TransitionPQPFile Class Reference

This class supports reading and writing of PQP files. More...

#include <OpenMS/ANALYSIS/OPENSWATH/TransitionPQPFile.h>

Inheritance diagram for TransitionPQPFile:

Public Member Functions
void	convertTargetedExperimentToPQP (const char *filename, OpenMS::TargetedExperiment &targeted_exp)
	Write out a targeted experiment (TraML structure) into a PQP file. More...
void	convertPQPToTargetedExperiment (const char *filename, OpenMS::TargetedExperiment &targeted_exp, bool legacy_traml_id=false)
	Read in a PQP file and construct a targeted experiment (TraML structure) More...
void	convertPQPToTargetedExperiment (const char *filename, OpenSwath::LightTargetedExperiment &targeted_exp, bool legacy_traml_id=false)
	Read in a PQP file and construct a targeted experiment (Light transition structure) More...
	TransitionPQPFile ()
	Constructor. More...
	~TransitionPQPFile () override
	Destructor. More...
Public Member Functions inherited from TransitionTSVFile
void	convertTargetedExperimentToTSV (const char *filename, OpenMS::TargetedExperiment &targeted_exp)
	Write out a targeted experiment (TraML structure) into a tsv file. More...
void	convertTSVToTargetedExperiment (const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp)
	Read in a tsv/mrm file and construct a targeted experiment (TraML structure) More...
void	convertTSVToTargetedExperiment (const char *filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment &targeted_exp)
	Read in a tsv file and construct a targeted experiment (Light transition structure) More...
void	validateTargetedExperiment (const OpenMS::TargetedExperiment &targeted_exp)
	Validate a TargetedExperiment (check that all ids are unique) More...
	TransitionTSVFile ()
	Constructor. More...
	~TransitionTSVFile () override
	Destructor. More...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
	~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...
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...

Private Member Functions
void	readPQPInput_ (const char *filename, std::vector< TSVTransition > &transition_list, bool legacy_traml_id=false)
	Read PQP SQLite file. More...
void	writePQPOutput_ (const char *filename, OpenMS::TargetedExperiment &targeted_exp)
	Write a TargetedExperiment to a file. More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...
Protected Member Functions inherited from TransitionTSVFile
void	TSVToTargetedExperiment_ (std::vector< TSVTransition > &transition_list, OpenMS::TargetedExperiment &exp)
	Convert a list of TSVTransition to a TargetedExperiment. More...
void	TSVToTargetedExperiment_ (std::vector< TSVTransition > &transition_list, OpenSwath::LightTargetedExperiment &exp)
	Convert a list of TSVTransition to a LightTargetedExperiment. More...
TransitionTSVFile::TSVTransition	convertTransition_ (const ReactionMonitoringTransition *it, OpenMS::TargetedExperiment &targeted_exp)
void	updateMembers_ () override
	Synchronize members with param class. More...
Protected Member Functions inherited from DefaultParamHandler
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 ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
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...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class supports reading and writing of PQP files.

The PQP files are SQLite databases consisting of several tables representing the data contained in TraML files.

This class can convert TraML and PQP files into each other

Constructor & Destructor Documentation

TransitionPQPFile()

TransitionPQPFile

(

)

Constructor.

~TransitionPQPFile()

~TransitionPQPFile ( )

override

Destructor.

Member Function Documentation

convertPQPToTargetedExperiment() [1/2]

void convertPQPToTargetedExperiment	(	const char *	filename,
		OpenMS::TargetedExperiment &	targeted_exp,
		bool	legacy_traml_id = false
	)

Read in a PQP file and construct a targeted experiment (TraML structure)

Parameters

filename	The input file
targeted_exp	The output targeted experiment
legacy_traml_id	Should legacy TraML IDs be used (boolean)?

convertPQPToTargetedExperiment() [2/2]

void convertPQPToTargetedExperiment	(	const char *	filename,
		OpenSwath::LightTargetedExperiment &	targeted_exp,
		bool	legacy_traml_id = false
	)

Read in a PQP file and construct a targeted experiment (Light transition structure)

Parameters

filename	The input file
targeted_exp	The output targeted experiment
legacy_traml_id	Should legacy TraML IDs be used (boolean)?

convertTargetedExperimentToPQP()

void convertTargetedExperimentToPQP	(	const char *	filename,
		OpenMS::TargetedExperiment &	targeted_exp
	)

Write out a targeted experiment (TraML structure) into a PQP file.

Parameters

filename	The output file
targeted_exp	The targeted experiment

readPQPInput_()

void readPQPInput_ ( const char *  filename, std::vector< TSVTransition > &  transition_list, bool  legacy_traml_id = false  )

private

Read PQP SQLite file.

Parameters

filename	The input file
transition_list	The output list of transitions
legacy_traml_id	Should legacy TraML IDs be used (boolean)?

writePQPOutput_()

void writePQPOutput_ ( const char *  filename, OpenMS::TargetedExperiment &  targeted_exp  )

private

Write a TargetedExperiment to a file.

Parameters

filename	Name of the output file
targeted_exp	The data structure to be written to the file