutputFilename() const | XTandemInfile | |
| getOutputResults() 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 |
| isValid(const String &filename, std::ostream &os) | XMLFile | |
| MassType enum name | XTandemInfile | |
| max_precursor_charge_ | XTandemInfile | protected |
| max_valid_evalue_ | XTandemInfile | protected |
| modifications_ | XTandemInfile | protected |
| MONOISOTOPIC enum value | XTandemInfile | |
| number_of_missed_cleavages_ | XTandemInfile | protected |
| number_of_threads_ | XTandemInfile | protected |
| operator=(const XTandemInfile &rhs) | XTandemInfile | protected |
| output_filename_ | XTandemInfile | protected |
| output_results_ | 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 |
| save_(const String &filename, XMLHandler *handler) const | XMLFile | protected |
| schema_location_ | XMLFile | protected |
| schema_version_ | XMLFile | protected |
| semi_cleavage_ | XTandemInfile | protected |
| setAllowIsotopeError(const bool allow_isotope_error) | XTandemInfile | |
| setCleavageSite(const String &cleavage_site) | XTandemInfile | |
| 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 | |
| setNoiseSuppression(const bool noise_suppression) | XTandemInfile | |
| setNumberOfMissedCleavages(UInt missed_cleavages) | XTandemInfile | |
| setNumberOfThreads(UInt threads) | XTandemInfile | |
| setOutputFilename(const String &output) | XTandemInfile | |
| setOutputResults(String result) | XTandemInfile | |
| setPrecursorErrorType(MassType mono_isotopic) | XTandemInfile | |
| setPrecursorMassErrorUnit(ErrorUnit unit) | XTandemInfile | |
| setPrecursorMassToleranceMinus(double tol) | XTandemInfile | |
| setPrecursorMassTolerancePlus(double tol) | 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, bool ignore_member_parameters=false, bool force_default_mods=false) | XTandemInfile | |
| writeNote_(std::ostream &os, const String &label, const String &value) | XTandemInfile | protected |
| writeNote_(std::ostream &os, const String &label, const char *value) | XTandemInfile | protected |
| writeNote_(std::ostream &os, const String &label, bool value) | XTandemInfile | protected |
| writeTo_(std::ostream &os, bool ignore_member_parameters) | 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 |