OMSFileStore Class Reference

Helper class for storing .oms files (SQLite format) More...

#include <OpenMS/FORMAT/OMSFileStore.h>

Inheritance diagram for OMSFileStore:

Collaboration diagram for OMSFileStore:

Public Types
using	Key = qint64
	Type used for database keys. More...
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	OMSFileStore (const String &filename, LogType log_type)
	Constructor. More...
	~OMSFileStore ()
	Destructor. More...
void	store (const IdentificationData &id_data)
	Write data from an IdentificationData object to database. More...
void	store (const FeatureMap &features)
	Write data from a FeatureMap object to database. 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...

Private Member Functions
void	storeVersionAndDate_ ()
void	storeScoreTypes_ (const IdentificationData &id_data)
void	storeInputFiles_ (const IdentificationData &id_data)
void	storeProcessingSoftwares_ (const IdentificationData &id_data)
void	storeDBSearchParams_ (const IdentificationData &id_data)
void	storeProcessingSteps_ (const IdentificationData &id_data)
void	storeObservations_ (const IdentificationData &id_data)
void	storeParentSequences_ (const IdentificationData &id_data)
void	storeParentGroupSets_ (const IdentificationData &id_data)
void	storeIdentifiedCompounds_ (const IdentificationData &id_data)
void	storeIdentifiedSequences_ (const IdentificationData &id_data)
void	storeAdducts_ (const IdentificationData &id_data)
void	storeObservationMatches_ (const IdentificationData &id_data)
void	storeFeatures_ (const FeatureMap &features)
void	createTable_ (const String &name, const String &definition, bool may_exist=false)
void	createTableMoleculeType_ ()
void	createTableDataValue_ ()
Key	storeDataValue_ (const DataValue &value)
void	createTableCVTerm_ ()
Key	storeCVTerm_ (const CVTerm &cv_term)
void	createTableMetaInfo_ (const String &parent_table, const String &key_column="id")
void	storeMetaInfo_ (const MetaInfoInterface &info, const String &parent_table, Key parent_id)
void	createTableAppliedProcessingStep_ (const String &parent_table)
void	storeAppliedProcessingStep_ (const IdentificationData::AppliedProcessingStep &step, Size step_order, const String &parent_table, Key parent_id)
void	createTableIdentifiedMolecule_ ()
Key	getAddress_ (const IdentificationData::IdentifiedMolecule &molecule_var)
void	createTableParentMatches_ ()
void	storeParentMatches_ (const IdentificationData::ParentMatches &matches, Key molecule_id)
template<class MetaInfoInterfaceContainer >
void	storeMetaInfos_ (const MetaInfoInterfaceContainer &container, const String &parent_table)
template<class ScoredProcessingResultContainer >
void	storeScoredProcessingResults_ (const ScoredProcessingResultContainer &container, const String &parent_table)
void	storeFeature_ (const FeatureMap &features)
void	storeFeatureAndSubordinates_ (const Feature &feature, int &feature_id, int parent_id)
template<class FeatureContainer , class Predicate >
bool	anyFeaturePredicate_ (const FeatureContainer &features, const Predicate &pred)
	check whether a predicate is true for any feature (or subordinate thereof) in a container More...
void	storeMapMetaData_ (const FeatureMap &features)
void	storeDataProcessing_ (const FeatureMap &features)

Private Attributes
QString	db_name_
std::map< std::string, QSqlQuery >	prepared_queries_
	prepared queries for inserting data into different tables More...

Additional Inherited Members
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_
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Helper class for storing .oms files (SQLite format)

This class encapsulates the SQLite database in a .oms file and allows to write data to it.

Member Typedef Documentation

Key

using Key = qint64

Type used for database keys.

Constructor & Destructor Documentation

OMSFileStore()

OMSFileStore	(	const String &	filename,
		LogType	log_type
	)

Constructor.

Deletes the output file if it exists, then creates an SQLite database in its place. Opens the database and configures it for fast writing.

Parameters

filename	Path to the .oms output file (SQLite database)
log_type	Type of logging to use

Exceptions

Exception::FailedAPICall

Database cannot be opened

~OMSFileStore()

~OMSFileStore

(

)

Destructor.

Closes the connection to the database file.

Member Function Documentation

anyFeaturePredicate_()

bool anyFeaturePredicate_ ( const FeatureContainer &  features, const Predicate &  pred  )

inlineprivate

check whether a predicate is true for any feature (or subordinate thereof) in a container

createTable_()

void createTable_ ( const String &  name, const String &  definition, bool  may_exist = false  )

private

createTableAppliedProcessingStep_()

void createTableAppliedProcessingStep_ ( const String &  parent_table )

private

Referenced by OMSFileStore::storeScoredProcessingResults_().

createTableCVTerm_()

void createTableCVTerm_ ( )

private

createTableDataValue_()

void createTableDataValue_ ( )

private

createTableIdentifiedMolecule_()

void createTableIdentifiedMolecule_ ( )

private

createTableMetaInfo_()

void createTableMetaInfo_ ( const String &  parent_table, const String &  key_column = "id"  )

private

Referenced by OMSFileStore::storeMetaInfos_().

createTableMoleculeType_()

void createTableMoleculeType_ ( )

private

createTableParentMatches_()

void createTableParentMatches_ ( )

private

getAddress_()

Key getAddress_ ( const IdentificationData::IdentifiedMolecule &  molecule_var )

private

store() [1/2]

void store

(

const FeatureMap &

features

)

Write data from a FeatureMap object to database.

store() [2/2]

void store

(

const IdentificationData &

id_data

)

Write data from an IdentificationData object to database.

storeAdducts_()

void storeAdducts_ ( const IdentificationData &  id_data )

private

storeAppliedProcessingStep_()

void storeAppliedProcessingStep_ ( const IdentificationData::AppliedProcessingStep &  step, Size  step_order, const String &  parent_table, Key  parent_id  )

private

Referenced by OMSFileStore::storeScoredProcessingResults_().

storeCVTerm_()

Key storeCVTerm_ ( const CVTerm &  cv_term )

private

storeDataProcessing_()

void storeDataProcessing_ ( const FeatureMap &  features )

private

storeDataValue_()

Key storeDataValue_ ( const DataValue &  value )

private

storeDBSearchParams_()

void storeDBSearchParams_ ( const IdentificationData &  id_data )

private

storeFeature_()

void storeFeature_ ( const FeatureMap &  features )

private

storeFeatureAndSubordinates_()

void storeFeatureAndSubordinates_ ( const Feature &  feature, int &  feature_id, int  parent_id  )

private

storeFeatures_()

void storeFeatures_ ( const FeatureMap &  features )

private

storeIdentifiedCompounds_()

void storeIdentifiedCompounds_ ( const IdentificationData &  id_data )

private

storeIdentifiedSequences_()

void storeIdentifiedSequences_ ( const IdentificationData &  id_data )

private

storeInputFiles_()

void storeInputFiles_ ( const IdentificationData &  id_data )

private

storeMapMetaData_()

void storeMapMetaData_ ( const FeatureMap &  features )

private

storeMetaInfo_()

void storeMetaInfo_ ( const MetaInfoInterface &  info, const String &  parent_table, Key  parent_id  )

private

Referenced by OMSFileStore::storeMetaInfos_().

storeMetaInfos_()

void storeMetaInfos_ ( const MetaInfoInterfaceContainer &  container, const String &  parent_table  )

inlineprivate

References OMSFileStore::createTableMetaInfo_(), and OMSFileStore::storeMetaInfo_().

Referenced by OMSFileStore::storeScoredProcessingResults_().

storeObservationMatches_()

void storeObservationMatches_ ( const IdentificationData &  id_data )

private

storeObservations_()

void storeObservations_ ( const IdentificationData &  id_data )

private

storeParentGroupSets_()

void storeParentGroupSets_ ( const IdentificationData &  id_data )

private

storeParentMatches_()

void storeParentMatches_ ( const IdentificationData::ParentMatches &  matches, Key  molecule_id  )

private

storeParentSequences_()

void storeParentSequences_ ( const IdentificationData &  id_data )

private

storeProcessingSoftwares_()

void storeProcessingSoftwares_ ( const IdentificationData &  id_data )

private

storeProcessingSteps_()

void storeProcessingSteps_ ( const IdentificationData &  id_data )

private

storeScoredProcessingResults_()

void storeScoredProcessingResults_ ( const ScoredProcessingResultContainer &  container, const String &  parent_table  )

inlineprivate

References OMSFileStore::createTableAppliedProcessingStep_(), OMSFileStore::storeAppliedProcessingStep_(), and OMSFileStore::storeMetaInfos_().

storeScoreTypes_()

void storeScoreTypes_ ( const IdentificationData &  id_data )

private

storeVersionAndDate_()

void storeVersionAndDate_ ( )

private

Member Data Documentation

db_name_

QString db_name_

private

prepared_queries_

std::map<std::string, QSqlQuery> prepared_queries_

private

prepared queries for inserting data into different tables