Inheritance diagram for Epifany:

Public Member Functions
	Epifany ()

Public Member Functions inherited from TOPPBase
	TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={})
	Constructor. More...

virtual	~TOPPBase ()
	Destructor. More...

ExitCodes	main (int argc, const char **argv)
	Main routine of all TOPP applications. More...

Protected Member Functions
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument). More...

Param	getSubsectionDefaults_ (const String &) const override
	This method should return the default parameters for subsections. More...

pair< double, double >	checkExtremePSMScores_ (vector< PeptideIdentification > &mergedpeps)

void	convertPSMScores_ (vector< PeptideIdentification > &mergedpeps)

void	removeExtremeValues_ (vector< PeptideIdentification > &mergedpeps, double minscore, double maxscore)

ExitCodes	main_ (int, const char **) override
	The actual "main" method. main_() is invoked by main(). More...

Protected Member Functions inherited from TOPPBase
String	getParamArgument_ (const Param::ParamEntry &entry) const
	Utility function that determines a suitable argument value for the given Param::ParamEntry. More...

std::vector< ParameterInformation >	paramToParameterInformation_ (const Param &param) const
	Translates the given parameter object into a vector of ParameterInformation, that can be utilized for cl parsing. More...

ParameterInformation	paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const
	Transforms a ParamEntry object to command line parameter (ParameterInformation). More...

void	registerParamSubsectionsAsTOPPSubsections_ (const Param &param)

void	registerFullParam_ (const Param &param)
	Register command line parameters for all entries in a Param object. More...

void	registerStringOption_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers a string option. More...

void	setValidStrings_ (const String &name, const std::vector< String > &strings)
	Sets the valid strings for a string option or a whole string list. More...

void	setValidStrings_ (const String &name, const std::string vstrings[], int count)
	Sets the valid strings for a string option or a whole string list. More...

void	registerInputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
	Registers an input file option. More...

void	registerOutputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers an output file option. More...

void	setValidFormats_ (const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)
	Sets the formats for a input/output file option or for all members of an input/output file lists. More...

void	registerDoubleOption_ (const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)
	Registers a double option. More...

void	setMinInt_ (const String &name, Int min)
	Sets the minimum value for the integer parameter(can be a list of integers,too) `name`. More...

void	setMaxInt_ (const String &name, Int max)
	Sets the maximum value for the integer parameter(can be a list of integers,too) `name`. More...

void	setMinFloat_ (const String &name, double min)
	Sets the minimum value for the floating point parameter(can be a list of floating points,too) `name`. More...

void	setMaxFloat_ (const String &name, double max)
	Sets the maximum value for the floating point parameter(can be a list of floating points,too) `name`. More...

void	registerIntOption_ (const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)
	Registers an integer option. More...

void	registerIntList_ (const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of integers option. More...

void	registerDoubleList_ (const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of doubles option. More...

void	registerStringList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of strings option. More...

void	registerInputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
	Registers a list of input files option. More...

void	registerOutputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)
	Registers a list of output files option. More...

void	registerFlag_ (const String &name, const String &description, bool advanced=false)
	Registers a flag. More...

void	registerSubsection_ (const String &name, const String &description)
	Registers an allowed subsection in the INI file (usually from OpenMS algorithms). More...

void	registerTOPPSubsection_ (const String &name, const String &description)
	Registers an allowed subsection in the INI file originating from the TOPP tool itself. More...

void	addEmptyLine_ ()
	Adds an empty line between registered variables in the documentation. More...

String	getStringOption_ (const String &name) const
	Returns the value of a previously registered string option. More...

double	getDoubleOption_ (const String &name) const
	Returns the value of a previously registered double option. More...

Int	getIntOption_ (const String &name) const
	Returns the value of a previously registered integer option. More...

StringList	getStringList_ (const String &name) const
	Returns the value of a previously registered StringList. More...

IntList	getIntList_ (const String &name) const
	Returns the value of a previously registered IntList. More...

DoubleList	getDoubleList_ (const String &name) const
	Returns the value of a previously registered DoubleList. More...

bool	getFlag_ (const String &name) const
	Returns the value of a previously registered flag. More...

const ParameterInformation &	findEntry_ (const String &name) const
	Finds the entry in the parameters_ array that has the name `name`. More...

Param const &	getParam_ () const
	Return all parameters relevant to this TOPP tool. More...

void	checkParam_ (const Param &param, const String &filename, const String &location) const
	Checks top-level entries of `param` according to the information during registration. More...

void	fileParamValidityCheck_ (String &filename, const String &param_name, const ParameterInformation &p) const
	checks if an input file exists (respecting the flags) More...

void	checkIfIniParametersAreApplicable_ (const Param &ini_params)
	Checks if the parameters of the provided ini file are applicable to this tool. More...

void	printUsage_ ()
	Prints the tool-specific command line options and appends the common options. More...

void	writeLog_ (const String &text) const
	Writes a string to the log file and to std::cout. More...

void	writeDebug_ (const String &text, UInt min_level) const
	Writes a `text` to the log file and to std::cout if the debug level is at least `min_level`. More...

void	writeDebug_ (const String &text, const Param &param, UInt min_level) const
	Writes a String followed by a Param to the log file and to std::cout if the debug level is at least `min_level`. More...

String	makeTempDirectory_ () const
	Creates a unique temporary directory and returns its name (you have to clean it up yourself) More...

String	makeAutoRemoveTempDirectory_ (Int keep_debug=2)
	Creates a unique temporary directory and returns its name (will be cleaned up automatically if debug level is high enough) More...

void	removeTempDirectory_ (const String &dirname, Int keep_debug=2) const
	Removes a (temporary) directory. More...

ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const
	Runs an external process via QProcess and reports its status in the logs. More...

const String &	getIniLocation_ () const
	Returns the location of the ini file where parameters are taken from. E.g. if the command line was `TOPPTool -instance 17`, then this will be `"TOPPTool:17:"`. Note the ':' at the end. More...

const String &	toolName_ () const
	Returns the tool name. More...

void	inputFileReadable_ (const String &filename, const String &param_name) const
	Checks if an input file exists, is readable and is not empty. More...

void	outputFileWritable_ (const String &filename, const String &param_name) const
	Checks if an output file is writable. More...

bool	parseRange_ (const String &text, double &low, double &high) const
	Parses a range string ([a]:[b]) into two variables (doubles) More...

bool	parseRange_ (const String &text, Int &low, Int &high) const
	Parses a range string ([a]:[b]) into two variables (integers) More...

void	addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const
	Data processing setter for consensus maps. More...

void	addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const
	Data processing setter for feature maps. More...

void	addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const
	Data processing setter for peak maps. More...

DataProcessing	getProcessingInfo_ (DataProcessing::ProcessingAction action) const
	Returns the data processing information. More...

DataProcessing	getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const
	Returns the data processing information. More...

bool	writeCTD_ ()
	Write common tool description (CTD) file. More...

Additional Inherited Members
Public Types inherited from TOPPBase
enum	ExitCodes { EXECUTION_OK, INPUT_FILE_NOT_FOUND, INPUT_FILE_NOT_READABLE, INPUT_FILE_CORRUPT, INPUT_FILE_EMPTY, CANNOT_WRITE_OUTPUT_FILE, ILLEGAL_PARAMETERS, MISSING_PARAMETERS, UNKNOWN_ERROR, EXTERNAL_PROGRAM_ERROR, PARSE_ERROR, INCOMPATIBLE_INPUT_DATA, INTERNAL_ERROR, UNEXPECTED_RESULT }
	Exit codes. More...

Static Public Member Functions inherited from TOPPBase
static void	setMaxNumberOfThreads (int num_threads)
	Sets the maximal number of usable threads. More...

Protected Attributes inherited from TOPPBase
String	version_
	Version string (if empty, the OpenMS/TOPP version is printed) More...

String	verboseVersion_
	Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user. More...

bool	official_
	Flag indicating if this an official TOPP tool. More...

std::vector< Citation >	citations_
	Papers, specific for this tool (will be shown in '–help') More...

ProgressLogger::LogType	log_type_
	Type of progress logging. More...

bool	test_mode_
	Test mode. More...

Int	debug_level_
	Debug level set by -debug. More...

Static Protected Attributes inherited from TOPPBase
static String	topp_ini_file_
	.TOPP.ini file for storing system default parameters More...

static const Citation	cite_openms_
	The OpenMS citation. More...

Constructor & Destructor Documentation

◆ Epifany()

Epifany ( )

inline

Member Function Documentation

◆ checkExtremePSMScores_()

pair<double,double> checkExtremePSMScores_ ( vector< PeptideIdentification > & mergedpeps )

inlineprotected

◆ convertPSMScores_()

void convertPSMScores_ ( vector< PeptideIdentification > & mergedpeps )

inlineprotected

References String::toLower().

◆ getSubsectionDefaults_()

Param getSubsectionDefaults_ ( const String & section ) const

inlineoverrideprotectedvirtual

This method should return the default parameters for subsections.

It is called once for each registered subsection, when writing the example ini file.

Reimplement this method to set the defaults written in the 'write_ini' method.

Note: Make sure to set the 'advanced' flag of the parameters right in order to hide certain parameters from inexperienced users.

Reimplemented from TOPPBase.

References DefaultParamHandler::getParameters().

◆ main_()

ExitCodes main_	(	int	argc,
		const char **	argv
	)

inlineoverrideprotectedvirtual

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )

inlineoverrideprotectedvirtual

Sets the valid command line options (with argument) and flags (without argument).

The options '-ini' '-log' '-instance' '-debug' and the flag '–help' are automatically registered.

Implements TOPPBase.

◆ removeExtremeValues_()

void removeExtremeValues_	(	vector< PeptideIdentification > &	mergedpeps,
		double	minscore,
		double	maxscore
	)

inlineprotected

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ Epifany()

Member Function Documentation

◆ checkExtremePSMScores_()

◆ convertPSMScores_()

◆ getSubsectionDefaults_()

◆ main_()

◆ registerOptionsAndFlags_()

◆ removeExtremeValues_()