DBAdapter Class Reference [Database IO]

A class for accessing and storing data in a SQL database. More...

#include <OpenMS/FORMAT/DB/DBAdapter.h>

List of all members.

Public Member Functions
	DBAdapter (DBConnection &db_con)
	Constructor.
	~DBAdapter ()
	Destructor.
template<class ExperimentType >
void	storeExperiment (ExperimentType &exp)
	Stores a MSExperiment.
template<class ExperimentType >
void	loadExperiment (UID id, ExperimentType &exp)
	Reads a MSExperiment.
template<class SpectrumType >
void	loadSpectrum (UID id, SpectrumType &spec)
	Reads a MSSpectrum.
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
bool	checkDBVersion (bool warning)
	Returns true if the DB is up-to-date (Checks the version in ADMIN_Version table).
void	createDB ()
	Deletes all tables in the database and creates a new OpenMS database.
Private Member Functions
	DBAdapter ()
	Not implemented.
UID	storeMetaInfo_ (const String &parent_table, UID parent_id, const MetaInfoInterface &info)
	Stores, updates or deletes MetaInfo data.
UID	storeMetaInfo_ (const String &parent_table, UID parent_id, const Peak1D &peak)
	Overload for Peak1D that does nothing.
UID	storeMetaInfo_ (const String &parent_table, UID parent_id, const RichPeak1D &peak)
	Overloaded method for RichPeak1D, which is both a MetaInfoInterface and a Peak1D.
UID	storeMetaInfo_ (const String &parent_table, UID parent_id, const Precursor &peak)
	Overloaded method for RichPeak1D, which is both a MetaInfoInterface (via CVTermList) and a and a Peak1D.
void	loadMetaInfo_ (UID id, MetaInfoInterface &info)
	Loads MetaInfo data from database.
void	loadMetaInfo_ (UID id, Peak1D &peak)
	Overloaded method for Peak1D, which does nothing.
void	loadMetaInfo_ (UID id, RichPeak1D &peak)
	Overloaded method for RichPeak1D, which is both a MetaInfoInterface and a Peak1D.
void	loadMetaInfo_ (UID id, Precursor &peak)
	Overloaded method for Precursor, which is both a MetaInfoInterface (via CVTermList) and a Peak1D.
void	deleteMetaInfo_ (const String &parent_table, const String &condition)
	Conditionally deletes MetaInfo data from database.
UID	storeFile_ (const String &parent_table, UID parent_id, const SourceFile &file)
	Stores, updates or deletes file information.
void	loadFile_ (UID id, SourceFile &file)
	Loads file information.
UID	storeSample_ (const Sample &sample, UID exp_id, UID parent_id)
	Stores, updates or deletes sample information.
void	loadSample_ (UID id, Sample &sample)
	Loads sample information.
Private Attributes
DBConnection &	db_con_
	Reference to the DB connection handed over in the constructor.
PeakFileOptions	options_

---

Detailed Description

A class for accessing and storing data in a SQL database.

It can be used to create objects from the DB or store them in the DB.

Todo:

Add DataProcessing to MetaInfoDescription (Hiwi, Mathias)

Check if test is really complete (Hiwi, Mathias)

Check that all values are quoted (Hiwi, Mathias)

Implement StringDataArray and IntegerDataArray of spectrum (Hiwi, Mathias)

---

Constructor & Destructor Documentation

DBAdapter

(

DBConnection &

db_con

)

Constructor.

~DBAdapter

(

)

Destructor.

DBAdapter

(

)

[private]

Not implemented.

---

Member Function Documentation

bool checkDBVersion

(

bool

warning

)

Returns true if the DB is up-to-date (Checks the version in ADMIN_Version table).

Parameters:

warning

if this is set, a warning is issued to stderr if the db is not up-to-date.

Referenced by DBAdapter::loadExperiment(), DBAdapter::loadSpectrum(), and DBAdapter::storeExperiment().

void createDB

(

)

Deletes all tables in the database and creates a new OpenMS database.

void deleteMetaInfo_	(	const String &	parent_table,
		const String &	condition
	)			[private]

Conditionally deletes MetaInfo data from database.

Referenced by DBAdapter::storeExperiment().

const PeakFileOptions& getOptions

(

)

const

Non-mutable access to the options for loading/storing.

PeakFileOptions& getOptions

(

)

Mutable access to the options for loading/storing.

Referenced by TOPPViewBase::metadataDatabaseDialog().

void loadExperiment	(	UID	id,
		ExperimentType &	exp
	)

Reads a MSExperiment.

References DBAdapter::checkDBVersion(), DBAdapter::db_con_, DBConnection::executeQuery(), PeakFileOptions::getMetadataOnly(), PeakFileOptions::getMSLevels(), PeakFileOptions::getRTRange(), ProteinIdentification::getSearchParameters(), PeakFileOptions::hasMSLevels(), PeakFileOptions::hasRTRange(), DBAdapter::loadMetaInfo_(), DBAdapter::loadSample_(), DBAdapter::loadSpectrum(), DIntervalBase< D >::maxPosition(), DIntervalBase< D >::minPosition(), DBAdapter::options_, DateTime::set(), ProteinHit::setAccession(), MassAnalyzer::setAccuracy(), IonDetector::setAcquisitionMode(), IonDetector::setADCSamplingFrequency(), ContactPerson::setContactInfo(), ProteinIdentification::setDateTime(), ContactPerson::setEmail(), MassAnalyzer::setFinalMSExponent(), ContactPerson::setFirstName(), ProteinIdentification::setHigherScoreBetter(), ProteinIdentification::setHits(), IonSource::setInletType(), ContactPerson::setInstitution(), IonSource::setIonizationMethod(), MassAnalyzer::setIsolationWidth(), ContactPerson::setLastName(), MassAnalyzer::setMagneticFieldStrength(), Software::setName(), MassAnalyzer::setOrder(), IonSource::setOrder(), IonDetector::setOrder(), IonSource::setPolarity(), ProteinHit::setRank(), MassAnalyzer::setReflectronState(), MassAnalyzer::setResolution(), IonDetector::setResolution(), MassAnalyzer::setResolutionMethod(), MassAnalyzer::setResolutionType(), MassAnalyzer::setScanDirection(), MassAnalyzer::setScanLaw(), MassAnalyzer::setScanRate(), MassAnalyzer::setScanTime(), ProteinHit::setScore(), ProteinIdentification::setScoreType(), ProteinIdentification::setSearchEngine(), ProteinIdentification::setSearchEngineVersion(), ProteinIdentification::setSearchParameters(), ProteinHit::setSequence(), ProteinIdentification::setSignificanceThreshold(), MassAnalyzer::setTOFTotalPathLength(), MassAnalyzer::setType(), IonDetector::setType(), Software::setVersion(), and String::toQString().

Referenced by TOPPViewBase::addDataDB(), and TOPPViewBase::metadataDatabaseDialog().

void loadFile_	(	UID	id,
		SourceFile &	file
	)			[private]

Loads file information.

Referenced by DBAdapter::loadSpectrum().

void loadMetaInfo_	(	UID	id,
		Precursor &	peak
	)			[private]

Overloaded method for Precursor, which is both a MetaInfoInterface (via CVTermList) and a Peak1D.

void loadMetaInfo_	(	UID	id,
		MetaInfoInterface &	info
	)			[private]

Loads MetaInfo data from database.

Referenced by DBAdapter::loadExperiment(), and DBAdapter::loadSpectrum().

void loadMetaInfo_	(	UID	id,
		Peak1D &	peak
	)			[private]

Overloaded method for Peak1D, which does nothing.

void loadMetaInfo_	(	UID	id,
		RichPeak1D &	peak
	)			[private]

Overloaded method for RichPeak1D, which is both a MetaInfoInterface and a Peak1D.

void loadSample_	(	UID	id,
		Sample &	sample
	)			[private]

Loads sample information.

Referenced by DBAdapter::loadExperiment().

void loadSpectrum	(	UID	id,
		SpectrumType &	spec
	)

Reads a MSSpectrum.

References ScanWindow::begin, DBAdapter::checkDBVersion(), DBAdapter::db_con_, ScanWindow::end, DBConnection::executeQuery(), PeakFileOptions::getIntensityRange(), PeakFileOptions::getMZRange(), DataProcessing::getProcessingActions(), PeakFileOptions::hasIntensityRange(), PeakFileOptions::hasMZRange(), DBAdapter::loadFile_(), DBAdapter::loadMetaInfo_(), DIntervalBase< D >::maxPosition(), DIntervalBase< D >::minPosition(), DBAdapter::options_, DateTime::set(), PeptideHit::setAAAfter(), PeptideHit::setAABefore(), PeptideHit::setCharge(), DataProcessing::setCompletionTime(), PeptideIdentification::setHigherScoreBetter(), PeptideIdentification::setHits(), Acquisition::setIdentifier(), Software::setName(), InstrumentSettings::setPolarity(), Peak2D::setPosition(), InstrumentSettings::setScanMode(), PeptideHit::setScore(), PeptideIdentification::setScoreType(), PeptideHit::setSequence(), PeptideIdentification::setSignificanceThreshold(), DataProcessing::setSoftware(), Software::setVersion(), and InstrumentSettings::setZoomScan().

Referenced by DBAdapter::loadExperiment().

void storeExperiment

(

ExperimentType &

exp

)

Stores a MSExperiment.

References DBAdapter::checkDBVersion(), DBAdapter::db_con_, DBAdapter::deleteMetaInfo_(), DBConnection::executeQuery(), DBConnection::getAutoId(), HPLC::getColumn(), HPLC::getComment(), Instrument::getCustomizations(), Gradient::getEluents(), HPLC::getFlux(), HPLC::getInstrument(), Instrument::getIonOptics(), AcquisitionInfo::getMethodOfCombination(), Instrument::getModel(), Software::getName(), Gradient::getPercentages(), InstrumentSettings::getPolarity(), HPLC::getPressure(), InstrumentSettings::getScanMode(), InstrumentSettings::getScanWindows(), Instrument::getSoftware(), HPLC::getTemperature(), Gradient::getTimepoints(), Instrument::getVendor(), Software::getVersion(), InstrumentSettings::getZoomScan(), DBAdapter::storeFile_(), DBAdapter::storeMetaInfo_(), and DBAdapter::storeSample_().

UID storeFile_	(	const String &	parent_table,
		UID	parent_id,
		const SourceFile &	file
	)			[private]

Stores, updates or deletes file information.

Returns:

the id of the new META_File table row

Referenced by DBAdapter::storeExperiment().

UID storeMetaInfo_	(	const String &	parent_table,
		UID	parent_id,
		const Precursor &	peak
	)			[private]

Overloaded method for RichPeak1D, which is both a MetaInfoInterface (via CVTermList) and a and a Peak1D.

UID storeMetaInfo_	(	const String &	parent_table,
		UID	parent_id,
		const RichPeak1D &	peak
	)			[private]

Overloaded method for RichPeak1D, which is both a MetaInfoInterface and a Peak1D.

UID storeMetaInfo_	(	const String &	parent_table,
		UID	parent_id,
		const MetaInfoInterface &	info
	)			[private]

Stores, updates or deletes MetaInfo data.

Returns:

the id of the new META_MetaInfo table row

Referenced by DBAdapter::storeExperiment().

UID storeMetaInfo_	(	const String &	parent_table,
		UID	parent_id,
		const Peak1D &	peak
	)			[private]

Overload for Peak1D that does nothing.

UID storeSample_	(	const Sample &	sample,
		UID	exp_id,
		UID	parent_id
	)			[private]

Stores, updates or deletes sample information.

Returns:

the id of the new META_Sample table row

Referenced by DBAdapter::storeExperiment().

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Member Data Documentation

DBConnection& db_con_ [private]

Reference to the DB connection handed over in the constructor.

Referenced by DBAdapter::loadExperiment(), DBAdapter::loadSpectrum(), and DBAdapter::storeExperiment().

PeakFileOptions options_ [private]

Referenced by DBAdapter::loadExperiment(), and DBAdapter::loadSpectrum().