OpenMS  2.8.0
Public Member Functions | Static Private Attributes | List of all members
GNPSMGFFile Class Reference

#include <OpenMS/FORMAT/GNPSMGFFile.h>

Inheritance diagram for GNPSMGFFile:
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Collaboration diagram for GNPSMGFFile:
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Public Member Functions

 GNPSMGFFile ()
 
void run (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...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
ProgressLoggeroperator= (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 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 () const
 Ends the progress display. More...
 
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...
 
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. 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< Stringsubsections_
 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_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Constructor & Destructor Documentation

◆ GNPSMGFFile()

Member Function Documentation

◆ run()

void run ( const String consensus_file_path,
const StringList mzml_file_paths,
const String out 
) const

Create file for GNPS molecular networking.

Parameters
consensus_file_pathpath to consensusXML with spectrum references
mzml_file_pathspath to mzML files referenced in consensusXML. Used to extract spectra as MGF.
outMGF file with MS2 peak data for molecular networking.

Referenced by TOPPGNPSExport::main_().

Member Data Documentation

◆ DEF_COSINE_SIMILARITY

constexpr double DEF_COSINE_SIMILARITY = 0.9
staticconstexprprivate

◆ DEF_MERGE_BIN_SIZE

constexpr double DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES)
staticconstexprprivate

◆ DEF_MSMAP_CACHE

constexpr int DEF_MSMAP_CACHE = 50
staticconstexprprivate

◆ DEF_PEPT_CUTOFF

constexpr int DEF_PEPT_CUTOFF = 5
staticconstexprprivate