| OpenMS 2.5.0

XTandemInfile Member List

This is the complete list of members for XTandemInfile, including all inherited members.

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
parseBuffer_(const std::string &buffer, 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() override | XTandemInfile |