OpenMS
2.5.0
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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 ¶m, 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 ¶m_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 §ion) 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 ¶m_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, 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 |
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 ¶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 |
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 | inlineprotected |
prepareChromOutput(Interfaces::IMSDataConsumer **chromatogramConsumer, const boost::shared_ptr< ExperimentalSettings > &exp_meta, const OpenSwath::LightTargetedExperiment &transition_exp, const String &out_chrom) | TOPPOpenSwathBase | inlineprotected |
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_()=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 |
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 |
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 |
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 ¶m, UInt min_level) const | TOPPBase | protected |
writeLog_(const String &text) const | TOPPBase | protected |
~TOPPBase() | TOPPBase | virtual |