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