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

addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) const	TOPPBase	protected
addDataProcessing_(FeatureMap &map, const DataProcessing &dp) const	TOPPBase	protected
addDataProcessing_(PeakMap &map, const DataProcessing &dp) const	TOPPBase	protected
addEmptyLine_()	TOPPBase	protected
addText_(const std::string &text)	TOPPBase	private
ambiguous_mods_	NucleicAcidSearchEngine	protected
calculateAndFilterFDR_(IdentificationData &id_data, bool only_top_hits)	NucleicAcidSearchEngine	inlineprotected
calculatePrecursorMass_(double mz, Int charge, Int isotope, double adduct_mass, bool negative_mode)	NucleicAcidSearchEngine	inlineprotected
CANNOT_WRITE_OUTPUT_FILE enum value	TOPPBase
checkIfIniParametersAreApplicable_(const Param &ini_params)	TOPPBase	protected
checkParam_(const Param &param, const std::string &filename, const std::string &location) const	TOPPBase	protected
citations_	TOPPBase	protected
cite_openms	TOPPBase	static
ConstRibonucleotidePtr typedef	NucleicAcidSearchEngine	private
debug_level_	TOPPBase	protected
deisotopeAndSingleChargeMSSpectrum_(MSSpectrum &in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=true)	NucleicAcidSearchEngine	inlineprotected
enableLogging_() const	TOPPBase	private
EXECUTION_OK enum value	TOPPBase
ExitCodes enum name	TOPPBase
EXTERNAL_PROGRAM_ERROR enum value	TOPPBase
EXTERNAL_PROGRAM_NOTFOUND enum value	TOPPBase
fileParamValidityCheck_(const StringList &param_value, const std::string &param_name, const ParameterInformation &p) const	TOPPBase	protected
fileParamValidityCheck_(std::string &param_value, const std::string &param_name, const ParameterInformation &p) const	TOPPBase	protected
findEntry_(const std::string &name) const	TOPPBase	protected
fragment_ion_codes_	NucleicAcidSearchEngine	protected
generateLFQInput_(IdentificationData &id_data, const std::string &out_file)	NucleicAcidSearchEngine	inlineprotected
getDefaultParameters_() const	TOPPBase	private
getDocumentationURL() const	TOPPBase
getDoubleList_(const std::string &name) const	TOPPBase	protected
getDoubleOption_(const std::string &name) const	TOPPBase	protected
getFlag_(const std::string &name) const	TOPPBase	protected
getIniLocation_() const	TOPPBase	inlineprotected
getIntList_(const std::string &name) const	TOPPBase	protected
getIntOption_(const std::string &name) const	TOPPBase	protected
getModifications_(const set< std::string > &mod_names)	NucleicAcidSearchEngine	inlineprotected
getOutputDirOption(const std::string &name) const	TOPPBase	protected
getParam_(const std::string &key) const	TOPPBase	private
getParam_() const	TOPPBase	protected
getParamArgument_(const Param::ParamEntry &entry) const	TOPPBase	protected
getParamAsBool_(const std::string &key) const	TOPPBase	private
getParamAsDouble_(const std::string &key, double default_value=0) const	TOPPBase	private
getParamAsDoubleList_(const std::string &key, const DoubleList &default_value) const	TOPPBase	private
getParamAsInt_(const std::string &key, Int default_value=0) const	TOPPBase	private
getParamAsIntList_(const std::string &key, const IntList &default_value) const	TOPPBase	private
getParamAsString_(const std::string &key, const std::string &default_value="") const	TOPPBase	private
getParamAsStringList_(const std::string &key, const StringList &default_value) const	TOPPBase	private
getParameterByName_(const std::string &name)	TOPPBase	private
getProcessingInfo_(DataProcessing::ProcessingAction action) const	TOPPBase	protected
getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) const	TOPPBase	protected
getStringList_(const std::string &name) const	TOPPBase	protected
getStringOption_(const std::string &name) const	TOPPBase	protected
getSubsection_(const std::string &name) const	TOPPBase	private
getSubsectionDefaults_(const std::string &section) const	TOPPBase	privatevirtual
getSubsectionDefaults_() const	TOPPBase	private
getToolPrefix() const	TOPPBase
getToolUserDefaults_(const std::string &tool_name) const	TOPPBase	private
HitsByScore typedef	NucleicAcidSearchEngine	protected
ILLEGAL_PARAMETERS enum value	TOPPBase
INCOMPATIBLE_INPUT_DATA enum value	TOPPBase
ini_location_	TOPPBase	private
INPUT_FILE_CORRUPT enum value	TOPPBase
INPUT_FILE_EMPTY enum value	TOPPBase
INPUT_FILE_NOT_FOUND enum value	TOPPBase
INPUT_FILE_NOT_READABLE enum value	TOPPBase
inputFileReadable_(const std::string &filename, const std::string &param_name) const	TOPPBase	protected
instance_number_	TOPPBase	private
INTERNAL_ERROR enum value	TOPPBase
log_	TOPPBase	mutableprivate
log_type_	TOPPBase	protected
main(int argc, const char **argv)	TOPPBase
main_(int, const char **) override	NucleicAcidSearchEngine	inlineprotectedvirtual
MISSING_PARAMETERS enum value	TOPPBase
NucleicAcidSearchEngine()	NucleicAcidSearchEngine	inline
official_	TOPPBase	protected
outputFileWritable_(const std::string &filename, const std::string &param_name) const	TOPPBase	protected
param_	TOPPBase	private
param_cmdline_	TOPPBase	private
param_common_	TOPPBase	private
param_common_tool_	TOPPBase	private
param_inifile_	TOPPBase	private
param_instance_	TOPPBase	private
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const std::string &argument="", const std::string &full_name="") const	TOPPBase	protected
parameters_	TOPPBase	private
paramToParameterInformation_(const Param &param) const	TOPPBase	protected
PARSE_ERROR enum value	TOPPBase
parseAdduct_(const std::string &adduct)	NucleicAcidSearchEngine	inlineprotected
parseCommandLine_(const int argc, const char **argv, const std::string &misc="misc", const std::string &unknown="unknown")	TOPPBase	private
parseRange_(const std::string &text, double &low, double &high) const	TOPPBase	protected
parseRange_(const std::string &text, Int &low, Int &high) const	TOPPBase	protected
postProcessHits_(const PeakMap &exp, vector< HitsByScore > &annotated_hits, IdentificationData &id_data, bool negative_mode)	NucleicAcidSearchEngine	inlineprotected
preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool negative_mode, Int min_charge, Int max_charge, bool include_unknown_charge)	NucleicAcidSearchEngine	inlineprotected
printUsage_()	TOPPBase	protected
registerDoubleList_(const std::string &name, const std::string &argument, const DoubleList &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerDoubleOption_(const std::string &name, const std::string &argument, double default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerFlag_(const std::string &name, const std::string &description, bool advanced=false)	TOPPBase	protected
registerFullParam_(const Param &param)	TOPPBase	protected
registerInputFile_(const std::string &name, const std::string &argument, const std::string &default_value, const std::string &description, bool required=true, bool advanced=false, const StringList &tags=StringList())	TOPPBase	protected
registerInputFileList_(const std::string &name, const std::string &argument, const StringList &default_value, const std::string &description, bool required=true, bool advanced=false, const StringList &tags=StringList())	TOPPBase	protected
registerIntList_(const std::string &name, const std::string &argument, const IntList &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerIntOption_(const std::string &name, const std::string &argument, Int default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOptionsAndFlags_() override	NucleicAcidSearchEngine	inlineprotectedvirtual
registerOutputDir_(const std::string &name, const std::string &argument, const std::string &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOutputFile_(const std::string &name, const std::string &argument, const std::string &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOutputFileList_(const std::string &name, const std::string &argument, const StringList &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOutputPrefix_(const std::string &name, const std::string &argument, const std::string &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerParamSubsectionsAsTOPPSubsections_(const Param &param)	TOPPBase	protected
registerStringList_(const std::string &name, const std::string &argument, const StringList &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerStringOption_(const std::string &name, const std::string &argument, const std::string &default_value, const std::string &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerSubsection_(const std::string &name, const std::string &description)	TOPPBase	protected
registerTOPPSubsection_(const std::string &name, const std::string &description)	TOPPBase	protected
resolve_ambiguous_mods_	NucleicAcidSearchEngine	protected
resolveAmbiguousMods_(HitsByScore &hits)	NucleicAcidSearchEngine	inlineprotected
runExternalProcess_(const std::string &executable, const std::vector< std::string > &arguments, const std::string &workdir="", const std::map< std::string, std::string > &env={}) const	TOPPBase	protected
runExternalProcess_(const std::string &executable, const std::vector< std::string > &arguments, std::string &proc_stdout, std::string &proc_stderr, const std::string &workdir="", const std::map< std::string, std::string > &env={}) const	TOPPBase	protected
setMaxFloat_(const std::string &name, double max)	TOPPBase	protected
setMaxInt_(const std::string &name, Int max)	TOPPBase	protected
setMaxNumberOfThreads(int num_threads)	TOPPBase	static
setMinFloat_(const std::string &name, double min)	TOPPBase	protected
setMinInt_(const std::string &name, Int min)	TOPPBase	protected
setValidFormats_(const std::string &name, const std::vector< std::string > &formats, const bool force_OpenMS_format=true)	TOPPBase	protected
setValidStrings_(const std::string &name, const std::vector< std::string > &strings)	TOPPBase	protected
setValidStrings_(const std::string &name, const std::string vstrings[], int count)	TOPPBase	protected
subsections_	TOPPBase	private
subsections_TOPP_	TOPPBase	private
TAG_ADVANCED	TOPPBase	inlinestatic
TAG_INPUT_FILE	TOPPBase	inlinestatic
TAG_OUTPUT_DIR	TOPPBase	inlinestatic
TAG_OUTPUT_FILE	TOPPBase	inlinestatic
TAG_OUTPUT_PREFIX	TOPPBase	inlinestatic
TAG_REQUIRED	TOPPBase	inlinestatic
test_mode_	TOPPBase	protected
tool_description_	TOPPBase	private
tool_name_	TOPPBase	private
toolhandler_test_	TOPPBase	protected
toolName_() const	TOPPBase	protected
topp_ini_file_	TOPPBase	protectedstatic
TOPPBase()=delete	TOPPBase
TOPPBase(const TOPPBase &)=delete	TOPPBase
TOPPBase(const std::string &name, const std::string &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)	TOPPBase
UNEXPECTED_RESULT enum value	TOPPBase
UNKNOWN_ERROR enum value	TOPPBase
verboseVersion_	TOPPBase	protected
version_	TOPPBase	protected
writeDebug_(const std::string &text, UInt min_level) const	TOPPBase	protected
writeDebug_(const std::string &text, const Param &param, UInt min_level) const	TOPPBase	protected
writeLogError_(const std::string &text) const	TOPPBase	protected
writeLogInfo_(const std::string &text) const	TOPPBase	protected
writeLogWarn_(const std::string &text) const	TOPPBase	protected
writeToolDescription_(Writer &writer, std::string write_type, std::string fileExtension)	TOPPBase	protected
~TOPPBase()	TOPPBase	virtual