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 | inlineprotected |
addEmptyLine_() | TOPPBase | protected |
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 |
EXECUTION_OK enum value | TOPPBase | |
ExitCodes enum name | TOPPBase | |
EXTERNAL_PROGRAM_ERROR enum value | TOPPBase | |
findEntry_(const String &name) const | TOPPBase | protected |
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 | 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 |
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 ¶m_name) const | TOPPBase | protected |
INTERNAL_ERROR enum value | TOPPBase | |
log_type_ | TOPPBase | protected |
main(int argc, const char **argv) | TOPPBase | |
main_(int, const char **) | TOPPRNPxl | inlineprotectedvirtual |
makeTempDirectory_() const | TOPPBase | protected |
MISSING_PARAMETERS enum value | TOPPBase | |
official_ | TOPPBase | protected |
outputFileWritable_(const String &filename, const String ¶m_name) const | TOPPBase | protected |
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const | TOPPBase | protected |
paramToParameterInformation_(const Param ¶m) const | TOPPBase | protected |
PARSE_ERROR enum value | TOPPBase | |
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, 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_() | TOPPRNPxl | 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 ¶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 |
removeTempDirectory_(const String &dirname, Int keep_debug=2) 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, bool id_tag_support=false, bool require_args=true, const String &version="") | TOPPBase | |
TOPPRNPxl() | TOPPRNPxl | inline |
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 |