| OpenMS 2.5.0

TOPPOpenSwathBase Member List

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
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 | protected static
debug_level_ | TOPPBase | protected
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
getDoubleList_(const String &name) const | TOPPBase | protected
getDoubleOption_(const String &name) const | TOPPBase | protected
getFlag_(const String &name) const | TOPPBase | protected
getIniLocation_() const | TOPPBase | inline protected
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 &param_name) const | TOPPBase | protected
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, Interfaces::IMSDataConsumer *plugin_consumer=nullptr) | TOPPOpenSwathBase | inline protected
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 | inline private
loadTransitionList(const FileTypes::Type &tr_type, const String &tr_file, const Param &tsv_reader_param) | TOPPOpenSwathBase | inline protected
log_type_ | TOPPBase | protected
main(int argc, const char **argv) | TOPPBase |
main_(int argc, const char **argv)=0 | TOPPBase | protected pure 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
paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const | TOPPBase | protected
paramToParameterInformation_(const Param &param) 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
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 load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out) | TOPPOpenSwathBase | inline protected
prepareChromOutput(Interfaces::IMSDataConsumer **chromatogramConsumer, const boost::shared_ptr< ExperimentalSettings > &exp_meta, const OpenSwath::LightTargetedExperiment &transition_exp, const String &out_chrom) | TOPPOpenSwathBase | inline 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 | protected pure 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
test_mode_ | TOPPBase | protected
toolName_() const | TOPPBase | protected
topp_ini_file_ | TOPPBase | protected static
TOPPBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}) | 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
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