OpenMS: Member List

| OpenMS 2.5.0

TOPPBase Member List

This is the complete list of members for TOPPBase, 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
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
debug_level_ | TOPPBase | protected
enableLogging_() const | TOPPBase | private
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
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
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
getToolUserDefaults_(const String &tool_name) const | 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 &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 argc, const char **argv)=0 | TOPPBase | protectedpure virtual
makeAutoRemoveTempDirectory_(Int keep_debug=2) | TOPPBase | protected
makeTempDirectory_() const | TOPPBase | protected
MISSING_PARAMETERS enum value | TOPPBase |
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 |
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 &param) | 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_()=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 &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
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
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, const std::vector< Citation > &citations={}) | 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
working_dir_ | TOPPBase | private
working_dir_keep_debug_lvl_ | TOPPBase | private
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