OMSFile Class Reference

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

#include <OpenMS/FORMAT/OMSFile.h>

Inheritance diagram for OMSFile:

Collaboration diagram for OMSFile:

Public Member Functions
	OMSFile (LogType log_type=LogType::NONE)
	Constructor (with option to set log type)
void	store (const std::string &filename, const IdentificationData &id_data)
	Write out an IdentificationData object to SQL-based OMS file.
void	store (const std::string &filename, const FeatureMap &features)
	Write out a feature map to SQL-based OMS file.
void	store (const std::string &filename, const ConsensusMap &consensus)
	Write out a consensus map to SQL-based OMS file.
void	load (const std::string &filename, IdentificationData &id_data)
	Read in an OMS file and construct an IdentificationData object.
void	load (const std::string &filename, FeatureMap &features)
	Read in an OMS file and construct a feature map.
void	load (const std::string &filename, ConsensusMap &consensus)
	Read in an OMS file and construct a consensus map.
void	exportToJSON (const std::string &filename_in, const std::string &filename_out)
	Read in an OMS file and write out the contents in JSON format.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Protected Attributes
LogType	log_type_
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class supports reading and writing of OMS files.

OMS files are SQLite databases consisting of several tables.

Constructor & Destructor Documentation

OMSFile()

OMSFile ( LogType  log_type = LogType::NONE )

inlineexplicit

Constructor (with option to set log type)

Member Function Documentation

exportToJSON()

void exportToJSON	(	const std::string &	filename_in,
		const std::string &	filename_out
	)

Read in an OMS file and write out the contents in JSON format.

Parameters

[in]	filename_in	The input file (OMS)
[out]	filename_out	The output file (JSON)

load() [1/3]

void load	(	const std::string &	filename,
		ConsensusMap &	consensus
	)

Read in an OMS file and construct a consensus map.

Parameters

[out]	filename	The input file
[in]	consensus	The consensus map

load() [2/3]

void load	(	const std::string &	filename,
		FeatureMap &	features
	)

Read in an OMS file and construct a feature map.

Parameters

[out]	filename	The input file
[in]	features	The feature map

load() [3/3]

void load	(	const std::string &	filename,
		IdentificationData &	id_data
	)

Read in an OMS file and construct an IdentificationData object.

Parameters

[out]	filename	The input file
[in]	id_data	The IdentificationData object

Referenced by NucleicAcidSearchEngine::main_().

store() [1/3]

void store	(	const std::string &	filename,
		const ConsensusMap &	consensus
	)

Write out a consensus map to SQL-based OMS file.

Parameters

[in]	filename	The output file
[in]	consensus	The consensus map

store() [2/3]

void store	(	const std::string &	filename,
		const FeatureMap &	features
	)

Write out a feature map to SQL-based OMS file.

Parameters

[in]	filename	The output file
[in]	features	The feature map

store() [3/3]

void store	(	const std::string &	filename,
		const IdentificationData &	id_data
	)

Write out an IdentificationData object to SQL-based OMS file.

Parameters

[in]	filename	The output file
[in]	id_data	The IdentificationData object

Referenced by NucleicAcidSearchEngine::main_().

Member Data Documentation

log_type_

LogType log_type_

protected