| addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) const | TOPPBase | protected | 
  | addDataProcessing_(FeatureMap< FeatureType > &map, const DataProcessing &dp) const | TOPPBase | inlineprotected | 
  | addDataProcessing_(MSExperiment< PeakType, CT > &map, const DataProcessing &dp) const | TOPPBase | inlineprotected | 
  | addEmptyLine_() | TOPPBase | protected | 
  | addText_(const String &text) | TOPPBase | private | 
  | CANNOT_WRITE_OUTPUT_FILE enum value | TOPPBase |  | 
  | checkIfIniParametersAreApplicable_(const Param &ini_params) | TOPPBase | protected | 
  | checkParam_(const Param ¶m, const String &filename, const String &location) const | TOPPBase | protected | 
  | debug_level_ | TOPPBase | protected | 
  | enableLogging_() const | TOPPBase | private | 
  | EXECUTION_OK enum value | TOPPBase |  | 
  | ExitCodes enum name | TOPPBase |  | 
  | EXTERNAL_PROGRAM_ERROR enum value | TOPPBase |  | 
  | findEntry_(const String &name) const | TOPPBase | protected | 
  | getDefaultParameters_() const | TOPPBase | private | 
  | getDocumentIDTagger_() const | TOPPBase | protected | 
  | 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 | 
  | 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, DoubleReal 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 §ion) const | TOPPBase | privatevirtual | 
  | getSubsectionDefaults_() const | TOPPBase | private | 
  | getToolUserDefaults_(const String &tool_name) const | TOPPBase | private | 
  | id_tag_support_ | TOPPBase | private | 
  | id_tagger_ | TOPPBase | private | 
  | 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 ¶m_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 argc, const char **argv)=0 | TOPPBase | protectedpure virtual | 
  | MISSING_PARAMETERS enum value | TOPPBase |  | 
  | official_ | TOPPBase | protected | 
  | outputFileWritable_(const String &filename, const String ¶m_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 ¶m) const | TOPPBase | protected | 
  | PARSE_ERROR enum value | TOPPBase |  | 
  | 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 | 
  | 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 ¶m) | TOPPBase | protected | 
  | 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) | 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_()=0 | TOPPBase | protectedpure virtual | 
  | 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 ¶m) | 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 | 
  | require_args_ | TOPPBase | private | 
  | setMaxFloat_(const String &name, DoubleReal max) | TOPPBase | protected | 
  | setMaxInt_(const String &name, Int max) | TOPPBase | protected | 
  | setMaxNumberOfThreads(int num_threads) | TOPPBase | static | 
  | setMinFloat_(const String &name, DoubleReal 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 | 
  | subsections_ | TOPPBase | private | 
  | subsections_TOPP_ | TOPPBase | private | 
  | test_mode_ | TOPPBase | protected | 
  | tool_description_ | TOPPBase | private | 
  | tool_name_ | TOPPBase | private | 
  | toolName_() const | TOPPBase | protected | 
  | topp_ini_file_ | TOPPBase | protectedstatic | 
  | TOPPBase(const String &name, const String &description, bool official=true, bool id_tag_support=false, bool require_args=true, const String &version="") | TOPPBase |  | 
  | TOPPBase() | TOPPBase | private | 
  | TOPPBase(const TOPPBase &) | TOPPBase | private | 
  | 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 ¶m, UInt min_level) const | TOPPBase | protected | 
  | writeLog_(const String &text) const | TOPPBase | protected | 
  | writeWSDL_(const String &filename) | TOPPBase | protected | 
  | ~TOPPBase() | TOPPBase | virtual |