GNPSMGFFile Class Reference

#include <OpenMS/FORMAT/GNPSMGFFile.h>

Inheritance diagram for GNPSMGFFile:

Collaboration diagram for GNPSMGFFile:

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 DefaultParamHandler &	operator= (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 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	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< 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_

Constructor & Destructor Documentation

GNPSMGFFile()

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_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_().

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