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NucleicAcidSearchEngine Member List

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

addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) constTOPPBaseprotected
addDataProcessing_(FeatureMap &map, const DataProcessing &dp) constTOPPBaseprotected
addDataProcessing_(PeakMap &map, const DataProcessing &dp) constTOPPBaseprotected
addEmptyLine_()TOPPBaseprotected
addText_(const String &text)TOPPBaseprivate
ambiguous_mods_NucleicAcidSearchEngineprotected
calculateAndFilterFDR_(IdentificationData &id_data, bool only_top_hits)NucleicAcidSearchEngineinlineprotected
calculatePrecursorMass_(double mz, Int charge, Int isotope, double adduct_mass, bool negative_mode)NucleicAcidSearchEngineinlineprotected
CANNOT_WRITE_OUTPUT_FILE enum valueTOPPBase
checkIfIniParametersAreApplicable_(const Param &ini_params)TOPPBaseprotected
checkParam_(const Param &param, const String &filename, const String &location) constTOPPBaseprotected
citations_TOPPBaseprotected
cite_openms_TOPPBaseprotectedstatic
ConstRibonucleotidePtr typedefNucleicAcidSearchEngineprivate
debug_level_TOPPBaseprotected
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)NucleicAcidSearchEngineinlineprotected
enableLogging_() constTOPPBaseprivate
EXECUTION_OK enum valueTOPPBase
ExitCodes enum nameTOPPBase
EXTERNAL_PROGRAM_ERROR enum valueTOPPBase
fileParamValidityCheck_(const StringList &param_value, const String &param_name, const ParameterInformation &p) constTOPPBaseprotected
fileParamValidityCheck_(String &param_value, const String &param_name, const ParameterInformation &p) constTOPPBaseprotected
findEntry_(const String &name) constTOPPBaseprotected
fragment_ion_codes_NucleicAcidSearchEngineprotected
generateLFQInput_(IdentificationData &id_data, const String &out_file)NucleicAcidSearchEngineinlineprotected
getDefaultParameters_() constTOPPBaseprivate
getDocumentationURL() constTOPPBase
getDoubleList_(const String &name) constTOPPBaseprotected
getDoubleOption_(const String &name) constTOPPBaseprotected
getFlag_(const String &name) constTOPPBaseprotected
getIniLocation_() constTOPPBaseinlineprotected
getIntList_(const String &name) constTOPPBaseprotected
getIntOption_(const String &name) constTOPPBaseprotected
getModifications_(const set< String > &mod_names)NucleicAcidSearchEngineinlineprotected
getParam_(const String &key) constTOPPBaseprivate
getParam_() constTOPPBaseprotected
getParamArgument_(const Param::ParamEntry &entry) constTOPPBaseprotected
getParamAsBool_(const String &key) constTOPPBaseprivate
getParamAsDouble_(const String &key, double default_value=0) constTOPPBaseprivate
getParamAsDoubleList_(const String &key, const DoubleList &default_value) constTOPPBaseprivate
getParamAsInt_(const String &key, Int default_value=0) constTOPPBaseprivate
getParamAsIntList_(const String &key, const IntList &default_value) constTOPPBaseprivate
getParamAsString_(const String &key, const String &default_value="") constTOPPBaseprivate
getParamAsStringList_(const String &key, const StringList &default_value) constTOPPBaseprivate
getParameterByName_(const String &name)TOPPBaseprivate
getProcessingInfo_(DataProcessing::ProcessingAction action) constTOPPBaseprotected
getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) constTOPPBaseprotected
getStringList_(const String &name) constTOPPBaseprotected
getStringOption_(const String &name) constTOPPBaseprotected
getSubsection_(const String &name) constTOPPBaseprivate
getSubsectionDefaults_(const String &section) constTOPPBaseprivatevirtual
getSubsectionDefaults_() constTOPPBaseprivate
getToolPrefix() constTOPPBase
getToolUserDefaults_(const String &tool_name) constTOPPBaseprivate
HitsByScore typedefNucleicAcidSearchEngineprotected
ILLEGAL_PARAMETERS enum valueTOPPBase
INCOMPATIBLE_INPUT_DATA enum valueTOPPBase
ini_location_TOPPBaseprivate
INPUT_FILE_CORRUPT enum valueTOPPBase
INPUT_FILE_EMPTY enum valueTOPPBase
INPUT_FILE_NOT_FOUND enum valueTOPPBase
INPUT_FILE_NOT_READABLE enum valueTOPPBase
inputFileReadable_(const String &filename, const String &param_name) constTOPPBaseprotected
instance_number_TOPPBaseprivate
INTERNAL_ERROR enum valueTOPPBase
log_TOPPBasemutableprivate
log_type_TOPPBaseprotected
main(int argc, const char **argv)TOPPBase
main_(int, const char **) overrideNucleicAcidSearchEngineinlineprotectedvirtual
MISSING_PARAMETERS enum valueTOPPBase
NucleicAcidSearchEngine()NucleicAcidSearchEngineinline
official_TOPPBaseprotected
outputFileWritable_(const String &filename, const String &param_name) constTOPPBaseprotected
param_TOPPBaseprivate
param_cmdline_TOPPBaseprivate
param_common_TOPPBaseprivate
param_common_tool_TOPPBaseprivate
param_inifile_TOPPBaseprivate
param_instance_TOPPBaseprivate
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") constTOPPBaseprotected
parameters_TOPPBaseprivate
paramToParameterInformation_(const Param &param) constTOPPBaseprotected
PARSE_ERROR enum valueTOPPBase
parseAdduct_(const String &adduct)NucleicAcidSearchEngineinlineprotected
parseCommandLine_(const int argc, const char **argv, const String &misc="misc", const String &unknown="unknown")TOPPBaseprivate
parseRange_(const String &text, double &low, double &high) constTOPPBaseprotected
parseRange_(const String &text, Int &low, Int &high) constTOPPBaseprotected
postProcessHits_(const PeakMap &exp, vector< HitsByScore > &annotated_hits, IdentificationData &id_data, bool negative_mode)NucleicAcidSearchEngineinlineprotected
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)NucleicAcidSearchEngineinlineprotected
printUsage_()TOPPBaseprotected
registerDoubleList_(const String &name, const String &argument, const DoubleList &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerDoubleOption_(const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerFlag_(const String &name, const String &description, bool advanced=false)TOPPBaseprotected
registerFullParam_(const Param &param)TOPPBaseprotected
registerInputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())TOPPBaseprotected
registerInputFileList_(const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())TOPPBaseprotected
registerIntList_(const String &name, const String &argument, const IntList &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerIntOption_(const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerOptionsAndFlags_() overrideNucleicAcidSearchEngineinlineprotectedvirtual
registerOutputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerOutputFileList_(const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerOutputPrefix_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerParamSubsectionsAsTOPPSubsections_(const Param &param)TOPPBaseprotected
registerStringList_(const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerStringOption_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)TOPPBaseprotected
registerSubsection_(const String &name, const String &description)TOPPBaseprotected
registerTOPPSubsection_(const String &name, const String &description)TOPPBaseprotected
resolve_ambiguous_mods_NucleicAcidSearchEngineprotected
resolveAmbiguousMods_(HitsByScore &hits)NucleicAcidSearchEngineinlineprotected
runExternalProcess_(const QString &executable, const QStringList &arguments, const QString &workdir="") constTOPPBaseprotected
runExternalProcess_(const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="") constTOPPBaseprotected
setMaxFloat_(const String &name, double max)TOPPBaseprotected
setMaxInt_(const String &name, Int max)TOPPBaseprotected
setMaxNumberOfThreads(int num_threads)TOPPBasestatic
setMinFloat_(const String &name, double min)TOPPBaseprotected
setMinInt_(const String &name, Int min)TOPPBaseprotected
setValidFormats_(const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)TOPPBaseprotected
setValidStrings_(const String &name, const std::vector< String > &strings)TOPPBaseprotected
setValidStrings_(const String &name, const std::string vstrings[], int count)TOPPBaseprotected
subsections_TOPPBaseprivate
subsections_TOPP_TOPPBaseprivate
test_mode_TOPPBaseprotected
tool_description_TOPPBaseprivate
tool_name_TOPPBaseprivate
toolhandler_test_TOPPBaseprotected
toolName_() constTOPPBaseprotected
topp_ini_file_TOPPBaseprotectedstatic
TOPPBase()=deleteTOPPBase
TOPPBase(const TOPPBase &)=deleteTOPPBase
TOPPBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)TOPPBase
UNEXPECTED_RESULT enum valueTOPPBase
UNKNOWN_ERROR enum valueTOPPBase
verboseVersion_TOPPBaseprotected
version_TOPPBaseprotected
writeDebug_(const String &text, UInt min_level) constTOPPBaseprotected
writeDebug_(const String &text, const Param &param, UInt min_level) constTOPPBaseprotected
writeLogError_(const String &text) constTOPPBaseprotected
writeLogInfo_(const String &text) constTOPPBaseprotected
writeLogWarn_(const String &text) constTOPPBaseprotected
writeToolDescription_(Writer &writer, std::string write_type, std::string fileExtension)TOPPBaseprotected
~TOPPBase()TOPPBasevirtual