OpenMS  2.4.0
Public Member Functions | Protected Member Functions | List of all members
Epifany Class Reference
Inheritance diagram for Epifany:
TOPPBase

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, doublecheckExtremePSMScores_ (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 StringgetIniLocation_ () 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 StringtoolName_ () 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...
 
ExitCodes writeWSDL_ (const String &filename)
 Write WSDL file and validate it. Returns EXECUTION_OK or INTERNAL_ERROR (if validation failed) More...
 
String getParamArgument_ (const Param::ParamEntry &entry) const
 Utility function that determines a suitable argument value for the given Param::ParamEntry. More...
 
std::vector< ParameterInformationparamToParameterInformation_ (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 ParameterInformationfindEntry_ (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 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< Citationcitations_
 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