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... | |
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... | |
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 | 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 ¶m, 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 ¶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... | |
String | makeTempDirectory_ () const |
Creates a unique temporary directory and returns its name. More... | |
void | removeTempDirectory_ (const String &dirname, Int keep_debug=2) const |
Removes a (temporary) directory. 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 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... | |
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... | |
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inlineprotectedvirtual |
The actual "main" method. main_() is invoked by main().
Implements TOPPBase.
References MSExperiment::addSpectrum(), PeptideIdentification::assignRanks(), MSExperiment::begin(), MSExperiment::end(), PeptideIdentification::getHits(), EmpiricalFormula::getMonoWeight(), MSExperiment::getPrimaryMSRunPath(), MSSpectrum::getRT(), RNPxlReportRowHeader::getString(), String::has(), OpenMS::Constants::k, MzMLFile::load(), IdXMLFile::load(), RNPxlModificationMassesResult::mod_combinations, RNPxlModificationMassesResult::mod_formula_idx, RNPxlModificationMassesResult::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(), PeptideIdentification::setMZ(), Peak1D::setMZ(), MSSpectrum::setName(), SpectrumSettings::setPrecursors(), ProteinIdentification::setPrimaryMSRunPath(), PeptideIdentification::setRT(), MSSpectrum::setRT(), MSExperiment::size(), MzMLFile::store(), IdXMLFile::store(), String::substitute(), String::toQString(), and DataValue::valueType().
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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 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13 |