NucleicAcidSearchEngine Member List

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 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 String &filename, const String &location) const	TOPPBase	protected
citations_	TOPPBase	protected
cite_openms_	TOPPBase	protectedstatic
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
fileParamValidityCheck_(const StringList &param_value, const String &param_name, const ParameterInformation &p) const	TOPPBase	protected
fileParamValidityCheck_(String &param_value, const String &param_name, const ParameterInformation &p) const	TOPPBase	protected
findEntry_(const String &name) const	TOPPBase	protected
fragment_ion_codes_	NucleicAcidSearchEngine	protected
generateLFQInput_(IdentificationData &id_data, const String &out_file)	NucleicAcidSearchEngine	inlineprotected
getDefaultParameters_() const	TOPPBase	private
getDocumentationURL() const	TOPPBase	private
getDoubleList_(const String &name) const	TOPPBase	protected
getDoubleOption_(const String &name) const	TOPPBase	protected
getFlag_(const String &name) const	TOPPBase	protected
getIniLocation_() const	TOPPBase	inlineprotected
getIntList_(const String &name) const	TOPPBase	protected
getIntOption_(const String &name) const	TOPPBase	protected
getModifications_(const set< String > &mod_names)	NucleicAcidSearchEngine	inlineprotected
getParam_(const String &key) const	TOPPBase	private
getParam_() const	TOPPBase	protected
getParamArgument_(const Param::ParamEntry &entry) const	TOPPBase	protected
getParamAsBool_(const String &key) const	TOPPBase	private
getParamAsDouble_(const String &key, double default_value=0) const	TOPPBase	private
getParamAsDoubleList_(const String &key, const DoubleList &default_value) const	TOPPBase	private
getParamAsInt_(const String &key, Int default_value=0) const	TOPPBase	private
getParamAsIntList_(const String &key, const IntList &default_value) const	TOPPBase	private
getParamAsString_(const String &key, const String &default_value="") const	TOPPBase	private
getParamAsStringList_(const String &key, const StringList &default_value) const	TOPPBase	private
getParameterByName_(const String &name)	TOPPBase	private
getProcessingInfo_(DataProcessing::ProcessingAction action) const	TOPPBase	protected
getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) const	TOPPBase	protected
getStringList_(const String &name) const	TOPPBase	protected
getStringOption_(const String &name) const	TOPPBase	protected
getSubsection_(const String &name) const	TOPPBase	private
getSubsectionDefaults_(const String &section) const	TOPPBase	privatevirtual
getSubsectionDefaults_() const	TOPPBase	private
getToolPrefix() const	TOPPBase
getToolUserDefaults_(const 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 String &filename, const 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 String &filename, const 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 String &argument="", const String &full_name="") const	TOPPBase	protected
parameters_	TOPPBase	private
paramToParameterInformation_(const Param &param) const	TOPPBase	protected
PARSE_ERROR enum value	TOPPBase
parseAdduct_(const String &adduct)	NucleicAcidSearchEngine	inlineprotected
parseCommandLine_(const int argc, const char **argv, const String &misc="misc", const String &unknown="unknown")	TOPPBase	private
parseRange_(const String &text, double &low, double &high) const	TOPPBase	protected
parseRange_(const 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 String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerDoubleOption_(const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerFlag_(const String &name, const String &description, bool advanced=false)	TOPPBase	protected
registerFullParam_(const Param &param)	TOPPBase	protected
registerIDMetaData_(IdentificationData &id_data, const String &in_mzml, const vector< String > &primary_files, const IdentificationData::DBSearchParam &search_param)	NucleicAcidSearchEngine	inlineprotected
registerInputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())	TOPPBase	protected
registerInputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())	TOPPBase	protected
registerIntList_(const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerIntOption_(const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOptionsAndFlags_() override	NucleicAcidSearchEngine	inlineprotectedvirtual
registerOutputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOutputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerParamSubsectionsAsTOPPSubsections_(const Param &param)	TOPPBase	protected
registerStringList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerStringOption_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerSubsection_(const String &name, const String &description)	TOPPBase	protected
registerTOPPSubsection_(const String &name, const String &description)	TOPPBase	protected
resolve_ambiguous_mods_	NucleicAcidSearchEngine	protected
resolveAmbiguousMods_(HitsByScore &hits)	NucleicAcidSearchEngine	inlineprotected
runExternalProcess_(const QString &executable, const QStringList &arguments, const QString &workdir="") const	TOPPBase	protected
runExternalProcess_(const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="") const	TOPPBase	protected
setMaxFloat_(const String &name, double max)	TOPPBase	protected
setMaxInt_(const String &name, Int max)	TOPPBase	protected
setMaxNumberOfThreads(int num_threads)	TOPPBase	static
setMinFloat_(const String &name, double min)	TOPPBase	protected
setMinInt_(const String &name, Int min)	TOPPBase	protected
setValidFormats_(const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)	TOPPBase	protected
setValidStrings_(const String &name, const std::vector< String > &strings)	TOPPBase	protected
setValidStrings_(const String &name, const std::string vstrings[], int count)	TOPPBase	protected
subsections_	TOPPBase	private
subsections_TOPP_	TOPPBase	private
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 String &name, const 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
writeCTD_()	TOPPBase	protected
writeDebug_(const String &text, UInt min_level) const	TOPPBase	protected
writeDebug_(const String &text, const Param &param, UInt min_level) const	TOPPBase	protected
writeLog_(const String &text) const	TOPPBase	protected
~TOPPBase()	TOPPBase	virtual