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OpenMS
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#include <OpenMS/FORMAT/GNPSMGFFile.h>
Public Member Functions | |
| GNPSMGFFile () | |
| void | store (const String &consensus_file_path, const StringList &mzml_file_paths, const String &out) const |
| Create file for GNPS molecular networking. More... | |
 Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages. More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor. More... | |
| virtual | ~DefaultParamHandler () |
| Destructor. More... | |
| DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More... | |
| void | setParameters (const Param ¶m) |
| Sets the parameters. More... | |
| const Param & | getParameters () const |
| Non-mutable access to the parameters. More... | |
| const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More... | |
| const String & | getName () const |
| Non-mutable access to the name. More... | |
| void | setName (const String &name) |
| Mutable access to the name. More... | |
| const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More... | |
| Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| virtual | ~ProgressLogger () |
| Destructor. More... | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. More... | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | setLogger (ProgressLoggerImpl *logger) |
| Sets the logger to be used for progress logging. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress (UInt64 bytes_processed=0) const |
| void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More... | |
Static Private Attributes | |
| static constexpr double | DEF_COSINE_SIMILARITY = 0.9 |
| static constexpr double | DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES) |
| static constexpr int | DEF_PEPT_CUTOFF = 5 |
| static constexpr int | DEF_MSMAP_CACHE = 50 |
Additional Inherited Members | |
| Public Types inherited from ProgressLogger | |
| enum | LogType { CMD , GUI , NONE } |
| Possible log types. More... | |
| Static Public Member Functions inherited from DefaultParamHandler | |
| static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
| Writes all parameters to meta values. More... | |
| Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. More... | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
| Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ |
| Container for current parameters. More... | |
| Param | defaults_ |
| Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
| std::vector< String > | subsections_ |
| Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
| String | error_name_ |
| Name that is displayed in error messages during the parameter checking. More... | |
| bool | check_defaults_ |
| If this member is set to false no checking if parameters in done;. More... | |
| bool | warn_empty_defaults_ |
| If this member is set to false no warning is emitted when defaults are empty;. More... | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
| GNPSMGFFile | ( | ) |
| void store | ( | const String & | consensus_file_path, |
| const StringList & | mzml_file_paths, | ||
| const String & | out | ||
| ) | const |
Create file for GNPS molecular networking.
| consensus_file_path | path to consensusXML with spectrum references |
| mzml_file_paths | path to mzML files referenced in consensusXML. Used to extract spectra as MGF. |
| out | MGF file with MS2 peak data for molecular networking. |
Referenced by TOPPGNPSExport::main_().
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1.9.1 
