 
  
 | Public Member Functions | |
| TOPPRNPxl () | |
|  Public Member Functions inherited from TOPPBase | |
| TOPPBase (const String &name, const String &description, bool official=true, bool id_tag_support=false, bool require_args=true, const String &version="") | |
| 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_ () | 
| Sets the valid command line options (with argument) and flags (without argument).  More... | |
| ExitCodes | main_ (int, const char **) | 
| 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... | |
| void | parseRange_ (const String &text, double &low, double &high) const | 
| Helper function that parses a range string ([a]:[b]) into two variables.  More... | |
| void | parseRange_ (const String &text, Int &low, Int &high) const | 
| Helper function that parses a range string ([a]:[b]) into two variables.  More... | |
| const DocumentIDTagger & | getDocumentIDTagger_ () const | 
| get DocumentIDTagger to assign DocumentIDs to maps  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< ParameterInformation > | paramToParameterInformation_ (const Param ¶m) 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 ¶m) | 
| void | registerFullParam_ (const Param ¶m) | 
| 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 | 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, DoubleReal 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, DoubleReal 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) | 
| 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... | |
| DoubleReal | 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 ¶m, const String &filename, const String &location) const | 
| Checks top-level entries of paramaccording 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 textto the log file and to std::cout if the debug level is at leastmin_level.  More... | |
| void | writeDebug_ (const String &text, const Param ¶m, 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... | |
| void | inputFileReadable_ (const String &filename, const String ¶m_name) const | 
| Checks if an input file exists, is readable and is not empty.  More... | |
| void | outputFileWritable_ (const String &filename, const String ¶m_name) const | 
| Checks if an output file is writeable.  More... | |
| void | addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const | 
| Data processing setter for consensus maps.  More... | |
| template<typename FeatureType > | |
| void | addDataProcessing_ (FeatureMap< FeatureType > &map, const DataProcessing &dp) const | 
| Data processing setter for feature maps.  More... | |
| template<typename PeakType , typename CT > | |
| void | addDataProcessing_ (MSExperiment< PeakType, CT > &map, const DataProcessing &dp) const | 
| Data processing setter for peak maps.  More... | |
| DataProcessing | getProcessingInfo_ (DataProcessing::ProcessingAction action) const | 
| Returns the the data processing information.  More... | |
| DataProcessing | getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const | 
| Returns the 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... | |
| 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... | |
| 
 | inline | 
| 
 | inlineprotectedvirtual | 
The actual "main" method. main_() is invoked by main().
Implements TOPPBase.
References MSExperiment< PeakT, ChromatogramPeakT >::addSpectrum(), PeptideIdentification::assignRanks(), MSExperiment< PeakT, ChromatogramPeakT >::begin(), MSExperiment< PeakT, ChromatogramPeakT >::end(), MarkerIonExtractor::extractMarkerIons(), PeptideIdentification::getHits(), EmpiricalFormula::getMonoWeight(), MSSpectrum< PeakT >::getRT(), RNPxlReportRowHeader::getString(), String::has(), initModificationMassesRNA(), OpenMS::Constants::k, IdXMLFile::load(), MzMLFile::load(), ModificationMassesResult::mod_combinations, ModificationMassesResult::mod_formula_idx, ModificationMassesResult::mod_masses, RNPxlReportRow::no_id, OpenMS::Constants::PROTON_MASS_U, RT_FACTOR, RT_FACTOR_PRECISION, RT_MODULO_FACTOR, Precursor::setCharge(), SpectrumSettings::setComment(), PeptideIdentification::setHigherScoreBetter(), PeptideIdentification::setHits(), MetaInfoInterface::setMetaValue(), Peak1D::setMZ(), MSSpectrum< PeakT >::setName(), SpectrumSettings::setPrecursors(), MSSpectrum< PeakT >::setRT(), MSExperiment< PeakT, ChromatogramPeakT >::size(), IdXMLFile::store(), MzMLFile::store(), String::substitute(), String::toQString(), and DataValue::valueType().
| 
 | inlineprotectedvirtual | 
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.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5 |