This is the complete list of members for TOPPOpenSwathBase, 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	static
debug_level_	TOPPBase	protected
enableLogging_() const	TOPPBase	private
EXECUTION_OK enum value	TOPPBase
ExitCodes enum name	TOPPBase
EXTERNAL_PROGRAM_ERROR enum value	TOPPBase
fileParamValidityCheck_(const StringList &param_value, const String &param_name, const ParameterInformation &p) const	TOPPBase	protected
fileParamValidityCheck_(String &param_value, const String &param_name, const ParameterInformation &p) const	TOPPBase	protected
findEntry_(const String &name) const	TOPPBase	protected
getDefaultParameters_() const	TOPPBase	private
getDocumentationURL() const	TOPPBase
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
getOutputDirOption(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
getToolPrefix() const	TOPPBase
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
loadSwathFiles(const StringList &file_list, boost::shared_ptr< ExperimentalSettings > &exp_meta, std::vector< OpenSwath::SwathMap > &swath_maps, const bool split_file, const String &tmp, const String &readoptions, const String &swath_windows_file, const double min_upper_edge_dist, const bool force, const bool sort_swath_maps, const bool sonar, const bool prm, const bool pasef, Interfaces::IMSDataConsumer *plugin_consumer=nullptr)	TOPPOpenSwathBase	inlineprotected
loadSwathFiles_(const StringList &file_list, const bool split_file, const String &tmp, const String &readoptions, boost::shared_ptr< ExperimentalSettings > &exp_meta, std::vector< OpenSwath::SwathMap > &swath_maps, Interfaces::IMSDataConsumer *plugin_consumer)	TOPPOpenSwathBase	inlineprivate
loadTransitionList(const FileTypes::Type &tr_type, const String &tr_file, const Param &tsv_reader_param)	TOPPOpenSwathBase	inlineprotected
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 &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
performCalibration(String trafo_in, String irt_tr_file, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, Size debug_level, bool sonar, bool pasef, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out)	TOPPOpenSwathBase	inlineprotected
prepareChromOutput(Interfaces::IMSDataConsumer **chromatogramConsumer, const boost::shared_ptr< ExperimentalSettings > &exp_meta, const OpenSwath::LightTargetedExperiment &transition_exp, const String &out_chrom, const UInt64 run_id)	TOPPOpenSwathBase	inlineprotected
printUsage_()	TOPPBase	protected
registerDoubleList_(const String &name, const String &argument, const 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, const 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, const 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
registerOutputDir_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
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, const StringList &default_value, const String &description, bool required=true, bool advanced=false)	TOPPBase	protected
registerOutputPrefix_(const String &name, const String &argument, const String &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, const 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
runExternalProcess_(const QString &executable, const QStringList &arguments, const QString &workdir="") const	TOPPBase	protected
runExternalProcess_(const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, 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
TAG_ADVANCED	TOPPBase	inlinestatic
TAG_INPUT_FILE	TOPPBase	inlinestatic
TAG_OUTPUT_DIR	TOPPBase	inlinestatic
TAG_OUTPUT_FILE	TOPPBase	inlinestatic
TAG_OUTPUT_PREFIX	TOPPBase	inlinestatic
TAG_REQUIRED	TOPPBase	inlinestatic
test_mode_	TOPPBase	protected
tool_description_	TOPPBase	private
tool_name_	TOPPBase	private
toolhandler_test_	TOPPBase	protected
toolName_() const	TOPPBase	protected
topp_ini_file_	TOPPBase	protectedstatic
TOPPBase()=delete	TOPPBase
TOPPBase(const TOPPBase &)=delete	TOPPBase
TOPPBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)	TOPPBase
TOPPOpenSwathBase(String name, String description, bool official=true)	TOPPOpenSwathBase	inline
UNEXPECTED_RESULT enum value	TOPPBase
UNKNOWN_ERROR enum value	TOPPBase
verboseVersion_	TOPPBase	protected
version_	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
writeLogError_(const String &text) const	TOPPBase	protected
writeLogInfo_(const String &text) const	TOPPBase	protected
writeLogWarn_(const String &text) const	TOPPBase	protected
writeToolDescription_(Writer &writer, std::string write_type, std::string fileExtension)	TOPPBase	protected
~TOPPBase()	TOPPBase	virtual