| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Attributes | List of all members
TOPPGNPSExport Class Reference
Inheritance diagram for TOPPGNPSExport:

## Public Member Functions

| TOPPGNPSExport ()
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...
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...

## Private Attributes

double | DEF_COSINE_SIMILARITY = 0.95
double | DEF_PRECURSOR_MZ_TOLERANCE = 0.0001
double | DEF_PRECURSOR_RT_TOLERANCE = 5

## 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

## ◆ TOPPGNPSExport()

TOPPGNPSExport | ( |  | ) |

inline

## Member Function Documentation

## ◆ main_()

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

inline override protected virtual

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

Implements TOPPBase.

References ConsensusFeature::begin(), BinnedSpectrum::DEFAULT_BIN_OFFSET_HIRES, BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES, ConsensusFeature::end(), ProgressLogger::endProgress(), BaseFeature::getCharge(), Peak1D::getMZ(), Peak2D::getMZ(), BaseFeature::getPeptideIdentifications(), Peak2D::getRT(), UniqueIdInterface::getUniqueId(), ConsensusXMLFile::load(), MzMLFile::load(), OPENMS_LOG_DEBUG, ProgressLogger::setLogType(), ProgressLogger::setProgress(), and ProgressLogger::startProgress().

## ◆ 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.

## Member Data Documentation

## ◆ DEF_COSINE_SIMILARITY

double DEF_COSINE_SIMILARITY = 0.95

private

## ◆ DEF_PRECURSOR_MZ_TOLERANCE

double DEF_PRECURSOR_MZ_TOLERANCE = 0.0001

private

## ◆ DEF_PRECURSOR_RT_TOLERANCE

double DEF_PRECURSOR_RT_TOLERANCE = 5

private