OpenMS: Member List

| OpenMS 2.5.0

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
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
EXECUTION_OK enum value | TOPPBase |
ExitCodes enum name | TOPPBase |
EXTERNAL_PROGRAM_ERROR enum value | TOPPBase |
fileParamValidityCheck_(String &filename, 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
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 | TOPPBase | protected
getParamArgument_(const Param::ParamEntry &entry) const | TOPPBase | protected
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
HitsByScore typedef | NucleicAcidSearchEngine | protected
ILLEGAL_PARAMETERS enum value | TOPPBase |
INCOMPATIBLE_INPUT_DATA enum value | TOPPBase |
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
INTERNAL_ERROR enum value | TOPPBase |
log_type_ | TOPPBase | protected
main(int argc, const char **argv) | TOPPBase |
main_(int, const char **) override | NucleicAcidSearchEngine | inlineprotectedvirtual
makeAutoRemoveTempDirectory_(Int keep_debug=2) | TOPPBase | protected
makeTempDirectory_() const | TOPPBase | protected
MISSING_PARAMETERS enum value | TOPPBase |
NucleicAcidSearchEngine() | NucleicAcidSearchEngine | inline
official_ | TOPPBase | protected
outputFileWritable_(const String &filename, const String &param_name) const | TOPPBase | protected
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const | TOPPBase | protected
paramToParameterInformation_(const Param &param) const | TOPPBase | protected
PARSE_ERROR enum value | TOPPBase |
parseAdduct_(const String &adduct) | NucleicAcidSearchEngine | inlineprotected
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_() | 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
removeTempDirectory_(const String &dirname, Int keep_debug=2) const | 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
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
test_mode_ | TOPPBase | protected
toolName_() const | TOPPBase | protected
topp_ini_file_ | TOPPBase | protectedstatic
TOPPBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}) | 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