, including all inherited members.
| AVERAGE enum value | XTandemInfile | |
| batch_size_ | XTandemInfile | [protected] |
| cleavage_site_ | 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] |