| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | List of all members
Epifany Class Reference
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
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 | printUsage_ ()
| Prints the tool-specific command line options and appends the common options. 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...
bool | writeCTD_ ()
| Write common tool description (CTD) file. More...
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 | 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...
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...
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...

## 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 | ) |

inline protected

## ◆ convertPSMScores_()

void convertPSMScores_ | ( | vector< PeptideIdentification > & | mergedpeps | ) |

inline protected

References String::toLower().

## ◆ getSubsectionDefaults_()

Param getSubsectionDefaults_ | ( | const String & | section | ) | const

inline override protected virtual

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
| ) |  |

inline override protected virtual

The actual "main" method. main_() is invoked by main().

Implements TOPPBase.

References ProteinIdentification::ProteinGroup::accessions, FalseDiscoveryRate::applyBasic(), PeptideProteinResolution::buildGraph(), Param::copy(), DefaultParamHandler::getParameters(), BayesianProteinInferenceAlgorithm::inferPosteriorProbabilities(), IdXMLFile::load(), OPENMS_LOG_INFO, IDFilter::removeUnreferencedProteins(), StopWatch::reset(), PeptideProteinResolution::resolveGraph(), DefaultParamHandler::setParameters(), Param::setValue(), StopWatch::start(), StopWatch::stop(), IdXMLFile::store(), StopWatch::toString(), and IDFilter::updateProteinGroups().

## ◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ | ( |  | ) |

inline override protected virtual

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
| ) |  |

inline protected