TOPPXFDR Member List

This is the complete list of members for TOPPXFDR, 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
arg_in_	TOPPXFDR	private
arg_in_type_	TOPPXFDR	private
arg_out_idXML_	TOPPXFDR	private
arg_out_mzid_	TOPPXFDR	private
arg_out_xquest_	TOPPXFDR	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
loadArguments_()	TOPPXFDR	inlineprivate
loadInputFile_(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)	TOPPXFDR	inlineprivate
log_	TOPPBase	mutableprivate
log_type_	TOPPBase	protected
logFatal(const String &message) const	TOPPXFDR	inlineprivate
main(int argc, const char **argv)	TOPPBase
main_(int, const char **) final	TOPPXFDR	inlineprotectedvirtual
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_in_	TOPPXFDR	privatestatic
param_in_type_	TOPPXFDR	privatestatic
param_inifile_	TOPPBase	private
param_instance_	TOPPBase	private
param_out_idXML_	TOPPXFDR	privatestatic
param_out_mzid_	TOPPXFDR	privatestatic
param_out_xquest_	TOPPXFDR	privatestatic
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_() final	TOPPXFDR	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 &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
TOPPXFDR()	TOPPXFDR	inline
UNEXPECTED_RESULT enum value	TOPPBase
UNKNOWN_ERROR enum value	TOPPBase
validateToolArguments_() const	TOPPXFDR	inlineprivate
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